[{"hash":"2126983566593039400","title":"ER Stress and Calcium Signaling","description":"GO terms point to unfolded protein response and translation initiation during ER stress, along with cellular calcium signaling and NFAT pathway regulation, suggesting a core theme of ER-stress\u2013driven translational control and calcium-dependent signaling. Some mitochondrial and biosynthetic terms may reflect broader stress-related remodeling, but the dominant signal is ER stress\u2013associated responses.","confidence":"Medium","size":29,"edges":406,"triangles":3654,"max_degree":28,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035690","count":4},{"id":"GO:0009236","count":3},{"id":"GO:0006744","count":3},{"id":"GO:0036494","count":3},{"id":"GO:0006986","count":3}]},{"hash":"2110774040847042309","title":"Renin-angiotensin system regulation","description":"Top GO terms indicate involvement in regulation of blood volume by the renin-angiotensin system, angiotensin maturation, and aldosterone production, suggesting a cohesive theme around cardiovascular/renal hormonal control. Other terms such as digestion, transcription, antigen processing, development, and amyloid beta metabolism appear ancillary, implying partial cohesion with the primary RAS-related functions.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007586","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0042985","count":4},{"id":"GO:0002016","count":4},{"id":"GO:0002018","count":4}]},{"hash":"678250140906150600","title":"Redox Detoxification and Oxidative Stress Response","description":"This cluster is dominated by redox-related GO terms: cellular oxidant detoxification, cell redox homeostasis, and cellular response to oxidative stress, with additional deglutathionylation, all pointing to a coordinated role in maintaining redox balance and protecting against oxidative damage. While a few terms like nucleotide biosynthesis and transcription regulation appear, they are likely secondary or multifunctional traits of some members. Overall, the redox/oxidative stress theme best explains the prominent terms and their occurrences.","confidence":"High","size":29,"edges":71,"triangles":165,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":10},{"id":"GO:0055114","count":9},{"id":"GO:0045454","count":9},{"id":"GO:0080058","count":6},{"id":"GO:0009263","count":6}]},{"hash":"86067877315839807","title":"Unknown","description":"The top GO terms span very disparate processes (thiamine biosynthesis, mitochondrial electron transport, immune and xenobiotic responses, neural development, and granulocyte differentiation) with no clear shared function, and the network is very sparse with many obsolete terms. There isn\u2019t a cohesive theme to label a specific function for this cluster.","confidence":"","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009228","count":9},{"id":"GO:0055114","count":9},{"id":"GO:0045964","count":8},{"id":"GO:0006120","count":8},{"id":"GO:0030851","count":8}]},{"hash":"1532618943676272057","title":"Retinoid Metabolism and Hormone Signaling","description":"The two strongest GO terms are retinal metabolic process and retinol metabolic process, pointing to retinoid (vitamin A) metabolism as the core function of this cluster. Additional terms like positive regulation of receptor signaling via JAK-STAT, cellular response to calcium ions, and response to thyroid hormone suggest broader endocrine signaling involvement. While some terms pertain to development, retinoid signaling is known to influence developmental processes, supporting a cohesive theme around retinoid metabolism linked to hormonal signaling.","confidence":"Medium","size":29,"edges":189,"triangles":787,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042574","count":10},{"id":"GO:0042572","count":10},{"id":"GO:0055114","count":9},{"id":"GO:0046427","count":6},{"id":"GO:0071277","count":6}]},{"hash":"1035371072963517140","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":4},{"id":"GO:0016554","count":2},{"id":"GO:1905639","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0001682","count":2}]},{"hash":"1599057655430674271","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0010019","count":3},{"id":"GO:0000961","count":3},{"id":"GO:0016554","count":2}]},{"hash":"569486932338697915","title":"RNA splicing regulation and processing","description":"The top GO terms are dominated by regulation of mRNA splicing via the spliceosome, splice-site recognition, and general mRNA processing, including regulatory ncRNA\u2013mediated gene silencing. This points to a coherent theme of RNA processing/splicing control, with a few peripheral terms (DNA replication/recombination, development) that are less central to the cluster\u2019s main function.","confidence":"High","size":29,"edges":69,"triangles":16,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":5},{"id":"GO:0000381","count":5},{"id":"GO:0006376","count":4},{"id":"GO:0006260","count":4}]},{"hash":"1197523331403112511","title":"Stress-Responsive Translation Regulation","description":"The top GO terms cluster around translation machinery and its regulation, including translational initiation and elongation, as well as increased regulation in response to endoplasmic reticulum stress and unfolded protein response, indicating a group of proteins coordinated to control protein synthesis under stress. A few terms like photosynthesis may reflect chloroplast context, but the core theme is stress-linked regulation of translation.","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0045901","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0015979","count":2}]},{"hash":"835034911480564785","title":"Genome maintenance and cell cycle control","description":"This cluster is dominated by terms related to nuclear processes essential for genome integrity and cell division, such as DNA replication, G2/M transition, and telomere maintenance, plus proteasome assembly. Peripheral terms about fat cell differentiation and muscle stretch may reflect broader growth/differentiation contexts, but the core signal points to genome maintenance and cell cycle regulation.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006397","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0045444","count":4},{"id":"GO:1904355","count":4}]},{"hash":"1682747182193405794","title":"DNA Transcription Regulation and Redox Homeostasis","description":"Based on the GO terms, the cluster is enriched for transcriptional control (DNA-templated transcription, regulation, and negative regulation of transcription by RNA Pol II), indicating a nuclear regulatory module. It is also associated with oxidative stress responses and redox balance (cellular response to oxidative stress, oxidant detoxification, and redox homeostasis), suggesting these proteins function together in gene expression control under oxidative stress conditions. While there are a few terms related to cell cycle and growth (chromosome segregation, positive regulation of cell size), the dominant themes are transcription regulation and redox/homeostatic stress responses, making this label representative of the cluster\u2019s core function.","confidence":"Medium","size":29,"edges":10,"triangles":1,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0007059","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0000122","count":4}]},{"hash":"1816142280589764609","title":"Meiosis and Germ Cell Chromosomal Dynamics","description":"The top GO terms cluster around meiotic processes: meiotic telomere attachment to the nuclear envelope, meiotic centromeric cohesion, replication-born double-strand break repair via sister chromatid exchange, and spermatid nucleus elongation. Together they indicate a theme of meiotic chromosome dynamics and germ cell development. A few terms like potassium ion transport and cerebrospinal fluid secretion seem peripheral, but the dominant signal points to meiosis-related roles.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0070197","count":2},{"id":"GO:1990414","count":2},{"id":"GO:0051754","count":2},{"id":"GO:0007588","count":2}]},{"hash":"1046118937095699039","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090503","count":2},{"id":"GO:0071039","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0032066","count":1},{"id":"GO:0034476","count":1}]},{"hash":"1979731176768504559","title":"Meiotic spindle and chromatid cohesion","description":"The top terms cluster around meiosis-specific processes such as meiotic spindle elongation, regulation of the meiotic cell cycle in oocytes, and centromeric/meiotic sister chromatid cohesion, suggesting the proteins participate in chromosome segregation during meiosis. Some terms are more general (tRNA processing, protein complex assembly), but the dominant theme is meiosis and chromosome cohesion/separation.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070262","count":1},{"id":"GO:0008033","count":1},{"id":"GO:0051232","count":1},{"id":"GO:0006461","count":1},{"id":"GO:1903538","count":1}]},{"hash":"197552233771586549","title":"Cardiac and neural development","description":"The cluster\u2019s top GO terms cluster around heart development, angiogenesis, and axonogenesis, with accompanying mitotic cell cycle transitions, pointing to developmental programs spanning cardiac, vascular, and neural lineages. While there are additional signals related to immune response and gene expression regulation, the dominant theme is development in heart, vessels, and neurons. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0000086","count":2},{"id":"GO:2000727","count":2},{"id":"GO:0006349","count":2}]},{"hash":"2130389175109245142","title":"Biosynthesis and Xenobiotic Detoxification","description":"The top terms span biosynthesis (antibiotic, biotin, cobalamin) and catabolic/detoxification processes (uracil catabolic, beta-ketoadipate, triglyceride breakdown, oxidant detoxification), plus xenobiotic response and regulation of endocannabinoid signaling. This suggests a broad metabolic cluster rather than a single protein complex.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0017000","count":10},{"id":"GO:0009102","count":8},{"id":"GO:0009236","count":6},{"id":"GO:0035690","count":6},{"id":"GO:0006212","count":6}]},{"hash":"223307988420866605","title":"Nociception and Thermoception Signaling","description":"This cluster is dominated by GO terms related to sensing painful and thermal stimuli (detection of mechanical stimulus involved in sensory perception of pain; thermoception; response to capsazepine), suggesting a focus on nociceptive and thermosensory signaling. While other terms (mRNA processing, NOD2 signaling, telomere regulation) appear, they are less indicative of the core function, so the label centers on pain and temperature sensing.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":9},{"id":"GO:0006397","count":8},{"id":"GO:0050966","count":8},{"id":"GO:0070431","count":8},{"id":"GO:0050955","count":8}]},{"hash":"747356826390113593","title":"Unknown","description":"The cluster shows a scattered mix of GO terms\u2014protein ubiquitination and cell cycle, plant development (root meristem growth, auxin transport), hypoxia response regulation, telomerase assembly, and even lung development. With zero edges and only shallow overlaps (mostly two members per term) there is no single dominant function or pathway tying the proteins together. Therefore a cohesive, high-level label cannot be assigned beyond Unknown.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0007049","count":2},{"id":"GO:1901407","count":2},{"id":"GO:0010449","count":2},{"id":"GO:0060430","count":2}]},{"hash":"1468224964084657933","title":"Mitochondrial lipid metabolism and apoptosis regulation","description":"The GO terms cluster around lipid handling (wax biosynthesis; long-chain fatty-acyl-CoA metabolism; phospholipid translocation/transport) and mitochondrial function (mitochondrial respiratory chain complex assembly; protein targeting to mitochondrion; regulation of cytochrome c release; p53-mediated DNA damage response). Together these suggest a theme of lipid-associated mitochondrial processes and control of intrinsic apoptosis in response to DNA damage, with a minority term (B cell chemotaxis) likely representing peripheral or pleiotropic roles in some proteins. The lack of edges/triangles indicates no known direct interactions within the cluster, so the association rests on shared mitochondrial\u2013lipid\u2013stress response functions. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010025","count":2},{"id":"GO:0035336","count":2},{"id":"GO:0035754","count":2},{"id":"GO:0045332","count":1},{"id":"GO:0090201","count":1}]},{"hash":"2187866193407228823","title":"Symbiont dormancy and stress response","description":"Label reflects enrichment for stress response and symbiont dormancy entry in host, with related signals for UV/pH/salt stress, GCN2 signaling, and receptor/internalization processes.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0085014","count":2},{"id":"GO:0006950","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0031623","count":2},{"id":"GO:0090529","count":1}]},{"hash":"585215636483049132","title":"Fe-S Cluster Assembly & Iron Homeostasis","description":"The top terms point to [2Fe-2S] cluster assembly and protein maturation via iron-sulfur clusters, plus transcriptional regulation in response to iron, suggesting a core function in Fe-S biogenesis and iron sensing. A few terms are obsolete or incidental, but the dominant theme ties to iron-sulfur cluster assembly and iron-responsive transcription. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097428","count":2},{"id":"GO:1903026","count":2},{"id":"GO:0051220","count":2},{"id":"GO:0044571","count":2},{"id":"GO:0036086","count":2}]},{"hash":"1010021787890291514","title":"Angiogenesis and vascular development","description":"The top GO terms are strongly centered on blood vessel formation and angiogenesis (including labyrinthine layer blood vessel development and positive regulation of angiogenesis), with supporting signals of wound response and cellular stress. While there are some DNA-templated transcription/replication terms, the dominant theme across the cluster appears to be angiogenic processes and vascular remodeling.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0009611","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0071333","count":2},{"id":"GO:0060716","count":2}]},{"hash":"1821975060824605770","title":"Cytoskeletal Polarity and Exocytosis Regulation","description":"Top terms indicate a focus on establishing and maintaining cellular polarity (epithelial polarity, cell shape), actin cytoskeleton dynamics (microspike assembly, cortical actin localization), and membrane trafficking processes (exocytosis, SNARE regulation, pinocytosis). The inclusion of Rho signaling and Wnt pathway hints at signaling cross-talk guiding polarity and cytoskeletal rearrangements. Taken together, this cluster appears to coordinate actin-driven polarity with vesicle trafficking.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035544","count":2},{"id":"GO:0006887","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0048549","count":2},{"id":"GO:1900042","count":2}]},{"hash":"2216409979113498839","title":"Cell signaling, polarity, and cytoskeletal regulation","description":"The cluster includes terms for epithelial polarity, neuron maturation and synaptic regulation, immune signaling (MyD88-TLR), actin filament severing, and cell-cycle/protein ubiquitination regulation, suggesting a general theme of signaling pathways coordinating cell architecture and developmental processes. This label captures the common thread of regulatory signaling affecting polarity, cytoskeleton, and development, though some terms are more specific or peripheral.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016336","count":2},{"id":"GO:0090394","count":2},{"id":"GO:0014041","count":2},{"id":"GO:1903125","count":2},{"id":"GO:0071287","count":2}]},{"hash":"1499238537556881492","title":"Neural Signaling and Sensory Perception Components","description":"This cluster centers on diverse signaling pathways (Wnt, NOD2 signaling, NF-kappaB regulation) and neural/sensory-related processes (pain detection, thermoception) plus oligodendrocyte differentiation. The common thread is involvement in signaling cascades that influence neural development and sensory responses, suggesting a cohesive theme around neural signaling and sensory perception rather than a single, narrow pathway.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0016055","count":3},{"id":"GO:0090501","count":2},{"id":"GO:0050966","count":2},{"id":"GO:0070431","count":2}]},{"hash":"47267867034629021","title":"Iron-sulfur cluster assembly and RNA modification","description":"The top GO terms show iron-sulfur cluster assembly and several RNA-related processes (translation, rRNA methylation/modification, and various methylations), suggesting a theme around Fe-S\u2013dependent protein maturation linked to RNA processing and ribosome function. While some outliers exist (nitrogen fixation, vitamin E biosynthesis), the strongest signal ties Fe-S biogenesis to RNA modification and translation machinery.","confidence":"Medium","size":28,"edges":378,"triangles":3276,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0016226","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0097428","count":2},{"id":"GO:0009399","count":2},{"id":"GO:0035573","count":1}]},{"hash":"1539001861493845538","title":"Organelle RNA Processing and Oxidative Stress","description":"Rationale: The cluster\u2019s prominent GO terms point to RNA metabolism in organelles, including chloroplast RNA processing, mitochondrial mRNA modification, and polycistronic RNA processing, with an additional indication of oxidative stress response (response to hydrogen peroxide). While some terms are unrelated or outdated, the core pattern suggests proteins involved in organellar RNA processing and redox regulation.","confidence":"Medium","size":28,"edges":378,"triangles":3276,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0042542","count":3},{"id":"GO:1903779","count":3},{"id":"GO:0006777","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009097","count":2}]},{"hash":"2003814584262128256","title":"Neural development and synaptic signaling","description":"This cluster centers on neural development and connectivity, highlighted by terms like substantia nigra development, negative regulation of axonogenesis, ephrin receptor signaling, and excitatory postsynaptic potential. While there are some general cellular processes (ER stress response, transcription, cell cycle) also represented, the prominent themes point to neurons\u2019 development and synaptic communication.","confidence":"High","size":28,"edges":20,"triangles":3,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034976","count":7},{"id":"GO:1903206","count":7},{"id":"GO:0048013","count":6},{"id":"GO:0007049","count":6},{"id":"GO:0006351","count":6}]},{"hash":"475094385594088940","title":"Cardiac development and detox-regulated transcription","description":"The top GO terms point to heart development and regulation of heart rate, suggesting a cardiac-focused cluster. Additional terms for cellular response to xenobiotic stimulus and oxidant detoxification indicate detox/oxidative stress involvement, while DNA-templated transcription and regulation of DNA binding imply transcriptional control. Overall, the cluster seems centered on cardiac development with linked transcriptional regulation and detox responses, though there are some metabolic biosynthesis terms present. ","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0017000","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0007507","count":2}]},{"hash":"1658199660978958768","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0001824","count":2},{"id":"GO:0016554","count":2},{"id":"GO:1905639","count":2},{"id":"GO:0080156","count":2}]},{"hash":"366608562081896571","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":140,"triangles":299,"max_degree":21,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":8},{"id":"GO:0006260","count":8},{"id":"GO:0009432","count":7},{"id":"GO:0000480","count":7},{"id":"GO:0071051","count":7}]},{"hash":"474896971621781207","title":"Glycosylation and polysaccharide biosynthesis","description":"This cluster is dominated by GO terms related to glycosylation (O-linked and N-linked) and biosynthesis of glycans and polysaccharide components (teichoic acid, cellulose, hyaluronan, UDP-glucose metabolism), as well as cell wall organization. Together these terms point to a common function in glycan modification and synthesis across diverse organisms, suggesting a cohesive role in glycosylation pathways and polysaccharide assembly. Immunoglobulin production appears tangential but may reflect glycoprotein-related processes rather than a core shared function.","confidence":"Medium","size":28,"edges":85,"triangles":34,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0018243","count":3},{"id":"GO:0002378","count":3},{"id":"GO:0036108","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0030244","count":3}]},{"hash":"807225955126624238","title":"Ubiquitin-dependent proteolysis","description":"The top GO terms show a strong emphasis on ubiquitin-mediated protein degradation (ubiquitin-dependent proteolysis and ERAD), suggesting a cluster centered on proteostasis. While other terms touch on neuronal development, endocytosis, and immune signaling, these can be linked to ubiquitin-regulated pathways that influence these processes. Overall, the main theme is ubiquitin-dependent proteolysis and its role in signaling and cellular regulation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0045792","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0046847","count":3}]},{"hash":"2125109097337564017","title":"Nuclear envelope dynamics and mitosis control","description":"The top GO terms cluster around nuclear envelope reassembly, nucleus organization, and regulation of mitotic spindle assembly and centriole elongation, pointing to roles in cell division and nuclear architecture. Additional terms about endosome transport and MVB sorting suggest linked intracellular trafficking during the cell cycle, but the strongest signal is nuclear/mmitotic regulation, justifying this label. ","confidence":"Medium","size":28,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1902187","count":3},{"id":"GO:0014070","count":2},{"id":"GO:1903723","count":2},{"id":"GO:0031468","count":2},{"id":"GO:0071454","count":2}]},{"hash":"1939836210044922487","title":"Xenobiotic and sugar transmembrane transporters","description":"The top GO terms are dominated by xenobiotic and general transmembrane transport (xenobiotic transmembrane transport, xenobiotic transport, potassium ion transmembrane transport) and specific sugar-related substrates (sialic acid transport, fucose metabolism/transport, 4-hydroxyphenylacetate transport). This pattern strongly points to a cluster of membrane transporter proteins handling xenobiotics and sugar-like substrates. A few terms about microtubule localization and GTPase activity regulation are less directly related, possibly reflecting broader cellular roles or annotation noise.","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:0035372","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0006004","count":2}]},{"hash":"174728004137189112","title":"ADP-ribosylation\u2013mediated signaling regulation","description":"This cluster centers on regulation of signaling with emphasis on ADP-ribosylation as a post-translational modification, including poly- and auto-ADP-ribosylation, and modulation of synaptic signaling (SNARE assembly, synaptic plasticity) as well as broader pathways like Wnt/ephrin signaling. Some terms about telomere maintenance and mitotic cohesion are present but weaker. Therefore the ADP-ribosylation\u2013mediated signaling regulation label captures the main shared function.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035544","count":3},{"id":"GO:0070212","count":3},{"id":"GO:1904357","count":3},{"id":"GO:1901187","count":3},{"id":"GO:0070213","count":3}]},{"hash":"619695511369921733","title":"Neuronal development and cytoskeletal remodeling","description":"This cluster centers on terms related to neuron development and dentate gyrus development, plus actin filament network formation and microtubule cytoskeleton organization, indicating coordinated neural differentiation with cytoskeletal changes. The presence of alpha-tubulin acetylation and even a connection to NLRP3 inflammasome regulation via microtubules aligns with cytoskeletal remodeling influencing signaling and development, while transcriptional regulation terms suggest gene expression changes during neural differentiation. Overall, the dominant theme is neural development linked to cytoskeletal dynamics.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051639","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0045598","count":1},{"id":"GO:0048666","count":1}]},{"hash":"727338668784578481","title":"Neural development and sensory perception","description":"The top terms point to neural differentiation and signaling (oligodendrocyte differentiation, dendrite development, ephrin pathway regulation) together with somatosensory functions (thermoception, detection of mechanical stimulus, response to capsazepine). While a few terms are non-neural, the predominant theme across the terms is neural development and sensory/pain signaling, suggesting the proteins function in neuronal differentiation and somatosensory processing.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090501","count":1},{"id":"GO:0050966","count":1},{"id":"GO:0070431","count":1},{"id":"GO:0050955","count":1},{"id":"GO:0070212","count":1}]},{"hash":"1808833021459594887","title":"Cell cycle, proteostasis, and chromatin assembly","description":"The top GO terms cluster around core cellular maintenance and division processes: proteasome assembly, ERAD-related quality control, ER-Golgi transport, microtubule severing, CENP-A chromatin assembly, and cell division. Although a few terms relate to development or cardiac signaling, the strongest common theme is maintenance of protein/homeostasis, cytoskeletal dynamics, chromatin organization, and mitotic machinery. This supports labeling the cluster as a compact set of housekeeping and cell-cycle\u2013related functions.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070682","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0098907","count":3},{"id":"GO:0051013","count":2},{"id":"GO:0061641","count":2}]},{"hash":"325992203722269081","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050992","count":1},{"id":"GO:2000233","count":1},{"id":"GO:1901911","count":1},{"id":"GO:0006382","count":1},{"id":"GO:1901909","count":1}]},{"hash":"1945815967541789198","title":"GTPase/GPCR Signaling in Development","description":"The top GO terms emphasize positive regulation of GTPase activity and Rac signaling, along with GPCR pathway activity, pointing to a group of proteins involved in signaling regulation and cytoskeletal dynamics. While there are tissue-specific terms like heart development and cardiac contraction, these processes depend on such signaling, and terms related to epithelial polarity and spindle assembly reflect broader developmental and cellular regulation. Overall, the common theme is signaling regulation during development rather than a single tissue-specific function.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0007205","count":4},{"id":"GO:0035021","count":4},{"id":"GO:0007507","count":3},{"id":"GO:0033028","count":3}]},{"hash":"2169878010950190244","title":"Transcriptional Regulation in Embryogenesis","description":"This cluster combines transcription-related processes (negative regulation of RNA polymerase II region binding, DNA-templated transcription, mRNA splicing) with embryonic-development terms (placenta development, trophoblast differentiation, EMT in endocardial cushion formation, cartilage morphogenesis), suggesting a group of genes coordinating gene expression during embryonic development and morphogenesis.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903026","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0060806","count":1},{"id":"GO:0003323","count":1},{"id":"GO:0060707","count":1}]},{"hash":"2064798409339353702","title":"Hormone, lipid, and secondary metabolite biosynthesis","description":"This cluster is enriched for biosynthetic processes of hormones (glucocorticoids, retinoic acid), lipids (sphingolipids), as well as secondary metabolites (tropane alkaloids, antibiotics), suggesting a cohesive theme around production of signaling molecules and defensive compounds, rather than a single canonical pathway.","confidence":"Medium","size":27,"edges":63,"triangles":57,"max_degree":13,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0017000","count":7},{"id":"GO:0048333","count":6},{"id":"GO:0046677","count":6},{"id":"GO:0006355","count":6}]},{"hash":"1569626458389067895","title":"Proteostasis and RNA processing","description":"The GO terms are dominated by protein quality control and processing (chaperone-dependent refolding, ubiquitin-dependent ERAD, proteasome regulatory particle assembly) and RNA metabolism (mRNA processing), with additional, broader processes like synapse localization and development. This suggests a cluster centered on maintaining protein and RNA homeostasis, with developmental signals as secondary associations, rather than a single cohesive pathway. Confidence: Medium","confidence":"","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0070389","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0070682","count":2},{"id":"GO:0035418","count":2}]},{"hash":"2170731923395112627","title":"Mitochondrial Metabolite and Ion Transport","description":"Proteins in this cluster are tied to transport and regulation across mitochondrial membranes. Recurrent GO terms include transmembrane transport of CoA, citrate, NAD, deoxynucleotides, iron, manganese, and magnesium, as well as regulation of mitochondrial membrane permeability. Together, they point to a cohesive theme of mitochondrial metabolite/ion transport and membrane control, with one outlier term (liver regeneration) not altering the overall mitochondrial focus.","confidence":"High","size":27,"edges":35,"triangles":1,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":16},{"id":"GO:0035349","count":16},{"id":"GO:0006843","count":16},{"id":"GO:0046902","count":16},{"id":"GO:0030302","count":16}]},{"hash":"1769106151806871411","title":"Broad immune and sensory signaling pathways","description":"The proteins appear to participate in multiple signaling cascades, including NOD2 signaling, GPCR signaling, NF-kB regulation, and ephrin receptor pathways, along with processes like cell migration and sensory perception (pain and thermoception). This suggests a cluster of general signal transduction components linking immune sensing, migration, and sensory responses, rather than a single cohesive function. Some terms are obsolete, adding noise to the signal.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070431","count":4},{"id":"GO:0007205","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0032088","count":4},{"id":"GO:0016477","count":4}]},{"hash":"1404266977963288516","title":"Unknown","description":"The GO terms show a highly heterogeneous mix of metabolic and detoxification processes (response to toxic substance, cellular oxidant detoxification, antibiotic biosynthetic process, various catabolic pathways) with no clear shared function. Additionally, there are no edges between proteins (Edges: 0, Max Degree: 0), suggesting no coherent cluster-level interaction. This makes it inappropriate to assign a specific functional label beyond Unknown.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0006212","count":3},{"id":"GO:0042952","count":3},{"id":"GO:0046839","count":3}]},{"hash":"254732554194185218","title":"Plant sugar transport and nectar secretion","description":"The cluster is enriched for plant-specific carbohydrate processes, notably sucrose transport, fructose export from the vacuole, and nectar secretion, suggesting a theme around sugar mobilization and nectar production in plants. Auxin signaling regulation also aligns with plant developmental regulation linked to nutrient allocation. Lipid-related terms (triglyceride homeostasis, long-chain fatty-acyl-CoA metabolism, cholesterol biosynthesis) and other terms appear more peripheral, indicating broader metabolic links but not a single cohesive pathway beyond plant carbohydrate management.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010930","count":1},{"id":"GO:0015770","count":1},{"id":"GO:1902334","count":1},{"id":"GO:0071836","count":1},{"id":"GO:0006695","count":1}]},{"hash":"2081491946382473389","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061158","count":2},{"id":"GO:1903883","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0010586","count":2},{"id":"GO:1903265","count":2}]},{"hash":"918136294898293341","title":"Unknown","description":"The GO terms are scattered across transcription, redox/detoxification, lipid metabolism, and a few unrelated specialized processes (bone resorption, plant metabolite catabolism). There is no single dominant function linking most members, and the graph has no edges, so a coherent label cannot be inferred. ","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2},{"id":"GO:1902349","count":2},{"id":"GO:0045453","count":2}]},{"hash":"676111593428554454","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010025","count":3},{"id":"GO:0042761","count":3},{"id":"GO:0009718","count":2},{"id":"GO:0009243","count":2},{"id":"GO:0016126","count":2}]},{"hash":"1391202890407122674","title":"Unknown","description":"Top terms cover intracellular signaling, response to mechanical stimulus, ubiquitination, and a scattered mix of plant, circadian, and immune-related terms. No single theme dominates, and there are no edges connecting proteins, indicating a heterogeneous or poorly connected cluster. As such, no cohesive function can be assigned.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0045496","count":1},{"id":"GO:0009638","count":1}]},{"hash":"594209599666235743","title":"TORC1-regulated autophagy under amino acid starvation","description":"The cluster is dominated by GO terms linking autophagy, cellular response to amino acid starvation, regulation of autophagosome assembly, and TORC1 signaling, pointing to a cohesive module where autophagy is controlled by TORC1 in response to amino acid scarcity. Some developmental terms and yeast pseudohyphal growth likely reflect pleiotropic or conserved stress-response roles rather than a different primary function, but the core signal is nutrient-sensing\u2013driven autophagy.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006914","count":2},{"id":"GO:0007124","count":1},{"id":"GO:0060021","count":1},{"id":"GO:0048738","count":1},{"id":"GO:1903833","count":1}]},{"hash":"1893106805401233580","title":"Ciliary and Flagellar Assembly and Motility","description":"The top GO terms cluster around cilia and flagella: microtubule severing, sperm axoneme assembly, flagellated sperm motility, epithelial cilium movement, and regulation of axon extension. The presence of tubulin post-translational modifications (polyglutamylation and polyglycylation) also supports a role in axoneme function and motility. A few terms like transcription initiation and mitotic cell cycle appear incidental, not altering the main ciliary theme.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051013","count":2},{"id":"GO:0007288","count":2},{"id":"GO:1905419","count":2},{"id":"GO:0003351","count":2},{"id":"GO:0030516","count":2}]},{"hash":"1256164596729208610","title":"Embryonic and placental development","description":"The top GO terms cluster around embryonic and extraembryonic tissue differentiation, including placenta development, trophoblast differentiation, and related organogenesis processes (endocrine system, cartilage morphogenesis, left-right patterning). This suggests a coherent theme of developmental programs active in early embryo and placenta, despite diverse tissue specifics.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060806","count":2},{"id":"GO:0003323","count":2},{"id":"GO:0060707","count":2},{"id":"GO:0003198","count":2},{"id":"GO:0060536","count":2}]},{"hash":"538128037265216308","title":"Plastid Gene Expression and Metabolism","description":"This cluster shows enrichment for plastid-related functions: chloroplast RNA processing, plastid transcription, and chorismate biosynthesis, as well as metabolic pathways like the pentose phosphate shunt and fructose metabolism that are active in plastids. The presence of an outlier term on cardiac conduction is unlikely to define the cluster, so the dominant theme appears to be plastid-associated gene expression and metabolism.","confidence":"Medium","size":26,"edges":319,"triangles":2460,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:1903779","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0031425","count":2},{"id":"GO:0000961","count":2},{"id":"GO:0042793","count":2}]},{"hash":"1244275119072480181","title":"Glucocorticoid and xenobiotic stress response","description":"Top GO terms show responses to corticosterone and xenobiotics, along with redox homeostasis and negative regulation of inflammation; developmental terms are present but likely reflect shared signaling contexts. Overall, the cluster appears to coordinate stress signaling and redox/inflammation regulation, rather than a single, narrow pathway.","confidence":"Medium","size":26,"edges":83,"triangles":52,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051412","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0001701","count":2}]},{"hash":"235821118723329179","title":"Oxidative stress response and redox homeostasis","description":"The cluster is dominated by GO terms tied to redox balance and detoxification (cell redox homeostasis, cellular oxidant detoxification, cellular response to oxidative stress) and redox-related post-translational modification (protein deglutathionylation). This cohesive set points to a shared function in managing oxidative stress. A few outlier terms related to transcriptional regulation or development appear incidental rather than central to the cluster\u2019s primary theme.","confidence":"High","size":26,"edges":124,"triangles":345,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":10},{"id":"GO:0098869","count":8},{"id":"GO:0055114","count":7},{"id":"GO:0080058","count":5},{"id":"GO:1903026","count":5}]},{"hash":"1248972865890346245","title":"Unknown","description":"Top GO terms span heart and brain development, muscle differentiation, transcription regulation, xenobiotic response, cobalamin biosynthesis, aerobic respiration, and general cell growth, indicating no single cohesive function tying the proteins together. With no edges or connected interactions, the cluster lacks a unified theme, so Unknown is the appropriate label.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0014898","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0035690","count":2}]},{"hash":"1325866633420713538","title":"Placental development and immune signaling","description":"The top terms include maternal placenta development and labyrinthine layer blood vessel development, pointing to placental tissue formation. Immune-related terms such as interleukin-4 production and NK T cell differentiation also appear, suggesting an immune signaling component in the placental context. While additional terms cover broader cellular processes (DNA repair, cell migration, apoptosis), the repeated placenta- and immune-associated terms support a cohesive theme around placental development with immune modulation.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:2001275","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0006281","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0001893","count":3}]},{"hash":"1719347638510001419","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035278","count":4},{"id":"GO:0061158","count":3},{"id":"GO:1903883","count":3},{"id":"GO:0010586","count":3},{"id":"GO:1903265","count":3}]},{"hash":"1087143692867842451","title":"Unknown","description":"The top GO terms span heart development and regulation of cardiac hypertrophy, neural processes like long-term synaptic potentiation and memory, miRNA processing, and metanephric (kidney) development, plus a few general apoptosis terms. This spread across heart, brain, and kidney development with no single unifying function or pathway linking them, suggesting the cluster does not reflect a cohesive biological theme.","confidence":"","size":26,"edges":5,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903244","count":11},{"id":"GO:1900271","count":10},{"id":"GO:1903799","count":10},{"id":"GO:0072205","count":10},{"id":"GO:0006919","count":10}]},{"hash":"1279327838541185465","title":"Unknown","description":"The top GO terms cover a wide range of processes\u2014from development (cartilage condensation, Wnt signaling) to reproduction (sperm capacitation), immune responses (defense to Gram-positive bacteria, response to fungal origin), metabolism (response to glucose), transcription, and other signaling activities. This breadth suggests the proteins do not share a single coherent function or pathway, but rather reflect a heterogeneous cluster. Therefore, no concise, unified label is apparent beyond Unknown.","confidence":"","size":26,"edges":5,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001502","count":10},{"id":"GO:0071226","count":10},{"id":"GO:0046827","count":9},{"id":"GO:0006351","count":9},{"id":"GO:0071333","count":8}]},{"hash":"992702462643223575","title":"Neural development and cell-cycle regulation","description":"The cluster is enriched for core gene-regulatory and cell-division processes: DNA-templated transcription, DNA replication, and the mitotic cell cycle are highly represented, alongside neural development terms such as forebrain development and neural tube closure. While some other terms (skeletal development, immune defense, ER-stress-induced apoptosis) appear, the dominant signal is developmentally oriented transcriptional control coupled with cell division, with a notable emphasis on neural development.","confidence":"Medium","size":26,"edges":12,"triangles":2,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":17},{"id":"GO:0006260","count":16},{"id":"GO:0000278","count":16},{"id":"GO:0001501","count":15},{"id":"GO:0030900","count":15}]},{"hash":"1120801145971552899","title":"Vacuolar amino acid and ion transporters","description":"The proteins are enriched for GO terms describing transmembrane transport into and out of the vacuole for several amino acids (lysine, arginine, glutamate, tyrosine, histidine, proline) and for lithium and potassium ions, plus a note on cellular response to potassium starvation. This points to a cohesive set of vacuolar membrane transporters handling amino acids and ions, potentially coordinated by GTPase-regulated trafficking. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0090517","count":2},{"id":"GO:1990818","count":2},{"id":"GO:0090518","count":2},{"id":"GO:0090515","count":2}]},{"hash":"1301691468672640241","title":"Unknown","description":"The GO terms cover a wide range of unrelated cellular processes (DNA replication and repair, intracellular transport, cell division, organelle-specific export, metal response, meiosis-related condensation, transport of amino acids, and immunity), with no single cohesive function tying all proteins together. Therefore a meaningful, specific label cannot be assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":4},{"id":"GO:0006289","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0090529","count":2},{"id":"GO:0046689","count":2}]},{"hash":"1843257584579218474","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":149,"triangles":453,"max_degree":22,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":12},{"id":"GO:0048026","count":12},{"id":"GO:0010610","count":11},{"id":"GO:0000398","count":10},{"id":"GO:0006378","count":8}]},{"hash":"2049438839490498112","title":"Spliceosome and ER stress response","description":"This cluster combines strong signals for mRNA splicing and spliceosome/snRNP assembly with ER stress\u2013related processes (unfolded protein response, chaperone-assisted refolding, ERAD, and regulation of translation initiation during ER stress), suggesting a link between RNA processing and protein quality control under stress. Some other GO terms (DNA replication, gluconeogenesis regulation) may be incidental. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0000387","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1037593394711680320","title":"ER-Golgi vesicle transport and intracellular trafficking","description":"Dominant GO terms point to components of the secretory pathway, with strong representation of ER-to-Golgi vesicle transport, intracellular transport, and retrograde Golgi-ER transport, indicating a core trafficking function. Additional terms related to transcription, cell division, and various stress/nutrient responses suggest regulatory roles linked to transport. Thus the label emphasizes the main theme (trafficking) while acknowledging associated regulatory signals.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0006886","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1955257002187056902","title":"DNA repair and RNA processing","description":"The cluster prominently includes base-excision repair and DNA recombination terms, indicating genome maintenance functions, alongside RNA processing terms such as RNA splicing and regulation of mRNA stability. This combination suggests a group of proteins involved in nuclear genome maintenance and RNA metabolism. Some terms are obsolete or secondary (e.g., aging, positive regulation of nuclear receptor activity), but the core theme remains genome integrity and RNA processing.","confidence":"Medium","size":26,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":3},{"id":"GO:0008380","count":2},{"id":"GO:2000327","count":2},{"id":"GO:0080111","count":2},{"id":"GO:1900087","count":2}]},{"hash":"61295546792800360","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning DNA replication and cell cycle (nuclear processes), ER protein folding and unfolded protein response (proteostasis), heat response, translational frameshifting, and regulation of nuclear export, plus photosynthesis and visual perception (plant/sensory processes). The combination does not reveal a single cohesive function, and the cluster shows weak connectivity (edges 4, no triangles). Therefore no clear, shared theme can be assigned.","confidence":"","size":26,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0009408","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0007049","count":2}]},{"hash":"899159611141635837","title":"ER Protein Quality Control and Unfolded Protein Response","description":"The dominant terms cluster around ER-based protein folding and quality control, including response to unfolded protein, chaperone-assisted refolding, and ER-associated degradation (ERAD). While RNA processing and transcription terms appear as background cellular processes, they do not negate the central ER stress/quality-control theme; pancreas-related terms may reflect secretory cell context but are less central to the core function. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008380","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0060707","count":2}]},{"hash":"1757843556080725832","title":"Transcription and ribosome biogenesis core machinery","description":"The GO terms show core nuclear processes: transcription by RNA polymerases I, II, and III, RNA-templated transcription, and RNA processing, plus ribosome biogenesis and protein homooligomerization, indicating proteins involved in fundamental gene expression and ribosome assembly. While there are a few broad terms like apoptotic process and T cell differentiation, the dominant theme is transcription/biogenesis.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0042254","count":1},{"id":"GO:0006360","count":1},{"id":"GO:0042797","count":1}]},{"hash":"994336380353573971","title":"Innate antiviral defense","description":"This cluster is dominated by GO terms pointing to innate immune activity and antiviral defenses (innate immune response, defense response to virus). While there are additional terms related to RNA processing and ubiquitination present, the strongest signals center on antiviral immunity, suggesting a grouping of proteins involved in host defense rather than a single cohesive molecular process. The lack of edges also suggests annotations drive the clustering rather than tight functional connectivity, so I assign a medium level of confidence.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":4},{"id":"GO:1901407","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0006378","count":3}]},{"hash":"991166241065592209","title":"Mitosis exit, microtubule nucleation, and nuclear import","description":"The top GO terms converge on mitotic progression (exit from mitosis, G2/M transition), microtubule nucleation, and nuclear import (NLS-bearing proteins), with supporting signals for GTPase regulation and RNA handling. This points to a coherent module coordinating cell division with cytoskeletal dynamics and nuclear-cytoplasmic transport, despite sparse direct interactions in the cluster.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0010458","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0007020","count":3},{"id":"GO:0051028","count":3}]},{"hash":"171929674770492694","title":"DNA Replication and Repair Machinery","description":"The top GO terms are dominated by DNA repair and replication processes (base-excision repair, nucleotide-excision repair, Okazaki fragment processing in mitotic replication, DNA biosynthesis, and DNA-templated transcription) along with cell division. This suggests the cluster consists of proteins involved in maintaining and duplicating the genome. Some other terms are older/obsolete annotations but do not change the overall theme.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006288","count":2},{"id":"GO:0006297","count":2},{"id":"GO:1903461","count":2},{"id":"GO:0071897","count":2},{"id":"GO:0051301","count":2}]},{"hash":"2023088176212834948","title":"Signal transduction and actin dynamics","description":"Top terms point to GPCR signaling, Rho/Ras regulation, lamellipodium assembly, and vesicle priming, all indicative of signal transduction coupled to actin remodeling and membrane trafficking. This suggests the cluster centers on coordinated signaling and cytoskeletal/membrane remodeling that underlies cell movement and exocytosis-related processes.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0060313","count":3},{"id":"GO:0007340","count":3}]},{"hash":"118170199420236076","title":"Neural development and transcriptional regulation","description":"These proteins show enrichment for neural development terms (forebrain development, hippocampus development, neural tube closure) and for DNA-templated transcription regulation (DNA-templated transcription, mitotic cell cycle). The mix points to a cluster of factors coordinating neural development through transcriptional control, with some additional stress- or regulation-related roles that can arise in developmental contexts.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0001501","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006349","count":3}]},{"hash":"645242483737178543","title":"Unknown","description":"The GO terms in this cluster are highly heterogeneous, with centriole/centrosome-related processes appearing alongside diverse physiological processes (hypoxia response, erythrocyte maturation, muscle contraction, renal absorption, hepatic stellate cell activation, etc.). There isn\u2019t a single cohesive function linking the majority of terms, so a specific, representative label cannot be confidently assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007099","count":1},{"id":"GO:0051298","count":1},{"id":"GO:0010457","count":1},{"id":"GO:2000490","count":1},{"id":"GO:0051291","count":1}]},{"hash":"1242785411221779041","title":"Mitochondrial Translation and RNA Modification","description":"The top GO terms point to mitochondrial protein synthesis (mitochondrial translation) and RNA modification activities (rRNA base methylation, tRNA methylation, tRNA queuosine biosynthesis), suggesting a cohesive module around mitochondrial gene expression and RNA processing. Co-factor biosynthesis terms (molybdopterin, biotin, PQQ, porphyrin-related) may reflect metabolic support for mitochondrial enzymes, reinforcing a broader mitochondrial biosynthesis module. Confidence: Medium","confidence":"Medium","size":25,"edges":300,"triangles":2300,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0006777","count":3},{"id":"GO:0032543","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006782","count":2},{"id":"GO:0018189","count":2}]},{"hash":"853637399948403133","title":"Multi-substrate membrane transporters","description":"This cluster is dominated by GO terms for transmembrane transport of diverse substrates\u2014ions (potassium, phosphate, nitrate), xenobiotics, and several sugars (arabinose, galactose, fucose, sialic acid)\u2014indicating a common theme of broad membrane transport activity.","confidence":"High","size":25,"edges":27,"triangles":0,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0042891","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0035435","count":3},{"id":"GO:0006855","count":3}]},{"hash":"540718288328212299","title":"Bacterial stress and metabolism cluster","description":"The terms point to cellular responses to various stresses (cadmium, hydrogen peroxide) and a set of core metabolic/biosynthetic processes (gluconeogenesis, LPS biosynthesis, cell division, 2-oxobutyrate biosynthesis). The mix suggests a bacterial module combining stress response pathways with basic metabolism rather than a single specialized pathway. Some obsolete GO terms and an odd \u201cresponse to morphine\u201d term appear as noise, but the overall theme remains stress and metabolism.","confidence":"Medium","size":25,"edges":126,"triangles":292,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043278","count":7},{"id":"GO:0071276","count":5},{"id":"GO:0070301","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0009103","count":5}]},{"hash":"2225056363115331955","title":"Protein acetylation pathways","description":"The top GO terms are dominated by acetylation-related processes (N-terminal acetylation, various peptidyl and histone acetylations, spermine acetylation), suggesting a unifying theme around acetyltransferase activity across diverse substrates. Additional terms reflect metabolic contexts that use acetylation steps (N-acetylglucosamine metabolism, melatonin biosynthesis, mycothiol biosynthesis), supporting a broad acetylation-centered cluster. Some terms (like angiogenesis) are less direct but may reflect regulatory roles of acetylation in signaling. Confidence reflects a plausible, cohesive theme but not a perfectly tight one due to some broader terms.","confidence":"Medium","size":25,"edges":11,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046208","count":10},{"id":"GO:0001525","count":10},{"id":"GO:0030187","count":9},{"id":"GO:0017196","count":9},{"id":"GO:0043967","count":9}]},{"hash":"1758848540541500976","title":"Cell-cycle Regulation and Developmental Signaling","description":"This cluster is dominated by terms related to cell-cycle control (G2/M transition, mitotic cell cycle) and tissue development (Schwann cell development, myoblast fusion, cardiac muscle proliferation regulation), with supporting signals from pathways like Wnt and polarity/localization processes (kinetochore localization, bud site selection). While there are some neuronal signaling terms, the overall theme ties cell division to developmental signaling across different cell types.","confidence":"Medium","size":25,"edges":112,"triangles":196,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":17},{"id":"GO:0014044","count":17},{"id":"GO:0060079","count":17},{"id":"GO:0071333","count":16},{"id":"GO:0000086","count":16}]},{"hash":"2134830528807598781","title":"Stress-Response Transcription and Signaling","description":"The cluster centers on transcriptional regulation and RNA processing (DNA-templated transcription, mRNA processing, transcription factor activity) with stress-activated signaling (p38 MAPK cascade). It also includes immune- and metal-stress responses (cellular response to cadmium, LPS, neutrophil clearance) and proteostasis (proteasomal ubiquitin-dependent degradation), suggesting a cohesive role in adjusting gene expression and signaling under environmental and inflammatory stress, alongside protein turnover.","confidence":"Medium","size":25,"edges":76,"triangles":176,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0090090","count":8},{"id":"GO:0032436","count":8},{"id":"GO:0006397","count":8},{"id":"GO:0071276","count":8}]},{"hash":"369073786705933393","title":"Developmental transcription and cytoskeletal regulation","description":"This cluster is dominated by GO terms tied to transcription and chromatin processes (DNA-templated transcription, mRNA splicing, nucleosome assembly, ubiquitin-dependent protein catabolic process) and also to cytoskeletal remodeling and development (actin filament bundle assembly, cell migration, heart and uterus development, Wnt signaling). The combination suggests proteins that coordinate gene expression programs during development while also regulating the cytoskeleton for morphogenesis and tissue formation. The lack of direct edges in the graph notwithstanding, the functional themes point to developmental transcriptional control coupled with cytoskeletal dynamics.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0007507","count":2},{"id":"GO:0010735","count":2},{"id":"GO:0090263","count":2}]},{"hash":"494988279673970630","title":"Unknown","description":"The 25 proteins map to a wide range of GO terms spanning metabolism, signaling, development, translation, and immune activation, with no dominant shared function or pathway. The absence of cohesive theme and no network edges make it inappropriate to assign a specific label beyond Unknown.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045723","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0042921","count":2},{"id":"GO:0048339","count":2},{"id":"GO:0006144","count":1}]},{"hash":"36628143955586682","title":"Regulation of signaling, apoptosis, and cell migration","description":"This cluster is dominated by terms about negative regulation of signaling pathways (Ras, GTPase) and processes tied to cell survival and movement (apoptosis, cell polarity, migration). While several terms are development-specific, the shared theme is regulatory control over signaling and cellular outcomes, including proliferation, survival, and migration.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046580","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0060313","count":2},{"id":"GO:0060268","count":2}]},{"hash":"281393918121971568","title":"Unknown","description":"The top terms show a mix of redox-related processes, post-translational modifications, cell division and spindle checkpoint regulation, glucose metabolism regulation, and distinct biosynthetic pathways (antibiotics and wybutosine). This scattered collection lacks a single coherent biological theme or function that would unify the cluster, suggesting either a heterogeneous set of proteins or annotation noise. Therefore I cannot assign a specific, representative name with confidence.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0018401","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0032364","count":1},{"id":"GO:1901874","count":1}]},{"hash":"905362627514946728","title":"Nuclear RNA processing and cell-cycle regulation","description":"The cluster\u2019s top GO terms cluster around RNA splicing and regulation of alternative splicing, plus negative regulation of transcription by RNA Pol II, pointing to nuclear gene-expression control. Also present are cell-cycle related terms (G2/M transition, exit from mitosis) and DNA repair/ubiquitin-dependent degradation, suggesting coordination between RNA processing, transcription, and cell-cycle progression. Some terms like viral process and cytoplasmic translation regulation appear ancillary, but the core theme remains nuclear RNA processing linked to cell-cycle control.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008380","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0042787","count":1},{"id":"GO:0070911","count":1}]},{"hash":"1094105328190268335","title":"Ubiquitin-dependent protein degradation","description":"This cluster is defined by GO terms centered on ubiquitination and related protein-removal pathways (K48-linked ubiquitination, autoubiquitination, and ubiquitin-dependent ERAD), pointing to ubiquitin-mediated protein regulation and turnover as the core function. Other terms touch on telomere maintenance and DNA repair, but the dominant signal is ubiquitin-driven degradation and regulation of protein fate.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006471","count":3},{"id":"GO:0061587","count":2},{"id":"GO:0000723","count":2},{"id":"GO:0070936","count":2},{"id":"GO:0019433","count":2}]},{"hash":"454485151625937370","title":"Neural Sensory Signaling and Development","description":"The dominant terms point to neural sensory signaling and development: detection of mechanical stimuli for pain, thermoception, and capsazepine response, along with ephrin signaling and oligodendrocyte differentiation. These together suggest nervous system\u2013related sensory perception and development. Some terms, like cell cycle and telomere maintenance, don\u2019t fit as neatly and imply broader roles for some proteins, so the cohesion isn\u2019t perfect. Overall, the cluster centers on neural sensory perception and development.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":6},{"id":"GO:0090501","count":5},{"id":"GO:0050966","count":5},{"id":"GO:0070431","count":5},{"id":"GO:0050955","count":5}]},{"hash":"1381698936088187107","title":"Endomembrane Trafficking and Autophagy Regulation","description":"The top GO terms point to membrane-related processes such as endomembrane organization, phosphatidylinositol phosphate biosynthesis, endocytosis (pinocytosis), focal adhesion/membrane linkage, and autophagosome assembly, with ubiquitination as a regulatory layer. While a couple terms are less directly related (myelin assembly, androgen receptor signaling), the dominant pattern is vesicle trafficking and autophagy control.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0060765","count":2},{"id":"GO:0032288","count":2},{"id":"GO:0048041","count":2},{"id":"GO:0042070","count":2}]},{"hash":"2252324722513361749","title":"Ribosome biogenesis and translation initiation","description":"Top terms strongly point to ribosome assembly and translation control, with emphasis on ribosome biogenesis (GO:0042254), formation of the translation preinitiation complex (GO:0001731), translation reinitiation (GO:0002188), and maturation of SSU rRNA (GO:0000462), plus GCN2-mediated signaling indicating stress-related translation regulation. While Arp2/3-related actin nucleation terms appear, the core theme is the biogenesis of the translation machinery and its regulation.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0060733","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0036265","count":3}]},{"hash":"491997873205964185","title":"Diverse Catabolic Pathways","description":"The top GO terms show multiple substrate-specific catabolic processes (chlorophyll, triglycerides, uracil) and a major aromatic compound degradation pathway (beta-ketoadipate). While there are some biosynthetic and detoxification terms also present, the clear recurring theme is the breakdown of diverse compounds, indicating a cluster centered on catabolic metabolism across substrates.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0015996","count":7},{"id":"GO:0017000","count":6},{"id":"GO:0098869","count":6},{"id":"GO:0009102","count":5},{"id":"GO:0008284","count":5}]},{"hash":"2301204423831294777","title":"Chromatin Regulation and Neural Development","description":"This cluster centers on GO terms related to chromatin modification (histone methylation) and transcription (DNA-templated transcription), with several terms pointing to neural development processes (cerebellar cortex development, gliogenesis, regulation of differentiation). While some terms are broader (cell cycle, immune-related regulation), the combination suggests a group of proteins involved in chromatin-mediated transcriptional control during neural development. Confidence reflects partial alignment due to some non-neural terms, hence a Medium score.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051567","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0032088","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1736892389418870576","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061158","count":4},{"id":"GO:1903883","count":4},{"id":"GO:0035278","count":4},{"id":"GO:0010586","count":4},{"id":"GO:1903265","count":4}]},{"hash":"403954116124424522","title":"GABAergic Signaling and Neurite Morphogenesis","description":"These proteins cluster around GABAergic synaptic transmission and cytoskeletal remodeling for neurite outgrowth, with small GTPase signaling and actin dynamics (filopodium assembly, axon extension) and associated Golgi trafficking, suggesting a module involved in neuronal communication and growth.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045792","count":3},{"id":"GO:0000266","count":3},{"id":"GO:1900026","count":3},{"id":"GO:0046847","count":3},{"id":"GO:0051932","count":3}]},{"hash":"1200587170466869805","title":"Transmembrane Transporters and Small-Molecule Metabolism","description":"The top GO terms show several transmembrane transport processes (potassium, phosphate, xenobiotic, etc.) along with metabolism of small molecules like fucose and arabinose. This points to a cluster of membrane transport proteins handling ions and small metabolites, with some accompanying metabolic activities. The lack of interactions within the cluster does not undermine this functional theme, though a few terms are obsolete.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0002088","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0008209","count":2},{"id":"GO:0042891","count":1}]},{"hash":"1300954599064331201","title":"Calcium-dependent signaling in neural and cardiac development","description":"This cluster centers on calcium-regulated signaling pathways, notably the calcineurin-NFAT cascade, which ties to neural differentiation and morphology (dendrite morphogenesis, miRNA processing regulation) and to heart development. The presence of neural-associated terms (visual perception, dendrite morphogenesis) alongside heart development supports a shared theme of calcium-dependent signals governing neural and cardiac development, with broader signaling regulation indicated by kinase activity terms.","confidence":"Medium","size":24,"edges":108,"triangles":105,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0055114","count":3},{"id":"GO:1903799","count":2},{"id":"GO:0007507","count":2}]},{"hash":"1489700152741962453","title":"Metabolism and Signaling Regulation","description":"This cluster includes diverse GO terms spanning metabolism (amino acid catabolism, oxaloacetate and kynurenine pathways, porphyrinogen and biotin biosynthesis) as well as signaling and transcription (Notch signaling, cellular response to insulin, DNA-templated transcription), suggesting a broad network where metabolic state interfaces with signaling and gene regulation rather than a single pathway.","confidence":"Medium","size":24,"edges":195,"triangles":979,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042853","count":10},{"id":"GO:0019878","count":9},{"id":"GO:0007219","count":9},{"id":"GO:0032869","count":9},{"id":"GO:0097053","count":9}]},{"hash":"1370847293314794220","title":"ER Stress and DNA Repair","description":"The top GO terms cluster around proteostasis and stress responses: ubiquitin-dependent ERAD, unfolded protein response, and heat-related protein response indicate ER and proteostasis stress. Additional terms for DNA damage tolerance and nucleotide-excision repair suggest a linked genome maintenance response under stress. A few terms touch immune signaling or kidney development, which may reflect multifunctionality, but the dominant theme appears to be cellular stress response with emphasis on protein quality control and DNA repair.","confidence":"Medium","size":24,"edges":20,"triangles":1,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0009408","count":3},{"id":"GO:0006986","count":3},{"id":"GO:0070911","count":2}]},{"hash":"1521026229201166394","title":"Cerebellar development and neurotransmitter metabolism","description":"The top GO terms point to cerebellar development (Purkinje cell layer morphogenesis) and neural signaling (Wnt pathway) with neurotransmitter aspects (L-glutamate biosynthetic process). Additional metabolic terms for sterol/ubiquinone biosynthesis and oxidation-reduction suggest mitochondrial-related metabolism common in neurons. The mix indicates a cluster centered on cerebellar development with accompanying metabolic and signaling processes.","confidence":"Medium","size":24,"edges":15,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0016126","count":2},{"id":"GO:0016049","count":2},{"id":"GO:1901006","count":2},{"id":"GO:0021692","count":2}]},{"hash":"2202161007618722842","title":"Embryonic morphogenesis and placental development","description":"Based on the enriched GO terms, the cluster centers on developmental tissue formation, especially placental morphogenesis, trophoblast differentiation, EMT in heart-associated structures, and cartilage development. These themes point to a cohesive role in embryonic morphogenesis and placental development, with EMT processes contributing to tissue remodeling during embryogenesis.","confidence":"High","size":24,"edges":13,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051096","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0060669","count":2},{"id":"GO:0048260","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1085356680962359484","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":272,"triangles":1938,"max_degree":23,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":20},{"id":"GO:0048026","count":20},{"id":"GO:1903608","count":14},{"id":"GO:0000398","count":14},{"id":"GO:0071031","count":13}]},{"hash":"632514409252437957","title":"Cranial skeletal and nervous system development","description":"This cluster is dominated by GO terms tied to embryonic cranial skeleton morphogenesis, overall skeletal system development, and nervous system development, with related signaling pathways (ephrin receptor signaling, JNK cascade) and processes common in developing tissues (calcium-dependent exocytosis, translation regulation). The combination points to a cohesive developmental program guiding cranial skeletal formation alongside neural development; the other terms align with proliferative and signaling activities typical of embryonic cells.","confidence":"High","size":24,"edges":14,"triangles":0,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":19},{"id":"GO:0006260","count":19},{"id":"GO:0007399","count":19},{"id":"GO:0045956","count":19},{"id":"GO:0045727","count":18}]},{"hash":"835347944877995193","title":"Splicing, Translation, and Cytoskeleton in Development","description":"The terms indicate both fundamental gene expression processes (mRNA splicing via spliceosome; translation initiation and reinitiation) and cytoskeletal dynamics (Arp2/3 actin nucleation; microtubule-based movement), along with several development-related processes (spinal cord development; lens fiber cell differentiation; prostate gland development; multicellular organism growth) and nutrient response. Taken together, the proteins likely participate in core cellular machinery that drives development and tissue formation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0021510","count":3},{"id":"GO:0007018","count":3},{"id":"GO:0070306","count":3}]},{"hash":"1125997671845018839","title":"Diverse microbial metabolism","description":"This cluster includes proteins associated with a broad range of metabolic pathways, including antibiotic and biotin biosynthesis, PHB biosynthesis, uracil catabolism, beta-ketoadipate degradation, triglyceride catabolism, and phospholipid turnover, plus a general response to toxic substances. The lack of a single dominant pathway and the diversity of GO terms suggest a general metabolic collection rather than a tightly connected function, so a label reflecting broad microbial metabolism is most representative.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0042619","count":5},{"id":"GO:0009102","count":4},{"id":"GO:0006212","count":3}]},{"hash":"2218577251220683222","title":"Redox metabolism and detoxification","description":"The cluster centers on oxidation-reduction processes, cellular redox homeostasis, and detoxification, with supporting signals from aromatic compound degradation and secondary metabolism (antibiotic biosynthesis, beta-ketoadipate, PHBV). This suggests a unifying theme of redox-balanced metabolism and processing of xenobiotics/metabolites.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0042619","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0034720","count":2}]},{"hash":"1159394095349041281","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0007568","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0036265","count":4}]},{"hash":"642159633353589843","title":"Neural development and dopaminergic signaling","description":"These proteins show a clear emphasis on neural development and dopamine-related signaling, with terms like nervous system development, substantia nigra development, branching morphogenesis of a nerve, and positive regulation of dopamine receptor signaling. Wnt signalosome assembly supports neural morphogenesis, while other terms reflect general cellular processes; overall, the dominant theme ties to neural/dopaminergic function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035690","count":5},{"id":"GO:1904887","count":4},{"id":"GO:0060161","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0042088","count":4}]},{"hash":"1151051201348878043","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0098789","count":2},{"id":"GO:0045657","count":2},{"id":"GO:0000480","count":2}]},{"hash":"28761340852425976","title":"Mitochondrial gene expression and metabolism","description":"The strongest connected terms point to mitochondrial functions: DNA-templated transcription (reflecting mitochondrial gene expression), protein import into the mitochondrial matrix, and regulation of mitochondrial membrane permeability, complemented by metabolic processes such as triglyceride biosynthesis and amino acid catabolism. While other terms (e.g., cell cycle and viral processes) appear, the core cluster centers on mitochondrial-associated transcription, import, and metabolism.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0042219","count":1},{"id":"GO:0046902","count":1},{"id":"GO:1903740","count":1},{"id":"GO:2000134","count":1}]},{"hash":"1478797797323814275","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010192","count":3},{"id":"GO:0006295","count":3},{"id":"GO:0006284","count":2},{"id":"GO:0000717","count":2},{"id":"GO:0006363","count":2}]},{"hash":"1346094769526735485","title":"Ubiquitination and Proteasomal Degradation","description":"The terms are dominated by ubiquitination-related processes (K48-, K6-, K11-linked ubiquitination, autoubiquitination, ubiquitin-dependent protein catabolic process) and histone catabolic process, indicating a cluster of proteins involved in tagging substrates for degradation and chromatin-related regulation, with links to TNF signaling and necroptosis regulation.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070936","count":9},{"id":"GO:0051865","count":9},{"id":"GO:0042787","count":9},{"id":"GO:0036205","count":8},{"id":"GO:1903265","count":8}]},{"hash":"1446792448292537911","title":"Porphyrin, Heme, and Chlorophyll Biosynthesis","description":"The cluster\u2019s most prominent GO terms are directly related to tetrapyrrole biosynthesis: protoporphyrinogen IX biosynthetic process, heme biosynthetic process, and chlorophyll biosynthetic process, indicating a shared function in producing porphyrin-based pigments. A few transport-related terms appear less central and may reflect incidental annotations. Overall, the core theme strongly supports a biosynthetic focus on porphyrin/heme/chlorophyll pathways.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006782","count":2},{"id":"GO:0015995","count":2},{"id":"GO:0006783","count":2},{"id":"GO:0048388","count":1}]},{"hash":"87215838974230243","title":"Unknown","description":"The GO terms are highly heterogeneous, including xenobiotic stimulus response, immobilization stress, cGMP signaling, smell perception, retinal cone development, neutrophil homeostasis, and regulation of cardiac muscle contraction. There isn\u2019t a clear, single functional theme linking these processes, and the lack of connections (edges/triangles) supports an Unknown label with None confidence.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0035902","count":3},{"id":"GO:0045737","count":3},{"id":"GO:0071321","count":2},{"id":"GO:0007608","count":2}]},{"hash":"361828921601801455","title":"Unknown","description":"The GO terms span diverse processes with no single shared function, including cell division, mitotic cycle, DNA repair, ubiquitin-related protein turnover, and vesicle trafficking, plus development and metabolism. This heterogeneity suggests no cohesive cluster function; thus Unknown.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0010449","count":2},{"id":"GO:0090526","count":2},{"id":"GO:0070914","count":2},{"id":"GO:0035523","count":2}]},{"hash":"1597978899542784006","title":"ER Stress Signaling and Protein Phosphorylation","description":"The terms point to an ER-centric stress and signaling theme, with intrinsic apoptotic signaling in response to ER stress, the ubiquitin-dependent ERAD pathway, and TORC1 signaling, alongside widespread phosphorylation events (protein phosphorylation; phosphorylation). Additional RNA-related terms (mRNA transport; negative regulation of endoribonuclease activity) suggest a broader stress-related post-transcriptional regulation. Several terms (brain development, antibiotic response, invasive growth in glucose limitation) are less cohesive with the core theme, but the dominant GO annotations support a cluster centered on ER stress\u2013driven signaling and phosphorylation. Confidence: Medium","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0070059","count":2}]},{"hash":"145410766198750150","title":"Mechanosensory and Post-Translational Signaling","description":"The cluster is enriched for mechanical sensing terms (thermoception, detection of mechanical stimulus, response to muscle stretch) and post-translational modification processes (protein ubiquitination, PARylation and auto-PARylation), with an immune signaling hint via the NOD2 pathway. This suggests a theme where mechanical stress signals are modulated by ubiquitin- and ADP-ribosylation-based signaling, making a mechanosensation-plus-PTM focus most representative.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0016032","count":3},{"id":"GO:0050966","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0050955","count":3}]},{"hash":"1509054337267200573","title":"Developmental transcriptional regulators and organogenesis","description":"These proteins are linked to broad embryonic development and organ formation. GO terms include DNA-templated transcription and processes such as heart development, placenta and pancreatic cell development, left-right patterning, cartilage morphogenesis, and EMT-related events in heart formation. This pattern suggests a set of transcriptional regulators coordinating lineage specification and organogenesis rather than a single pathway.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0060806","count":3},{"id":"GO:0003323","count":3},{"id":"GO:0060707","count":3},{"id":"GO:0003198","count":3}]},{"hash":"387962081634289707","title":"Embryogenesis and Organogenesis","description":"The top GO terms center on development and tissue formation\u2014placental and pancreatic cell development, trophoblast differentiation, EMT in heart cushion formation, cartilage morphogenesis, and endocrine system development\u2014highlighting broad organogenesis and differentiation processes. A few terms pull toward neural development (learning, glutamatergic synaptic transmission), but the dominant signal is embryonic organ formation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060806","count":2},{"id":"GO:0003323","count":2},{"id":"GO:0060707","count":2},{"id":"GO:0003198","count":2},{"id":"GO:0060536","count":2}]},{"hash":"1755299477559283763","title":"Retinoid and steroid lipid metabolism","description":"This cluster is enriched mainly for biosynthetic and metabolic processes related to vitamin A derivatives (retinol, retinal, retinoic acid) and lipid/steroid pathways (glucocorticoid biosynthesis, sphingolipid biosynthesis, androgen catabolic), suggesting a cohesive theme around biosynthesis and turnover of lipid-soluble signaling molecules and retinoids. Some terms like antibiotic biosynthesis may be outliers, but the dominant signal supports retinoid and steroid lipid metabolism.","confidence":"Medium","size":23,"edges":10,"triangles":0,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":10},{"id":"GO:0055114","count":10},{"id":"GO:0042574","count":9},{"id":"GO:0042572","count":9},{"id":"GO:0006355","count":9}]},{"hash":"608409090348260650","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":247,"triangles":1649,"max_degree":22,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0000463","count":4},{"id":"GO:0000480","count":4}]},{"hash":"588983150958441215","title":"Developmental growth and cytoskeletal remodeling","description":"The GO terms cluster around tissue development and morphogenesis (heart morphogenesis, spinal cord development), overall organism growth, and dynamic cytoskeletal processes (lamellipodium assembly, Arp2/3 regulation, actin nucleation) plus growth signaling (TORC1) and basic cell processes like division and splicing. This suggests a theme of developmental growth coordinated with cytoskeletal regulation, with a few peripheral terms such as splicing contributing to gene expression. Overall, a coherent but broad link to development and cytoskeleton.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003007","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0034316","count":2}]},{"hash":"328727612303573054","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":3},{"id":"GO:0090502","count":3},{"id":"GO:1905639","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0042793","count":2}]},{"hash":"185875473785392820","title":"Mitochondrial Metabolite and Ion Transport","description":"The top GO terms point to transport and regulation related to mitochondria, including CoA transmembrane transport, citrate transport, deoxynucleotide transport, and import/export of Mg2+, Mn2+, and Fe into mitochondria, as well as regulation of mitochondrial membrane permeability. This suggests a function group focused on mitochondrial exchange of metabolites and metal ions, rather than a single signaling or structural role. The occasional obsolete terms and a liver regeneration term likely reflect annotation noise rather than a core function, but the mitochondrial transport theme is strong enough to justify the label.","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097274","count":4},{"id":"GO:0000002","count":3},{"id":"GO:0035349","count":3},{"id":"GO:0006843","count":3},{"id":"GO:0046902","count":3}]},{"hash":"1139925764541164020","title":"Developmental transcriptional regulation and lineage differentiation","description":"The enrichment centers on DNA-templated transcription and multiple lineage-differentiation terms (placental/trophoblast, cartilage, pancreatic, megakaryocytes), pointing to transcriptional control of embryonic development and lineage specification.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0043046","count":5},{"id":"GO:0000122","count":4},{"id":"GO:0045654","count":4},{"id":"GO:0060806","count":4}]},{"hash":"1177923229672056260","title":"Unknown","description":"The GO terms span DNA repair, cardiac development, immune lineage commitment, growth, and various stress responses, with no clear shared function and no edges connecting proteins, so there is no cohesive theme to name this cluster.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0003179","count":1},{"id":"GO:0048738","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0002360","count":1}]},{"hash":"1385286995519319753","title":"Inflammatory and stress signaling regulation","description":"GO terms center on down-regulation of inflammatory signaling pathways (NF-\u03baB, TNF, LPS response) and related cellular stress responses. While there are some developmental terms and mentions of other pathways (Wnt, DNA damage\u2013p53\u2013apoptosis, mismatch repair), the recurring theme is modulation of inflammatory/stress signaling rather than a single cohesive enzymatic function.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042347","count":1},{"id":"GO:0033209","count":1},{"id":"GO:0034051","count":1},{"id":"GO:0042771","count":1},{"id":"GO:0071222","count":1}]},{"hash":"1821363059337452507","title":"Immune-Metabolic Signaling","description":"The top GO terms point to immune processes (hemopoiesis, interleukin-4 production, B cell maturation) and metabolic/endocrine signaling (gluconeogenesis, insulin signaling, platelet activation, cardiac contraction). This suggests a cluster of proteins involved in broad signaling crosstalk between immune and metabolic pathways, with some cardiovascular-related functions represented as well. The terms are diverse, so the label reflects a general theme rather than a single precise pathway.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":3},{"id":"GO:0030097","count":2},{"id":"GO:1901998","count":2},{"id":"GO:0032633","count":2},{"id":"GO:0002344","count":2}]},{"hash":"53433745582849037","title":"Ubiquitin-Mediated NF-kappaB Signaling","description":"The cluster shows strong enrichment for ubiquitination and proteasomal degradation processes (autoubiquitination, K48-linked, K6-linked), plus NF-kappaB pathway components (I-kappaB phosphorylation, NIK activation) and TNF signaling. This pattern suggests a cohesive module where ubiquitin tagging governs protein turnover and drives NF-kappaB signaling.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":8},{"id":"GO:1903265","count":8},{"id":"GO:0042787","count":8},{"id":"GO:0036205","count":7},{"id":"GO:0033209","count":7}]},{"hash":"1692086004425647945","title":"DNA recombination and repair in meiosis and immunity","description":"The GO terms cluster around DNA damage response, repair, and recombination, including meiotic mismatch repair, gene conversion, intra-S checkpoint signaling, and maintenance of DNA repeats, as well as somatic hypermutation and IgA isotype switching. This points to a cohesive theme of genome stability through recombination and repair across meiosis and antibody diversification.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031573","count":4},{"id":"GO:0045910","count":2},{"id":"GO:0007534","count":2},{"id":"GO:0010777","count":2},{"id":"GO:0043570","count":2}]},{"hash":"996372220558979808","title":"Kidney development and morphogenesis","description":"The GO terms cluster around embryonic organ formation with a strong emphasis on kidney-related processes: kidney development, branching involved in ureteric bud morphogenesis, and pronephros morphogenesis. Additional terms reflect broader developmental patterning (cartilage condensation, left-right asymmetry) and signaling. The mix suggests a developmental program centered on nephrogenesis rather than a single molecular pathway. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031587","count":1},{"id":"GO:0007259","count":1},{"id":"GO:0001502","count":1},{"id":"GO:0001822","count":1},{"id":"GO:0001658","count":1}]},{"hash":"645830608964632057","title":"Diverse Signaling and Stimulus Response","description":"The top GO terms point to various signaling pathways and responses to stimuli (heat, salicylic acid, vitamin D, vasopressin signaling, sensory/pain signals) as well as post-transcriptional gene regulation (mRNA stability) and development-related processes. This mix suggests a broad network of proteins involved in general signal transduction and stimulus-response rather than a single, cohesive function.","confidence":"Low","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043488","count":3},{"id":"GO:1900383","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0060743","count":2},{"id":"GO:0009408","count":2}]},{"hash":"1990163658814733265","title":"Unknown","description":"The top GO terms are diverse across species and processes: transcription, heart development, hypoxia response, cell cycle, mRNA transport, and even fungal sporulation events. The list lacks a cohesive shared function or tissue context, and there are cross-kingdom terms (ascospore formation, karyogamy) that don\u2019t align with a single cluster theme. Because of this heterogeneity, there isn\u2019t a clear, representative label beyond Unknown.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0008284","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0006469","count":2}]},{"hash":"409572109565408429","title":"Chromatin remodeling and histone acetylation","description":"The top GO terms cluster around chromatin regulation and histone modification, including transcription initiation-coupled chromatin remodeling, N-terminal lysine acetylation, and histone acetylation (H2B/H3-K9). These points suggest a cohesive function in epigenetic control of transcription. A few terms about uterine development appear unrelated to core function and may reflect broader or misannotated associations, but do not override the dominant chromatin-related pattern.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902661","count":2},{"id":"GO:0045815","count":2},{"id":"GO:1903709","count":2},{"id":"GO:0043969","count":2},{"id":"GO:0035948","count":2}]},{"hash":"1569012875353898236","title":"Unknown","description":"The Top Terms span DNA replication, translation, metabolism, multiple developmental processes, immune differentiation, cardiac hypertrophy, and ion transport, with no shared functional cue and no edges linking members, indicating a highly heterogeneous set rather than a coherent single-function cluster.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0035753","count":2},{"id":"GO:0014898","count":2}]},{"hash":"1719708273614701620","title":"Mitochondrial Transporters and Ion Homeostasis","description":"The cluster shows a strong enrichment for mitochondrial-related transport activities: transport of coenzymes (CoA, NAD), nucleotides, citrate, and iron/manganese/magnesium ions, along with regulation of mitochondrial membrane permeability. This points to a cohesive set of mitochondrial transporter proteins and channels that coordinate metabolite flux and ionic balance within mitochondria. One term (liver regeneration) appears as an outlier, likely a misannotation, but does not undermine the central mitochondrial transport theme.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":21},{"id":"GO:0035349","count":21},{"id":"GO:0006843","count":21},{"id":"GO:0046902","count":21},{"id":"GO:0030302","count":21}]},{"hash":"723096038815065699","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":181,"triangles":733,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":2},{"id":"GO:0031425","count":2},{"id":"GO:0000961","count":2},{"id":"GO:0001975","count":2},{"id":"GO:0051412","count":2}]},{"hash":"969998213315115569","title":"MAPK/ERK and Insulin Signaling Regulation","description":"This cluster centers on modulation of signaling pathways, especially negative regulation of the ERK1/ERK2 cascade and the insulin receptor signaling pathway, plus components involved in dephosphorylation and ubiquitin-mediated protein sorting. Together these terms point to coordinated control of cell proliferation and signal attenuation, with links to endothelial barrier processes, rather than a single enzymatic function. ","confidence":"High","size":22,"edges":86,"triangles":146,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070373","count":9},{"id":"GO:0000173","count":8},{"id":"GO:2001275","count":8},{"id":"GO:0008285","count":8},{"id":"GO:0008286","count":8}]},{"hash":"1627384424809782871","title":"PNS Myelination and NFAT Signaling","description":"Dominated by terms for peripheral nervous system myelination and calcineurin-NFAT signaling, with supporting terms on postsynaptic calcium regulation and excitatory synaptic potential, suggesting a neural development/synaptic signaling module centered on NFAT activity.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0022011","count":4},{"id":"GO:0051533","count":4},{"id":"GO:1903799","count":3},{"id":"GO:0033173","count":3},{"id":"GO:0050774","count":3}]},{"hash":"1008834158714609381","title":"ER stress\u2013linked protein quality control","description":"The terms cluster around chaperone-assisted refolding, ERAD/ubiquitin-proteasome\u2013mediated degradation, and regulation of translation under ER stress, plus nuclear QC. This points to a common theme of maintaining proteome quality during stress, especially in the endoplasmic reticulum.","confidence":"High","size":22,"edges":21,"triangles":1,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070389","count":4},{"id":"GO:1900035","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0031204","count":4},{"id":"GO:0090084","count":4}]},{"hash":"701089673704767415","title":"Membrane transport and neurotransmitter loading","description":"The top GO terms cluster around transmembrane transport of various ions and metabolites (potassium, sodium, nitrate, sialic acid, fucose, xenobiotics, 4-hydroxyphenylacetate) and a key neuronal function, neurotransmitter loading into synaptic vesicles. This combination strongly suggests proteins involved in membrane transport and vesicular loading rather than a single substrate pathway. Some terms appear noisy (e.g., heart development, obsolete transport) but do not override the dominant transport theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0006004","count":2},{"id":"GO:0015739","count":2},{"id":"GO:1900754","count":2}]},{"hash":"1539892668820717005","title":"DNA replication, repair, and ribosome biogenesis","description":"The top GO terms cluster around core cellular maintenance: DNA replication, DNA repair, cell division, and ribosome biogenesis, pointing to genome maintenance and protein synthesis machinery as the main theme. Additional signals for autophagy and Golgi-related protein retention suggest supporting roles in protein turnover and trafficking, but the dominant signal is fundamental growth and genome upkeep.","confidence":"Medium","size":22,"edges":17,"triangles":7,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0010124","count":3}]},{"hash":"269145531655868486","title":"Rhizobial transcription and RNA modification with nodulation","description":"The terms cluster around transcriptional control (DNA-templated transcription, negative regulation of transcription by RNA polymerase II) and multiple RNA modification processes (rRNA methylation, tRNA wobble uridine modification, RNA guanine-N7 methylation, arginine methylation). The presence of nodulation and cobalamin biosynthesis, plus antibiotic biosynthesis, suggests a Rhizobium-like bacterial context with secondary metabolism and plant-symbiosis traits. Overall, it points to bacterial gene expression control and RNA modification in a nodulation-capable, metabolically versatile microbe.","confidence":"Medium","size":22,"edges":114,"triangles":280,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0017000","count":7},{"id":"GO:0031167","count":6},{"id":"GO:0000122","count":5},{"id":"GO:0002098","count":5}]},{"hash":"2293709045271932575","title":"Lipid and nucleotide metabolism with antibiotic response","description":"This cluster groups proteins associated with lipid catabolic processes (triglyceride, monoacylglycerol, phosphatidylserine catabolism), nucleotide catabolism (uracil), and antibiotic-related processes (antibiotic biosynthesis and response), along with general metabolic terms like nitrogen utilization and PHB biosynthesis. The common thread is metabolism and breakdown of lipids and small molecules, with some antibiotic-related activity, suggesting a metabolism-focused cluster rather than signaling or structural roles.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0017000","count":5},{"id":"GO:0042619","count":4},{"id":"GO:0019433","count":4},{"id":"GO:2000124","count":4}]},{"hash":"2258099463903741662","title":"DNA replication and genome maintenance","description":"The top GO terms point to core nuclear processes: DNA replication, mitotic centrosome separation, RNA quality control via nonsense-mediated decay, and a DNA damage response (SOS). Taken together, these reflect a theme of genome maintenance and replication stress response, with a few outlier terms (e.g., certain developmental annotations) likely representing annotation noise. ","confidence":"Medium","size":22,"edges":6,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0007100","count":8},{"id":"GO:0000184","count":8},{"id":"GO:0006268","count":8},{"id":"GO:0009432","count":8}]},{"hash":"1044075711269434546","title":"Neural polarity and membrane trafficking","description":"The cluster is dominated by GO terms tied to brain/nervous system development, formation of radial glial scaffolds, and establishment of neuronal polarity (apical/basal localization). It also includes trafficking-related terms (Golgi to plasma membrane transport, protein localization to Golgi) and synaptic vesicle budding, pointing to neurons coordinating development with membrane trafficking and synaptic readiness. ER stress response appears in neural contexts, supporting cellular quality control during development, reinforcing a cohesive neural development and trafficking theme.","confidence":"High","size":22,"edges":144,"triangles":565,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0045197","count":19},{"id":"GO:0007420","count":19},{"id":"GO:0043001","count":19},{"id":"GO:0034976","count":19},{"id":"GO:0045176","count":19}]},{"hash":"1268446356796546761","title":"Ubiquitination and Proteasomal Degradation","description":"The top GO terms are centered on ubiquitin-dependent processes: autoubiquitination, ubiquitin-dependent protein catabolic processes, and specific ubiquitin linkages (K6, K48) related to tagging proteins for degradation, including ERAD. Additional terms like histone catabolic processes and TNF-mediated signaling reflect the broader roles of ubiquitination in turnover and signaling. Together, these points indicate a cohesive cluster of proteins involved in ubiquitination pathways and proteasomal/ERAD degradation mechanisms.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":10},{"id":"GO:0042787","count":10},{"id":"GO:0030433","count":8},{"id":"GO:0036205","count":8},{"id":"GO:1903265","count":8}]},{"hash":"1200479515206966163","title":"Synaptic signaling and plasticity","description":"The top GO terms include excitatory postsynaptic potential and long-term synaptic potentiation, indicating a focus on neuronal signaling and synaptic plasticity. Other terms (hormone stimulus response, heart development, cell cycle regulation) are less representative of the cluster\u2019s core function, but the neural signaling themes are dominant. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071374","count":3},{"id":"GO:0043065","count":2},{"id":"GO:1903799","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0006469","count":2}]},{"hash":"306783533130206353","title":"Developmental signaling and gene regulation","description":"Top terms span development (ectoderm, organ identity, cuticle patterning) and regulation of signaling and gene expression (TORC1, GTPase activity, STAT dephosphorylation, mRNA transport, serine dephosphorylation), suggesting a cluster of proteins involved in developmental signaling and post-translational regulation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0048496","count":3},{"id":"GO:0042518","count":3},{"id":"GO:0051028","count":3},{"id":"GO:0035293","count":3}]},{"hash":"1739606054536736586","title":"Developmental transcriptional regulation and chromatin modification","description":"Top GO terms center on transcriptional control by RNA polymerase II and chromatin modifications, with developmental contexts like heart development and endodermal fate commitment. Despite no observed edges or interactions in the network, the repeated themes point to a coordinated transcriptional program during development, involving Pol II-driven transcription and histone modification processes.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0070527","count":2},{"id":"GO:0033314","count":2},{"id":"GO:0007507","count":2}]},{"hash":"917317326355224565","title":"Membrane transporters for xenobiotics and sugars","description":"This cluster shows multiple GO terms tied to transport across membranes for a variety of substrates, including xenobiotics, sugars (sialic acid, urate, fucose), aromatic compounds (4-hydroxyphenylacetate), and potassium ions. The prominence of \"xenobiotic transport\" and related transmembrane transport terms, along with a cellular response to glucose starvation, points to a cohesive group of transporter proteins handling diverse substrates and metabolic stress. The outlier term about replicative senescence is less connected to transport function and likely noise. Overall, the dominant theme is membrane transport activity for inorganic and organic substrates.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042891","count":3},{"id":"GO:0006004","count":3},{"id":"GO:1904728","count":3},{"id":"GO:0015739","count":3},{"id":"GO:0042908","count":3}]},{"hash":"1318804808237912133","title":"TLR-driven bacterial component sensing and inflammasome activation","description":"These proteins cluster around innate immune recognition of bacterial components, as shown by GO terms for defense against Gram-positive bacteria, detection of lipopolysaccharide, and cellular responses to LPS. They also include signals for Toll-like receptor pathways (TLR2, TLR3) and the MyD88-dependent axis, along with NLRP3 inflammasome assembly and non-canonical NF-kB signaling, pointing to a coherent module of TLR-guided sensing that can activate inflammasome responses in bacterial contexts.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":4},{"id":"GO:0071222","count":3},{"id":"GO:1900227","count":3},{"id":"GO:0032497","count":3},{"id":"GO:0071726","count":3}]},{"hash":"729693718656402451","title":"NFAT Calcium Signaling Regulators","description":"The strongest signals in this cluster are terms related to regulation of the calcineurin-NFAT signaling cascade (positive and negative regulation), pointing to a core theme of calcium-dependent transcriptional regulation. Other terms (sulfur amino acid biosynthesis and root hair development) appear peripheral or collateral, suggesting some annotation noise but not conflicting with the NFAT-centered motif.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001015","count":2},{"id":"GO:0070886","count":2},{"id":"GO:0051533","count":2},{"id":"GO:0019379","count":1},{"id":"GO:0006750","count":1}]},{"hash":"906020637170772209","title":"GPCR-driven kinase signaling and synaptic plasticity","description":"This cluster is dominated by GO terms tied to G protein-coupled receptor (GPCR) signaling and regulation of kinase activities, including positive regulation of GTPase activity, autophosphorylation, and serine/threonine kinase activity. Terms like cellular response to hypoxia, short-term memory, and regulation of long-term synaptic potentiation hint at neuronal signaling and plasticity, suggesting the proteins function in signaling cascades that modulate synaptic strength. A few terms (ABA signaling, mitotic cell cycle, mRNA transport) may reflect broader signaling roles or cross-species annotations, but the central theme appears to be GPCR-mediated kinase signaling and its link to plasticity. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":7},{"id":"GO:0043547","count":6},{"id":"GO:0031954","count":6},{"id":"GO:0071902","count":6},{"id":"GO:0071456","count":5}]},{"hash":"471677120853464550","title":"DNA replication and cell cycle regulation","description":"This cluster is driven by core cell-cycle and genome-maintenance terms: DNA replication (GO:0006260), DNA repair (GO:0006281), mitotic cell cycle (GO:0000278), and G2/M transition (GO:0000086), suggesting a cohesive theme around genome integrity during cell division. Some developmental and signaling terms appear but do not override the dominant DNA/cell-cycle signal.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0048240","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000086","count":2}]},{"hash":"1013897068725065224","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning melanin biosynthesis, lung development, chloroplast RNA processing, mitochondrial RNA modification, cytidine-to-uridine editing, embryo seed dormancy, and antibiotic response, with several obsolete terms. There is no clear shared function linking these terms, suggesting either noisy annotations or a mixed organism dataset rather than a single cohesive protein cluster.","confidence":"","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0042438","count":3},{"id":"GO:0030324","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0090502","count":2}]},{"hash":"361153440524182139","title":"Protein quality control and stress response","description":"The cluster features GO terms tied to translation, heat response, and detection of misfolded proteins, plus involvement in ROS regulation and inflammatory signaling (IL-6 production). Together these point to a cellular stress/homeostasis program focusing on protein quality control, folding, and stress-induced responses, rather than a single specific pathway. Some terms like virion assembly and telomere localization are less obviously connected and may reflect context-specific roles or annotation noise, but the dominant pattern supports a stress/quality-control theme.","confidence":"Medium","size":21,"edges":202,"triangles":1200,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0019068","count":9},{"id":"GO:0051301","count":6},{"id":"GO:0006412","count":5},{"id":"GO:2000778","count":5},{"id":"GO:1904851","count":5}]},{"hash":"2197498083677631118","title":"Neuronal vesicle trafficking and endocytosis","description":"Based on the top GO terms, there is a clear signal for synaptic vesicle dynamics and membrane trafficking (synaptic vesicle uncoating; endocytosis; neurotransmitter receptor transport from endosome to postsynaptic membrane; proteins localizing to membranes). Additional terms about GTPase activity regulation and cell polarity support roles in vesicle movement and membrane organization. Some terms appear unrelated (e.g., subtelomeric chromatin, kidney development), but the strongest cluster centers on neuronal vesicle trafficking and receptor handling, suggesting this label captures the core function of the group.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000747","count":4},{"id":"GO:0016191","count":3},{"id":"GO:1903778","count":3},{"id":"GO:0031532","count":3},{"id":"GO:0006897","count":3}]},{"hash":"1828968238192664783","title":"Ribosome biogenesis and translation","description":"This cluster is enriched for GO terms related to ribosome assembly, ribosomal biogenesis, and translation, including cytoplasmic translation and ribosomal subunit export, indicating a core function in protein synthesis. The cell cycle and septum assembly terms may reflect coordination between growth, division, and ribosome biogenesis in the organism.","confidence":"High","size":21,"edges":108,"triangles":245,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042274","count":6},{"id":"GO:0042254","count":6},{"id":"GO:0007049","count":6},{"id":"GO:0051301","count":6}]},{"hash":"2091118234716643566","title":"DNA Transcription Regulation and Ubiquitin Pathways","description":"This cluster centers on transcription regulation (DNA-templated) and ubiquitin-related proteostasis (ubiquitin recycling, ubiquitin ligase regulation, ERAD-related processes), with additional links to stress signaling and cell fate (necroptosis). The common theme ties transcription control to ubiquitin-mediated proteolysis, though some terms appear noisy or unrelated.","confidence":"Medium","size":21,"edges":18,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1903070","count":2},{"id":"GO:0035019","count":2},{"id":"GO:0060013","count":1}]},{"hash":"1959496192213352191","title":"Regulatory Signaling and Differentiation","description":"The terms indicate regulatory roles across development and signaling, including adipocyte differentiation, oligodendrocyte differentiation, NOD2 and ephrin signaling, and regulatory processes such as mRNA stability and PARylation. The presence of thermoception and mechanosensation terms adds a sensory dimension, suggesting broad regulatory functions across tissues rather than a single pathway. Overall, this appears to be a broad regulatory cluster rather than a specific functional module.","confidence":"Low","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":3},{"id":"GO:0043488","count":3},{"id":"GO:0090501","count":2},{"id":"GO:0050966","count":2},{"id":"GO:0070431","count":2}]},{"hash":"751728327090336637","title":"Cerebellar development and neural cell-cycle signaling","description":"The cluster shows strong enrichment for cerebellar cortex formation and Bergmann glial differentiation, indicating a cerebellum-focused neural development theme. It also includes cell-cycle regulation terms (negative regulation of CDK activity, mitotic centrosome separation, kinetochore localization) and axon regeneration, suggesting coordination between neural development, cell-cycle control, and neural repair. Metabolic signaling is indicated by insulin signaling and glucose import in response to insulin, adding a metabolic dimension to the neural development program. Overall, a coherent theme around cerebellar neurodevelopment with cell-cycle and metabolic regulation.","confidence":"Medium","size":21,"edges":112,"triangles":278,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021697","count":10},{"id":"GO:0050852","count":10},{"id":"GO:0008285","count":10},{"id":"GO:0045736","count":10},{"id":"GO:0034501","count":10}]},{"hash":"2062183172878080414","title":"Embryonic Development and Stress Response","description":"Most terms cluster around embryonic development (skeletal system, forebrain, neural tube closure) and regulation of transcription, with additional links to stress responses (ER stress\u2013induced apoptosis, cadmium response) and cell-cycle control. This pattern suggests a developmental program that coordinates gene expression with growth and cellular stress management rather than a single specialized function.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001501","count":4},{"id":"GO:0030900","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0006349","count":4},{"id":"GO:0050830","count":4}]},{"hash":"503115695513831557","title":"Developmental gene regulation and DNA replication","description":"This cluster is driven by terms related to developmental processes (forebrain development, neural tube closure, skeletal system development) together with core gene expression and DNA-level processes (DNA-templated transcription, DNA replication, mitotic cell cycle). While there are some stress and defense-related terms present (ER-stress\u2013induced apoptosis, defense response to Gram-positive bacteria), the dominant signal points to regulation of gene expression during development and the associated DNA replication/cell cycle machinery. Overall, a concise label that captures both the developmental and transcription/replication aspects fits best.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0001501","count":4},{"id":"GO:0030900","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0006349","count":4}]},{"hash":"966411132980358940","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":6,"triangles":1,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000480","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3}]},{"hash":"1893409673358484377","title":"Transcription and ribosome biogenesis machinery","description":"The cluster centers on core gene-expression processes: ribosome biogenesis, RNA maturation, and DNA-templated transcription (plus RNA methylation). Development-related terms appear as secondary associations, with a small signal for actin nucleation. This combination indicates a cohesive set of proteins involved in transcriptional control and ribosome assembly.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0006349","count":2}]},{"hash":"210084369131907055","title":"Ion and small-molecule transmembrane transport","description":"The cluster features GO terms centered on transporting ions (potassium, nitrate, phosphate), sugars, and other small molecules across membranes, plus xenobiotic transport, indicating a unified theme of transmembrane transport of diverse solutes. ","confidence":"Medium","size":21,"edges":20,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0042891","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0035435","count":3},{"id":"GO:0006855","count":3}]},{"hash":"1894614903532702954","title":"Glycan biosynthesis and protein O-glycosylation","description":"The top GO terms cluster around carbohydrate construction and modification: glycogen and galactose metabolism, multiple O-glycosylation pathways (via mannose and via N-acetyl-galactosamine), and plant cell wall polysaccharide biosynthesis (cell wall organization, plant-type secondary cell wall biogenesis, homogalacturonan biosynthesis). While some developmental terms appear, the dominant theme is glycan biosynthesis and glycosylation, justifying this label as representative of the cluster.","confidence":"Medium","size":21,"edges":20,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":5},{"id":"GO:0006012","count":4},{"id":"GO:0071555","count":4},{"id":"GO:0030324","count":3},{"id":"GO:0043403","count":3}]},{"hash":"1018520873657617844","title":"DNA replication and mitosis core","description":"The most represented terms are DNA replication (GO:0006260) with 18 annotations and mitotic cell cycle (GO:0000278) with 17, indicating a strong cell-cycle focus. A secondary signal comes from protein localization to the nuclear periphery (GO:1990139), which can relate to nuclear envelope dynamics during cell division. Several terms about development and neuronal processes (e.g., cerebellar cortex formation and glutamatergic synaptic transmission) appear but are less coherent with the core cell-cycle theme and may reflect broad or contextual annotations or noise. Overall, the cluster seems best characterized by cell-cycle and DNA replication machinery.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":18},{"id":"GO:0000278","count":17},{"id":"GO:1990139","count":16},{"id":"GO:2000686","count":16},{"id":"GO:0033129","count":16}]},{"hash":"1913727063890685122","title":"Metabolic Signaling and Transcription Regulation","description":"Centered on signaling pathways (insulin receptor, glucose signaling, SMAD) and transcriptional regulation (RNA Pol II/III), suggesting a cohesive theme of signal transduction feeding into transcription control. Some associations like foam cell differentiation are ancillary.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0075297","count":1},{"id":"GO:0060395","count":1},{"id":"GO:0070898","count":1},{"id":"GO:0060261","count":1}]},{"hash":"626754029377782749","title":"Bone development and cytoskeletal remodeling","description":"These proteins collectively map to skeletal development (cranial skeletal system development; osteoblast fate commitment) and cytoskeletal/membrane dynamics (podosome assembly; positive regulation of GTPase activity; membrane tubulation; cellular fusion). The co-occurrence of bone formation signals with actin-driven membrane remodeling suggests a theme around bone remodeling processes involving osteoblast/osteoclast activity and cytoskeletal rearrangements. The link is coherent but not uniformly strong across all terms, justifying a Medium confidence.","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0007329","count":2},{"id":"GO:0051044","count":2},{"id":"GO:1904888","count":2},{"id":"GO:0071800","count":2}]},{"hash":"1176233518572832201","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0032066","count":1},{"id":"GO:0044806","count":1}]},{"hash":"1139108102753086236","title":"ER Protein Folding and Stress Response","description":"The cluster\u2019s top GO terms center on protein quality control in the endoplasmic reticulum, notably unfolded protein response, ER protein folding, and heat response, which together indicate ER stress and protein-folding homeostasis. Other terms touch on development and general cellular signaling, but the strongest signal remains ER-associated folding and stress processes. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006986","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0035690","count":3}]},{"hash":"174174998114319189","title":"Transmembrane transport of xenobiotics and metabolites","description":"Most terms point to membrane transport of small molecules and xenobiotics (xenobiotic transport/transmembrane transport, sialic acid transport, urate transport, potassium ion transmembrane transport). A couple of outlier terms exist (fucose metabolic process, replicative senescence), but the dominant signal is transport activity. This label captures the core function of the cluster.","confidence":"High","size":21,"edges":17,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0006004","count":2},{"id":"GO:1904728","count":2},{"id":"GO:0015739","count":2}]},{"hash":"99429691783710683","title":"Gene Expression and Translation","description":"The top GO terms cluster around transcription, RNA processing (splicing), and translation (including initiation), plus cell-cycle processes like mitotic division and development, indicating a broad theme of gene expression control and protein synthesis.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007568","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0000398","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0006351","count":4}]},{"hash":"449642417429152637","title":"Mitotic spindle regulation and cell cycle control","description":"This cluster is dominated by terms related to mitosis and spindle dynamics\u2014positive regulation of microtubule polymerization, attachment of spindle microtubules to kinetochores, sister chromatid biorientation, exit from mitosis, meiotic spindle disassembly, and regulation of the cell cycle (including CDK activity). While a couple of terms touch on stress or immune signaling, the core signal is spindle assembly/disassembly and cell cycle progression.","confidence":"High","size":21,"edges":9,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016239","count":2},{"id":"GO:0051987","count":2},{"id":"GO:0031116","count":2},{"id":"GO:1990758","count":2},{"id":"GO:0050860","count":1}]},{"hash":"293153979807898658","title":"Unknown","description":"The top GO terms span neural regulation, DNA repair, transcription, cardiac development, Wnt signaling, muscle contraction, GPCR internalization, and phosphorylation, with no clear single theme connecting them. There are no edges or interactions (Max Degree 0), suggesting heterogeneity or mis-clustering, so a coherent functional label is not apparent.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031914","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0003315","count":2},{"id":"GO:0032423","count":2}]},{"hash":"1727423014199561445","title":"Unknown","description":"The top GO terms span many unrelated cellular processes (transport, endosome organization, ribosome biogenesis, mitotic spindle assembly, cell division, development, fertilization, virion assembly). With no interactions among proteins and no cohesive shared function, there isn\u2019t a clear theme to label the cluster beyond Unknown.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015758","count":2},{"id":"GO:0007032","count":2},{"id":"GO:1901998","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0007018","count":2}]},{"hash":"1636004246781188812","title":"Ubiquitin-Mediated NF-\u03baB/TNF Signaling","description":"The cluster is dominated by ubiquitination-related processes (ubiquitin-dependent protein catabolic process, autoubiquitination, specific linkage types) and by positive regulation of canonical NF-\u03baB signaling and TNF-mediated signaling, indicating a module centered on ubiquitin-regulated inflammatory signaling.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1903265","count":12},{"id":"GO:0042787","count":12},{"id":"GO:0036205","count":11},{"id":"GO:0051865","count":11},{"id":"GO:0085020","count":11}]},{"hash":"991019359164684188","title":"Calcium signaling in heart and brain development","description":"This cluster is driven by terms linking calcium-dependent processes (calcineurin-NFAT signaling, regulation of postsynaptic calcium, cardiac contraction, heart/brain development) and stress responses (hypoxia). Together these suggest a cohesive theme where calcium signaling coordinates cardiac and neural development and function, with a few peripheral terms related to neuronal morphology and miRNA regulation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060048","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0007420","count":3},{"id":"GO:1903799","count":3},{"id":"GO:0007507","count":3}]},{"hash":"1956046497183518752","title":"Endocytosis and actin remodeling","description":"This cluster is dominated by GO terms related to synaptic vesicle endocytosis, actin filament organization, and plasma membrane remodeling, with several entries mentioning regulation of endocytosis and membrane tubulation, pointing to a shared theme of membrane trafficking coupled to cytoskeletal dynamics. While a few terms touch mitochondria or immune signaling, the strongest and most representative signals are endocytosis and actin remodeling, justifying this label.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048488","count":3},{"id":"GO:0097320","count":2},{"id":"GO:0038095","count":2},{"id":"GO:0007015","count":2},{"id":"GO:0030100","count":2}]},{"hash":"869668834767686477","title":"Golgi\u2013endosomal vesicle trafficking and receptor recycling","description":"GO terms cluster around vesicle trafficking through the Golgi and endosomes, including Golgi-to-plasma membrane transport, retrograde transport from endosome to Golgi, intra-Golgi vesicle transport, and receptor recycling with exocytic receptor delivery. Together these point to a coherent membrane trafficking and receptor recycling program, with metabolic cues like insulin signaling and mitochondrial potential playing secondary roles.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":2},{"id":"GO:0051881","count":2},{"id":"GO:0043001","count":1},{"id":"GO:0042147","count":1},{"id":"GO:0050775","count":1}]},{"hash":"539930691255071984","title":"Capsule and cell wall polysaccharide biosynthesis","description":"The top GO terms point to capsule polysaccharide biosynthetic process and cell wall polysaccharide biosynthetic process, indicating the cluster is centered on building polysaccharide components of the cell envelope. Additional terms about transport across the plasma membrane (calcium and amino acids) and cell shape regulation suggest related envelope-associated processes, but the polysaccharide biosynthesis signal is the strongest and most specific theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:1990034","count":2},{"id":"GO:0032973","count":2},{"id":"GO:0019516","count":1},{"id":"GO:0070592","count":1}]},{"hash":"364879142689974788","title":"Unknown","description":"The top GO terms span diverse processes (bone morphogenesis, endosome and receptor recycling, histone methylation, transcription regulation, synaptic transmission, peroxisome organization, and Rho signaling) with no shared functional thread; the cluster has no edges or coherent interactions, making a specific, representative label untenable. ","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003413","count":2},{"id":"GO:0010909","count":2},{"id":"GO:0034968","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0051036","count":1}]},{"hash":"66078174135156429","title":"Endothelial actin remodeling via Rho/Rac GTPase signaling","description":"This cluster is centered on actin cytoskeleton organization and small GTPase pathways (Rho/Rac), with links to endothelial cell behavior such as tube lumen extension and blood vessel remodeling, including both positive and negative regulation of GTPase signaling.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0097498","count":3},{"id":"GO:0035021","count":3},{"id":"GO:0051497","count":3},{"id":"GO:0035024","count":3}]},{"hash":"2047292661170836530","title":"Regulation of Signaling and Metabolism","description":"Based on the top GO terms, this cluster centers on regulation rather than action: regulation of GPCR signaling, cGMP/cAMP signaling, and GTPase activity, along with mitochondrial and energetic processes (membrane permeability, cellular respiration, and cardiac contraction). Although there are some outliers like DNA-templated transcription and smell perception, the dominant theme is proteins that participate in controlling signaling pathways and metabolic state, characteristic of regulatory proteins in cellular signaling and energy production.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0061087","count":2},{"id":"GO:0008277","count":2},{"id":"GO:0046902","count":2},{"id":"GO:0043457","count":2}]},{"hash":"1599464750727782637","title":"DNA Damage Repair and Apoptotic Response","description":"The cluster is dominated by GO terms for DNA repair pathways (base-excision, nucleotide-excision, UV-damage excision, interstrand cross-link repair) and a DNA-damage\u2013induced apoptotic signaling pathway, suggesting a cohesive role in genomic maintenance and damage-triggered cell fate decisions, with a couple of less-specific terms present.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070914","count":1},{"id":"GO:0008630","count":1},{"id":"GO:0006284","count":1},{"id":"GO:0000715","count":1},{"id":"GO:0035264","count":1}]},{"hash":"949166563252131898","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":174,"triangles":878,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0031425","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0031426","count":2},{"id":"GO:0009793","count":2},{"id":"GO:0090617","count":2}]},{"hash":"1719988001324881272","title":"Core metabolism and gene expression","description":"The terms emphasize central carbon metabolism (glycolysis, TCA), redox homeostasis, and essential cellular processes (translation and DNA replication), with tRNA wobble modification tying into translation. Xenobiotic response and embryonic development appear as secondary contexts; overall the cluster maps to core metabolic energy production coupled to gene expression machinery.","confidence":"High","size":20,"edges":55,"triangles":76,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0045454","count":3},{"id":"GO:0002098","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0006412","count":3}]},{"hash":"1646035131096361366","title":"Unknown","description":"Top terms span DNA replication and translation alongside disparate processes like morphogenesis, antibiotic biosynthesis, redox, plasmid maintenance, and intein-mediated splicing. The lack of a shared functional theme and minimal connectivity suggest no single cohesive function for this cluster. ","confidence":"","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0060349","count":2},{"id":"GO:0036342","count":2},{"id":"GO:0017000","count":2}]},{"hash":"1195448985710442145","title":"Ribosome biogenesis and RNA processing","description":"The cluster\u2019s top GO terms cluster around ribosome assembly and RNA metabolism\u2014ribosome biogenesis, SSU rRNA maturation, mRNA export, and spliceosome-mediated splicing, with secondary signals in translational initiation regulation and ncRNA-mediated silencing. Taken together, these proteins likely participate in nuclear RNA processing and ribosome assembly, consistent with a ribosome biogenesis/RNA processing module.","confidence":"High","size":20,"edges":25,"triangles":3,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0006605","count":2}]},{"hash":"16853286357419953","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":130,"triangles":402,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042493","count":3},{"id":"GO:0016554","count":2},{"id":"GO:1905639","count":2},{"id":"GO:0080156","count":2}]},{"hash":"667781726845978252","title":"Glucose metabolism and energy regulation","description":"The cluster is dominated by GO terms tied to glucose handling and energy pathways: phosphorylation, response to glucose, glycolytic process, and gluconeogenesis, with negative regulation of insulin secretion in response to glucose also present. While there are some development- and hormone signaling-related terms (male sex differentiation, steroid hormone receptor complex assembly, prostate gland development) at lower frequency, the primary signal centers on glucose metabolism and energy regulation. Confidence: Medium","confidence":"","size":20,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":3},{"id":"GO:0061179","count":3},{"id":"GO:0009749","count":2},{"id":"GO:0006096","count":2},{"id":"GO:0006094","count":2}]},{"hash":"1593608307825914456","title":"RNA processing and ribosome biogenesis","description":"The cluster combines strong signals for rRNA processing, ribosome biogenesis, and translation initiation complex formation, with several spliceosome-related mRNA processing terms, suggesting a cohesive role in RNA maturation and ribosome assembly.","confidence":"High","size":20,"edges":10,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046690","count":2},{"id":"GO:0006364","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0090305","count":2},{"id":"GO:0006376","count":2}]},{"hash":"1519596145813236649","title":"Chromatin methylation and transcription regulation","description":"The cluster groups proteins enriched for methylation-related processes (histone and protein methylation, peptidyl-lysine dimethylation, peptidyl-arginine methylation, rRNA methylation) and transcriptional control (DNA-templated transcription, negative regulation of RNA polymerase II, rDNA heterochromatin formation). This points to an epigenetic regulatory module centered on chromatin methylation guiding transcription. The cobalamin biosynthetic term appears less connected and may be an outlier.","confidence":"High","size":20,"edges":102,"triangles":231,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009236","count":4},{"id":"GO:0000183","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0031167","count":3},{"id":"GO:0000122","count":3}]},{"hash":"1371964775244586773","title":"Ubiquitin-mediated proteolysis and proteostasis","description":"The cluster\u2019s prominent GO terms center on ubiquitin tagging and proteasomal degradation (K48, K6, K11 linkages, proteasomal catabolic process, autoubiquitination) and stress-related responses (unfolded protein response, NF-kappaB signaling), indicating tight regulation of protein turnover and proteostasis. Additional terms related to transcription and metabolism suggest broader regulatory connections, but the core theme is ubiquitin-dependent protein degradation and its signaling networks. ","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032436","count":4},{"id":"GO:0006006","count":3},{"id":"GO:0046329","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0070936","count":3}]},{"hash":"937628019223549544","title":"Microtubule dynamics and intracellular transport","description":"Top GO terms indicate a strong focus on microtubule- and motor-driven processes: plus-end directed microtubule sliding, mitotic spindle elongation, and nuclear migration along microtubules are all classic cytoskeletal dynamics and transport functions. Regulation of GTPase activity frequently modulates cytoskeletal organization, supporting a microtubule-centric theme. Some terms touch on extracellular signaling affecting cell growth and neural tissue structural organization, which can rely on cytoskeletal architecture, while stress granule disassembly reflects a stress response that can intersect with cytoskeletal remodeling. Overall, the cluster appears to represent microtubule-driven dynamics and intracellular transport as its core function.","confidence":"Medium","size":20,"edges":149,"triangles":596,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019236","count":7},{"id":"GO:0043547","count":7},{"id":"GO:0000022","count":6},{"id":"GO:0000742","count":6},{"id":"GO:0035617","count":6}]},{"hash":"1252272781178721675","title":"Mitotic regulation and developmental signaling","description":"This cluster centers on mitosis and cell-cycle control (negative regulation of CDK activity, G2/M transition, kinetochore localization) but also includes development-related pathways (Wnt signaling, cerebellar cortex formation, myoblast fusion) and signaling in immune contexts (T cell receptor signaling). The common theme is coordination between cell division processes and broader developmental signaling, suggesting proteins that link mitotic control with tissue development and signaling cascades. ","confidence":"Medium","size":20,"edges":103,"triangles":253,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045736","count":13},{"id":"GO:0034501","count":13},{"id":"GO:0046827","count":12},{"id":"GO:0021697","count":11},{"id":"GO:0050852","count":11}]},{"hash":"1763180944949877407","title":"Multi-tissue development and differentiation","description":"The top GO terms point to developmental and differentiation processes across tissues (skeletal system, forebrain, adipose tissue) and associated activities like cell migration and responses to mechanical cues. There are also broader regulatory terms (mRNA processing, negative regulation of CdK activity, telomere maintenance) suggesting a general developmental/regulatory program rather than a single pathway. This supports a label centered on development and tissue differentiation with ancillary regulatory roles.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045736","count":12},{"id":"GO:0006397","count":12},{"id":"GO:0016477","count":12},{"id":"GO:0045444","count":12},{"id":"GO:1904355","count":12}]},{"hash":"2187853219162917114","title":"Cardiac development and muscle regulation","description":"The top GO terms point to heart rudiment formation and negative regulation of striated muscle contraction, with additional signals from Wnt pathway regulation and broader developmental processes (transcription, apoptosis, redox homeostasis). This pattern supports a theme around cardiac development and control of muscle function, rather than a single isolated process, hence a Cardiac development and muscle regulation label with moderate confidence.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0045944","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0003315","count":2}]},{"hash":"224798554690588433","title":"Gene Expression Machinery","description":"This cluster centers on core gene expression processes: DNA-templated transcription, RNA processing (mRNA splicing, RNA methylation), ribosome biogenesis, and translation initiation complex formation. While some developmental and stress-related terms appear, the dominant theme is transcription/processing and ribosome assembly, i.e., the machinery of gene expression.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0036265","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0001731","count":3}]},{"hash":"1902333703980798030","title":"Ubiquitination and ERAD Regulation","description":"This cluster is dominated by GO terms related to ubiquitination and ER-associated degradation (ERAD), including protein ubiquitination and ubiquitin-dependent ERAD pathways, and deubiquitination processes. The presence of regulatory terms around deubiquitinating enzymes and proteasomal degradation suggests these proteins share a function in ubiquitin-proteasome\u2013mediated protein quality control and turnover. Immune signaling and development terms are less central but may reflect broader regulatory roles tied to ubiquitin signaling. Overall, the core theme is ubiquitin-mediated proteolysis and ERAD regulation.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":5},{"id":"GO:0030433","count":4},{"id":"GO:2000157","count":4},{"id":"GO:1903094","count":4},{"id":"GO:1903071","count":4}]},{"hash":"1733279237629724978","title":"Ribosome biogenesis and translation machinery","description":"The top GO terms cluster around ribosome assembly (ribosome biogenesis, maturation of rRNA) and translation-related processes (formation of translation preinitiation complex, translation reinitiation), indicating a core role in protein synthesis. Other terms (transcription, proteasomal degradation, signaling) are broader gene-expression processes that may reflect pleiotropy but do not override the central ribosome/translation theme. Overall, this suggests a cohesive cluster centered on ribosome biogenesis and translation function. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0031146","count":3}]},{"hash":"1940795603919883132","title":"Mitotic cell cycle and proliferation signaling","description":"The cluster is dominated by GO terms tied to cell cycle progression and proliferation (mitotic cell cycle, cell division, positive regulation of cell population proliferation). We also see signaling-related terms such as positive regulation of GTPase activity and protein autophosphorylation, suggesting regulatory pathways that drive cell cycle events. While RNA processing terms are present, the strongest and most frequent signals relate to mitosis and proliferation. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0007205","count":6},{"id":"GO:0008284","count":5},{"id":"GO:0071456","count":5}]},{"hash":"2113597093328188070","title":"Cell cycle regulation and ubiquitin/ADP-ribosylation","description":"This cluster is dominated by GO terms related to the cell cycle (GO:0007049) and post-translational modifications, especially protein ubiquitination (GO:0016567) and ADP-ribosylation (GO:0070212/GO:0070213), plus a note on telomere maintenance and sister chromatid cohesion. While there are also terms tied to neural development and synaptic regulation, the strongest and most coherent signal is the interplay of cell-cycle control with ubiquitin and poly-ADP-ribose modifications that influence chromatin dynamics and chromosome maintenance. Confidence reflects the moderate coherence given the presence of outlier processes. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007049","count":7},{"id":"GO:0071260","count":6},{"id":"GO:0016567","count":6},{"id":"GO:0070213","count":5},{"id":"GO:1904908","count":5}]},{"hash":"2096633470139182293","title":"Mitochondrial import and ER stress response","description":"The cluster centers on mitochondrial-related processes\u2014regulation of mitochondrial membrane permeability and protein import into the mitochondrial matrix\u2014together with ER unfolded protein response, signaling a shared theme of organelle stress management. Additional terms like interferon-beta production and Pol III transcription hint at broader stress-responsive regulation and metabolic signaling that can accompany mitochondrial/ER dysfunction. While some terms are more general (cell cycle regulation, lipid biosynthesis), the dominant pattern points to mitochondrial function intertwined with ER stress signaling.","confidence":"Medium","size":20,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":1},{"id":"GO:1903740","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0010867","count":1}]},{"hash":"468364778433440084","title":"Transcription Regulation and Vesicle Transport","description":"This cluster is driven by GO terms for DNA-templated transcription and its regulation, plus ER-to-Golgi vesicle transport, pointing to a link between gene expression control and intracellular trafficking. The other terms (interferon-beta production, oogenesis, chaeta development, autophagy, nuclear migration) suggest additional, diverse roles or broad multifunctionality, but the strongest cohesive signal lies in transcriptional regulation paired with vesicle transport.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0032728","count":2},{"id":"GO:0007290","count":1},{"id":"GO:0008039","count":1}]},{"hash":"1275124319385264443","title":"Translational Initiation and RNA Regulation","description":"This cluster is dominated by GO terms for translation initiation and its regulation (formation of the translation preinitiation complex, IRES-dependent initiation, regulation of translational initiation), suggesting a common theme of translational control; a few terms touch on RNA surveillance or proteasome-related processes, which can relate to gene-expression regulation at the translational level. The absence of edges implies no tight interaction is shown, but the translational initiation theme best fits the data.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0000338","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0048140","count":2}]},{"hash":"1979704503824261742","title":"Unknown","description":"The terms span signaling pathways (Wnt, NOD2, ephrin), sensory perception (thermoception, mechanical stimulus), cell division, and telomere regulation, with no dominant theme tying all 20 proteins together. I cannot identify a single cohesive function to name the cluster.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":3},{"id":"GO:0035948","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0090501","count":2},{"id":"GO:0050966","count":2}]},{"hash":"72138326157896271","title":"Transcriptional Regulation and DNA Binding","description":"Most frequent GO terms here point to negative regulation of RNA polymerase II\u2013mediated transcription and DNA-templated transcription, plus regulation of DNA binding, suggesting a cluster of transcriptional regulators (DNA-binding factors) modulating RNAP II activity. Other terms are less central, so the core theme is transcription regulation and DNA binding.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0043388","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0080058","count":1},{"id":"GO:0018401","count":1}]},{"hash":"1465383529556046849","title":"Unknown","description":"No clear common function binds the 20 proteins; top GO terms span post-translational modification (ubiquitination, poly-ADP-ribosylation), metabolism, immune signaling, sensory perception, and telomere maintenance, with no edges linking them, so a cohesive label isn\u2019t supported.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0019740","count":2},{"id":"GO:0043304","count":1},{"id":"GO:0090501","count":1}]},{"hash":"1719024369470895485","title":"ER Stress Response and Protein Quality Control","description":"The cluster centers on ER proteostasis: protein folding in the ER, ER-associated degradation and ubiquitin-proteasome quality control, chaperone-assisted refolding, and ER stress\u2013related regulation of translation, suggesting a cohesive role in managing misfolded proteins and maintaining ER function.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0071630","count":2},{"id":"GO:0036494","count":2}]},{"hash":"923638675660979211","title":"Protein Targeting and Trafficking","description":"Top GO terms are dominated by SRP-dependent cotranslational protein targeting to membrane and related transport/targeting terms (to membrane, membrane rafts, nuclear pore assembly, ER-dependent peroxisome organization), suggesting a theme of protein targeting and organelle trafficking. A few terms (taste perception, ABA response) seem incidental and do not fit the core theme. Overall, the label captures the central trafficking-related function suggested by the prominent terms.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006614","count":1},{"id":"GO:0006617","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0090116","count":1},{"id":"GO:0009737","count":1}]},{"hash":"1056774015442932141","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0090162","count":3},{"id":"GO:0007264","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0071803","count":2}]},{"hash":"249655684896382265","title":"Mechanosensory signaling and protein modification","description":"The cluster is dominated by GO terms tied to sensing and responding to mechanical stimuli (cellular response to mechanical stimulus, detection of mechanical stimulus involved in sensory perception of pain, thermoception), suggesting a mechanosensory signaling theme. There are additional but weaker signals for protein regulation via ubiquitination and poly-ADP-ribosylation, plus some cell-cycle and telomere maintenance terms that may reflect broader stress responses. Overall, the mechanosensory signaling axis is the most representative functional thread.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0071260","count":8},{"id":"GO:0016567","count":7},{"id":"GO:0033280","count":6},{"id":"GO:0007049","count":5},{"id":"GO:0090501","count":5}]},{"hash":"309997646823787343","title":"Ras and small GTPase signaling","description":"These proteins cluster around GTPase signaling: strong terms include small GTPase-mediated signal transduction, regulation of GTPase activity, and Ras protein signal transduction; insulin receptor signaling is also present, consistent with RTK\u2013Ras pathways. A few terms (viral process, odor perception, sodium transport) seem unrelated noise. Overall, the group appears to function in Ras/small GTPase\u2013driven signaling networks.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0007264","count":3},{"id":"GO:0046825","count":2},{"id":"GO:0016032","count":2}]},{"hash":"405009471526149004","title":"Sterol biosynthesis and carbohydrate metabolism","description":"These proteins show both sterol biosynthetic processes (ergosterol and cholesterol biosynthesis) and a variety of carbohydrate-related catabolic and salvage pathways (glycolysis via fructose-6-phosphate, fructose and lactose catabolism, D-ribose catabolic, adenosine and AMP salvage). The cluster seems to reflect a broader metabolic theme around lipid and sugar metabolism rather than a single, narrow function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":2},{"id":"GO:0006696","count":2},{"id":"GO:0006695","count":2},{"id":"GO:0019303","count":1},{"id":"GO:0009750","count":1}]},{"hash":"467590342506720656","title":"Cardiac Development and Function","description":"The top terms are strongly centered on heart biology, including heart development, cardiac muscle contraction, and regulation of heart rate, suggesting the proteins cluster around cardiac function. Other terms like translation, tRNA aminoacylation, and autophagy regulation appear, but they seem peripheral and may reflect generic housekeeping functions or annotation noise. Overall, the dominant cardiac-related signals support labeling this cluster as Cardiac Development and Function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0007507","count":2},{"id":"GO:0060048","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0002027","count":2}]},{"hash":"70148734438636887","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046909","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0035646","count":2}]},{"hash":"1626145605966572876","title":"Unknown","description":"The top GO terms span cell division/cell cycle, immune/stress responses (interferon signaling, innate immunity, unfolded protein response), steroid receptor\u2013mediated regulation and development (prostate/male differentiation), plus an odd plant hormone term. There is no single cohesive biological theme linking these terms, so no clear label can represent the cluster beyond Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0071357","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0006463","count":2}]},{"hash":"978166773589574354","title":"Neural transcriptional regulation & ubiquitin signaling","description":"The cluster features GO terms focused on DNA-templated transcription and its regulation, along with ubiquitin-related processes (ubiquitin recycling and negative regulation of ubiquitin ligase activity), plus neural-related terms such as CNS morphogenesis and behavioral responses to ethanol. This suggests a cohesive theme around transcriptional control in neural development/function with modulation by ubiquitin signaling, despite the presence of some obsolete terms. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0060013","count":2},{"id":"GO:0035616","count":2},{"id":"GO:1904378","count":2},{"id":"GO:0006355","count":2}]},{"hash":"1452884368439813370","title":"Ciliary transport and Hedgehog signaling","description":"This cluster is dominated by GO terms pointing to intraciliary transport, cilium assembly, and the Smoothened (Hedgehog) signaling pathway, all hallmarks of ciliary function. Other terms touch on membrane tubulation and retinal photoreceptor-related processes, which can be linked to cilia-based trafficking and signaling in photoreceptors. Collectively, the proteins likely participate in cilium biogenesis and cilia-driven signal transduction.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042073","count":1},{"id":"GO:0007224","count":1},{"id":"GO:0060271","count":1},{"id":"GO:0010925","count":1},{"id":"GO:0033622","count":1}]},{"hash":"1447955482282347528","title":"Ribosome Biogenesis and Translation","description":"The proteins cluster around ribosome biogenesis and protein synthesis, with strong representation of translation (including cytoplasmic translation), tRNA modification, ribosomal large subunit assembly and export from nucleus, indicating a cohesive ribosome-related group.","confidence":"High","size":19,"edges":169,"triangles":935,"max_degree":18,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0002181","count":5},{"id":"GO:0006400","count":5},{"id":"GO:0000027","count":5},{"id":"GO:0000055","count":4}]},{"hash":"1100779227105909293","title":"Mitochondrial Translation and DNA Metabolism","description":"This cluster centers on mitochondrial functions: translation-related GO term, mitochondrial protein import, and mitochondrial DNA metabolic processes, with supporting redox-related terms, suggesting a cohesive module for mitochondrial protein synthesis and genome maintenance.","confidence":"High","size":19,"edges":166,"triangles":887,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0009097","count":2},{"id":"GO:0009099","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1227718167094437839","title":"Quinone and pigment biosynthesis","description":"The cluster shows strong enrichment for chlorophyll, plastoquinone, phylloquinone (vitamin K1), menaquinone, ubiquinone, and heme biosynthesis, pointing to a cohesive function in pigment and cofactor production, particularly in photosynthetic contexts. Some outlier terms (cell division, innate immune response) exist, but they don't override the dominant biosynthetic signal.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0042371","count":1},{"id":"GO:0048034","count":1},{"id":"GO:0015995","count":1},{"id":"GO:0010236","count":1}]},{"hash":"1903657597509017531","title":"Lysine Methylation\u2013Associated Transcription in Cardiac Stress","description":"This cluster is enriched for lysine methylation (peptidyl-lysine methylation/mono/di/tri-methylation) and RNA methylation terms, which point to epigenetic and translational regulation of gene expression. The presence of DNA-templated transcription and cardiac-related terms (heart development, cardiac muscle hypertrophy in response to stress) suggests a cardiac context where methylation-driven transcriptional control is relevant, possibly coordinated with protein kinase signaling. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":3},{"id":"GO:0018026","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0014898","count":2}]},{"hash":"565323408383214038","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":104,"triangles":333,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":9},{"id":"GO:0031047","count":8},{"id":"GO:0006260","count":6},{"id":"GO:0000462","count":6},{"id":"GO:0000398","count":6}]},{"hash":"2300853886455772367","title":"Mitotic chromosome segregation and DNA repair","description":"This label fits the strong mitosis signal: spindle assembly, centrosome separation, and metaphase chromosome alignment all point to chromosome segregation during cell division. Coupled with telomere maintenance via recombination and double-strand break repair pathways, the cluster also emphasizes genome integrity maintenance during division. Additional terms like mRNA transport and regulation of proliferation suggest regulatory layers coordinating these processes. Overall, the proteins seem to form a mitosis-plus-genome-stability module.","confidence":"High","size":19,"edges":34,"triangles":19,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007080","count":4},{"id":"GO:0048364","count":4},{"id":"GO:0007100","count":4},{"id":"GO:0090307","count":4}]},{"hash":"577826677212726220","title":"Membrane Transport Across Organelles","description":"This cluster shows a strong enrichment for transmembrane transport functions across different substrates (xenobiotics, vitamins, cysteine, phospholipids) and mitochondrial oligopeptide export, suggesting a core theme of membrane transport activity and transporter functions bridging organelles and substrates. Some outliers (mercury response, bacteriocin-related terms, stem cell proliferation) are less cohesive with the main signal, but do not override the dominant transport-related pattern.","confidence":"Medium","size":19,"edges":52,"triangles":38,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":17},{"id":"GO:0035461","count":17},{"id":"GO:0046689","count":14},{"id":"GO:0090374","count":14},{"id":"GO:0042883","count":14}]},{"hash":"1025905704276562534","title":"Cell signaling and cell cycle regulation","description":"The cluster shows enrichment for both signaling pathways (T cell receptor signaling, calcium-mediated signaling) and cell cycle processes (mitotic and meiotic cell cycles, CDK activity regulation). While there are additional terms related to extracellular matrix remodeling and immune defense, the strongest common theme is coordinated signaling that modulates cell cycle progression, suggesting a link between signaling cascades and cell cycle control.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0050852","count":2},{"id":"GO:0010614","count":2},{"id":"GO:0050850","count":2},{"id":"GO:1905050","count":2}]},{"hash":"339363174540564723","title":"RNA processing and translation initiation","description":"This cluster centers on mRNA processing steps (splicing, spliceosome assembly, polyadenylation) and translation control (initiation and reinitiation), plus stress-related mRNA stability. The co-occurrence of splice-related GO terms and translation initiation terms suggests proteins involved in RNA maturation and regulation of protein synthesis. Observed obsolescent terms do not negate the core theme.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":5},{"id":"GO:0010610","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0045292","count":5}]},{"hash":"1942881414727362584","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":2},{"id":"GO:0009243","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0019673","count":2},{"id":"GO:0097171","count":2}]},{"hash":"1193158777111337020","title":"NF-kappaB\u2013NOS inflammatory signaling","description":"The cluster\u2019s top GO terms center on positive regulation of nitric-oxide synthase activity and positive regulation of canonical NF-kappaB signaling, both hallmark players in inflammatory and innate immune responses. The presence of a diacyl lipopeptide response term further supports a pattern of innate immune signaling leading to NF-kB activation and NO production. Some terms are obsolete or peripheral (noise), but the core theme ties to inflammation-driven signaling pathways.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051000","count":2},{"id":"GO:0043123","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0072321","count":1},{"id":"GO:0006626","count":1}]},{"hash":"49489843264725799","title":"Developmental signaling and immune differentiation","description":"The top GO terms cover development (placenta, neuron, cell polarity) and immune signaling (T cell differentiation, Fc receptor signaling, JNK cascade, calcium signaling), suggesting a cluster of proteins involved in broad developmental signaling with immune regulation roles rather than a single narrow function.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001890","count":4},{"id":"GO:2000114","count":3},{"id":"GO:0050850","count":3},{"id":"GO:0048666","count":3},{"id":"GO:0009636","count":3}]},{"hash":"1026867872811283657","title":"ER-Golgi vesicle transport","description":"The strongest recurring GO terms point to vesicle trafficking between the endoplasmic reticulum and the Golgi (ER-to-Golgi and Golgi-to-ER transport) and general intracellular protein transport, with positive regulation of GTPase activity supporting trafficking regulation. Other terms such as pigmentation or defense response appear less central but may reflect broader roles in specialized cells; overall, the cluster is best described by ER-Golgi vesicle transport.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071456","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0050830","count":2}]},{"hash":"786317741394437679","title":"Actin Cytoskeleton Remodeling and Cell Adhesion","description":"The top GO terms cluster around actin cytoskeleton organization and dynamics (actin crosslink formation, actin filament bundle assembly, cortical patch localization), along with cell adhesion, epithelial/polarity establishment, Rho signaling regulation, and cell migration. This combination points to a cohesive module that drives actin-driven remodeling to support adhesion, polarity, and movement, with one outlier immune-related term (IL-2 production) likely incidental. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900042","count":2},{"id":"GO:0030035","count":2},{"id":"GO:0071963","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0007155","count":2}]},{"hash":"755410395883460808","title":"Actin cytoskeleton remodeling","description":"The cluster is characterized by GO terms tied to actin dynamics, including lamellipodium assembly, stress fiber assembly, and positive regulation of Rho signaling, pointing to cytoskeletal remodeling and cell motility. Additional terms reflect related roles in vascular permeability and development, but the strongest theme is actin cytoskeleton regulation, making this a concise label that captures the core function of the group.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032790","count":2},{"id":"GO:0043114","count":2},{"id":"GO:0051496","count":2},{"id":"GO:0030032","count":2},{"id":"GO:1904693","count":2}]},{"hash":"316142690244574018","title":"Intracellular vesicle trafficking","description":"The GO terms cluster around intracellular membrane transport, including plasma membrane\u2013to\u2013endosome transport and ER-to-Golgi vesicle trafficking, as well as regulation of vesicle fusion; while signaling terms (Rap, CDK, NFAT) may reflect associated regulation, the common theme appears to be membrane trafficking and its control.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048227","count":3},{"id":"GO:0031578","count":3},{"id":"GO:1902953","count":3},{"id":"GO:0032889","count":3},{"id":"GO:0032486","count":3}]},{"hash":"1713292237983290555","title":"Ribosome biogenesis and LSU assembly","description":"The cluster is dominated by GO terms related to ribosome biogenesis, maturation of LSU rRNA, and assembly of large subunit preribosomes, indicating a cohesive group of proteins involved in ribosome production and large subunit formation. Additional terms touching on mRNA transport and cell division likely reflect connections between ribosome assembly and nuclear/cellular cycle processes. Overall, the primary theme is ribosome biogenesis with emphasis on the large subunit. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0043547","count":4},{"id":"GO:1902626","count":3}]},{"hash":"1654118718090992634","title":"Unknown","description":"Top terms are highly diverse: viral process, protein oligomerization, regulation of synaptic vesicle exocytosis, various catabolic and mitochondrial-related processes, plus several obsolete terms. With no edges or cohesive shared function, there is no clear theme tying these proteins together.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0016032","count":4},{"id":"GO:0051291","count":4},{"id":"GO:2000300","count":3},{"id":"GO:0051289","count":3},{"id":"GO:0018189","count":3}]},{"hash":"1572700670888160682","title":"GPCR signaling and cell migration","description":"The top terms show intracellular signal transduction, GPCR-related signaling, and processes tied to cell movement such as cell migration and integrin activation, along with related adhesion and endocytic activities. Together, these point to a coherent theme of signaling pathways governing cytoskeletal dynamics, adhesion, and motility, with additional notes on mitochondrial fission and Ras regulation that fit within signaling and movement contexts.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0000266","count":3},{"id":"GO:0046580","count":3}]},{"hash":"1949549363783058884","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000967","count":1},{"id":"GO:0090305","count":1},{"id":"GO:0034427","count":1},{"id":"GO:0090503","count":1}]},{"hash":"608450251443229161","title":"Unknown","description":"The terms span several distinct biological processes (innate immune response, defense against virus, centrosome maintenance, mitotic regulation, actin filament network formation, mitochondrial fission, etc.). With no clear unifying function and minimal connectivity, there isn\u2019t a reliable theme to name this cluster beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0051661","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0090141","count":2},{"id":"GO:0051607","count":2}]},{"hash":"2139214691181742605","title":"Unknown","description":"The cluster's top GO terms span multiple, disparate processes: GPCR and ephrin signaling, Wnt signaling, synaptic plasticity regulation, telomere maintenance/capping, spindle assembly, and ADP-ribosylation. There isn't a single dominant function uniting these proteins, making a precise, specific label difficult. Therefore the appropriate label is Unknown with no confidence.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900383","count":2},{"id":"GO:0007205","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0032212","count":2}]},{"hash":"1601348978945898082","title":"Neural differentiation and synapse maintenance","description":"The top GO terms point to neuronal development (pyramidal neuron differentiation) and maintenance of synapses, supported by calcium signaling and NF-kappaB\u2013regulated pathways, indicating a neural connectivity and signaling focus. Some vascular-related terms appear but are peripheral to the core neural theme, which is why the cluster likely represents neural differentiation and synaptic maintenance.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043123","count":3},{"id":"GO:0005513","count":3},{"id":"GO:0008360","count":3},{"id":"GO:0006469","count":3},{"id":"GO:1900748","count":2}]},{"hash":"453932845994941109","title":"Mitochondrial fission and immune signaling","description":"The top GO terms cluster around mitochondrial fission and immune-related signaling (cellular response to GM-CSF), with supporting links to PI3K/AKT signaling, integrin activation, and membrane remodeling. This suggests a module where mitochondrial dynamics are coordinated with signal transduction and cytoskeletal/membrane changes in immune or hematopoietic contexts, rather than a single enzymatic pathway. Some terms are historical/obsolete, but the core theme remains mitochondrial dynamics coupled to signaling.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0000266","count":4},{"id":"GO:0097011","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0010925","count":3}]},{"hash":"12394166606272641","title":"Multi-tissue development and differentiation","description":"The top GO terms span development and differentiation across tissues (skeletal, neuromuscular, cardiac muscle differentiation; myelination; T cell differentiation) along with broad regulatory processes (transcription, DNA repair, signaling). The combination suggests a general regulatory/developmental program rather than a single, cohesive pathway, supported by the diversity of tissues involved and the presence of regulatory terms.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0045944","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0032088","count":3},{"id":"GO:0033138","count":3},{"id":"GO:0046638","count":2}]},{"hash":"325071741301542890","title":"Unknown","description":"The set of GO terms is highly diverse, spanning cardiovascular/endocrine regulation (renin, angiotensin, blood pressure), signaling pathways (MAPK, adrenergic signaling), immune/inflammatory responses, circadian regulation, sensory neuron guidance, hair follicle development, and temperature response. There isn\u2019t a single coherent biological theme tying these terms together, so a specific label isn\u2019t warranted beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007202","count":1},{"id":"GO:1905491","count":1},{"id":"GO:0071883","count":1},{"id":"GO:0002879","count":1},{"id":"GO:0042752","count":1}]},{"hash":"1542317646205053536","title":"Organelle RNA Processing and Lipid Metabolism","description":"The cluster centers on RNA processing in energy organelles (mitochondria and chloroplasts) and associated lipid metabolism (lipid homeostasis, ubiquinone/tocopherol biosynthesis, mitochondrial-related processes). An outlier term for cerebellar Purkinje cell morphogenesis is present but does not define the main theme. ","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0010795","count":1},{"id":"GO:1901006","count":1}]},{"hash":"209773713574290745","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051591","count":3},{"id":"GO:0045892","count":2},{"id":"GO:0031425","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0031426","count":2}]},{"hash":"1639245783382088388","title":"Unknown","description":"The terms include mitochondrial protein import and ATP synthesis alongside lipid biosynthesis and diverse development/immune signals (IL-2 production, T cell regulation, cerebellum morphogenesis). The wide spread of functions does not reveal a single coherent theme, so a precise label is not warranted.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051131","count":2},{"id":"GO:0045041","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0042775","count":1},{"id":"GO:0019432","count":1}]},{"hash":"1513791607761375550","title":"Neural development and cellular trafficking","description":"This cluster includes explicit brain development (GO:0007420) alongside terms for cell proliferation, ribosome biogenesis, mRNA transport, and ER-to-Golgi trafficking, as well as GTPase regulation and autophagy. The combination points to processes governing neural development with growth and intracellular transport, making the label representative, though the spread of terms yields only a Medium confidence.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0016237","count":4},{"id":"GO:0008284","count":3}]},{"hash":"1806492161476966353","title":"Transcription Regulation and Diverse Metabolite Biosynthesis","description":"The top terms emphasize transcriptional regulation (regulation of DNA-templated transcription; DNA-templated transcription) and broad biosynthetic processes (antibiotic, tropane alkaloid, glucocorticoid, retinoic acid, androgen-related), suggesting a cluster that spans regulatory functions combined with diverse metabolic biosynthesis activities.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0006355","count":6},{"id":"GO:0017000","count":6},{"id":"GO:0042619","count":6},{"id":"GO:0046677","count":6}]},{"hash":"587819015352939639","title":"Ubiquitin-Dependent Proteasomal Degradation","description":"These proteins show strong representation of ubiquitin-dependent protein catabolic processes, including autoubiquitination and SCF-dependent proteasomal degradation, across multiple ubiquitin linkage types (K48, K63, K6). The inclusion of histone catabolic process and regulatory links to TNF/JNK signaling suggests the cluster centers on ubiquitin-mediated protein turnover with broader roles in transcriptional and inflammatory signaling.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0051865","count":7},{"id":"GO:0070534","count":7},{"id":"GO:1903265","count":7},{"id":"GO:0046328","count":6}]},{"hash":"1523877948416404371","title":"Unknown","description":"The GO terms are highly diverse, including antibiotic and mercury/metal stress responses, translation, cell septum assembly, peptide transport/immunity, and even stem cell\u2013related processes. This spread suggests no single coherent function tying all proteins together, so a specific thematic label isn\u2019t supported.","confidence":"","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0046677","count":5},{"id":"GO:0006412","count":3},{"id":"GO:0090529","count":3},{"id":"GO:0046689","count":3},{"id":"GO:0090374","count":3}]},{"hash":"37736689074996702","title":"Developmental cell migration and cytoskeleton regulation","description":"The cluster is dominated by GO terms linking actin cytoskeleton dynamics and GTPase-regulated signaling (cell migration, actin organization, GTPase activity). These processes drive developmental morphogenesis, supported by terms for brain and organ development (zona limitans intrathalamica formation, midbrain dopaminergic neuron differentiation, lung induction) and germline/oocyte localization. Some cell division terms are present, but the core theme centers on cytoskeletal remodeling guiding developmental movements and patterning.","confidence":"High","size":18,"edges":15,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000281","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0000011","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0022006","count":3}]},{"hash":"1339711256540319336","title":"Cell Cycle and Migration Regulation","description":"The cluster centers on growth and motility regulation, with strong signals for cell division, cell migration, adhesion dynamics, and TORC1 signaling, plus GTPase-regulated cytoskeleton control. Transcription and mRNA transport reflect coordination of gene expression to support these processes; a potassium transport term is an outlier but can relate to membrane activity during movement. Overall, the theme is growth-linked cell cycle and migration signaling.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0051028","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0006813","count":5}]},{"hash":"283901128850988201","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0022417","count":2},{"id":"GO:0048680","count":2},{"id":"GO:0006458","count":2},{"id":"GO:0006939","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1867154169389197605","title":"Hypoxia signaling and transcription regulation","description":"Terms include detection of hypoxia and hypoxia-inducible factor-1alpha signaling, plus regulation of transcription, pointing to a hypoxia-driven transcriptional control theme. Peripheral terms like placenta development, meiosis, and drug response are less central to the core function. This makes the label a reasonable high-level summary of the cluster\u2019s dominant signal.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006457","count":2},{"id":"GO:0017006","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0000713","count":2},{"id":"GO:0070483","count":2}]},{"hash":"1309313495670076160","title":"Ubiquitin-regulated proteostasis and stress signaling","description":"The top GO terms point to ubiquitin-dependent regulation, including K48-linked and polyubiquitination, and peroxisome receptor recycling, which are central to protein turnover and trafficking. The presence of stress-response and cell-cycle terms (JNK cascade, exit from mitosis, nucleotide-excision repair) suggests a broader ubiquitin-mediated signaling role coordinating proteostasis with stress and division. Overall, the cluster appears to group proteins linked by ubiquitin-regulated proteostasis and stress responses.","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0051026","count":18},{"id":"GO:0070936","count":18},{"id":"GO:0016562","count":18},{"id":"GO:0090089","count":18},{"id":"GO:1902916","count":18}]},{"hash":"913494290663989861","title":"Cytoskeletal dynamics and cell cycle control","description":"This cluster is enriched for Arp2/3-mediated actin nucleation and positive regulation of GTPase activity, pointing to cytoskeletal remodeling. It also includes mitotic spindle assembly and negative regulation of G0 to G1 transition, which align with cell cycle progression. While there are additional hints of chromatin modification and development, the dominant theme tying most terms together is cytoskeleton remodeling coupled with cell cycle regulation. ","confidence":"Medium","size":18,"edges":32,"triangles":9,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0034314","count":6},{"id":"GO:0043981","count":6},{"id":"GO:0043982","count":6},{"id":"GO:0090307","count":6}]},{"hash":"125698771317102527","title":"Nucleocytoplasmic transport and ribosome biogenesis","description":"This cluster is dominated by GO terms related to moving molecules between the nucleus and cytoplasm (nuclear import/export, nuclear pore complex assembly, NLS-bearing protein import, ribosomal protein import into nucleus, ribosomal small subunit export, and mRNA export) and by processes connected to ribosome assembly. The presence of intraciliary transport is ancillary but fits within shared transport machinery themes. Overall, the terms cohere around nucleocytoplasmic trafficking and ribosome biogenesis.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0035735","count":5},{"id":"GO:0000060","count":5},{"id":"GO:0006610","count":5},{"id":"GO:0060188","count":5}]},{"hash":"2269757920761785620","title":"Vesicle Trafficking and Melanosome Biogenesis","description":"The top GO terms point to secretory pathway and vesicle trafficking (COPII coating; ER-to-Golgi and intra-Golgi transport) and pigment organelle formation (melanosome assembly; pigmentation). This suggests the cluster represents proteins involved in vesicle trafficking with a specific link to pigment-containing organelles, despite some related terms touching broader processes like autophagy or cytoskeletal dynamics.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048208","count":1},{"id":"GO:0006891","count":1},{"id":"GO:0006914","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0043473","count":1}]},{"hash":"1561187006096513144","title":"Developmental signaling and proliferation","description":"The cluster shows enrichment for developmental processes (multicellular and skin development) alongside cell-cycle and signaling regulation (mitotic cell cycle, regulation of GTPase activity, and kinase activity). This suggests a theme of coordinated development with growth and signaling control, rather than a single narrowly defined function. Additional terms like mRNA transport and hypoxia response indicate broader regulatory roles in gene expression under stress. Overall, the proteins likely participate in developmental processes intertwined with signaling pathways and proliferation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":7},{"id":"GO:0043588","count":7},{"id":"GO:0008284","count":6},{"id":"GO:0071456","count":6},{"id":"GO:0051028","count":6}]},{"hash":"1709299492048666433","title":"Transcriptional Regulation and mRNA Stability","description":"The top terms cluster around transcription control (negative regulation of transcription by RNA polymerase II, DNA-templated transcription) and post-transcriptional regulation (regulation of mRNA stability), with protein ubiquitination also represented, suggesting a core theme of gene expression regulation and protein turnover. While a few developmental and ER-related terms appear, they are less central to the cluster's major signal.","confidence":"Medium","size":18,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0043488","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0034620","count":1}]},{"hash":"580512009204732936","title":"Neural Sensory Signaling and Regulation","description":"This cluster shows enrichment for terms related to neural/sensory signaling (mechanical pain detection, thermoception, ephrin signaling) and neural differentiation (oligodendrocyte differentiation), along with regulatory processes such as ubiquitination and protein modification. The mix includes some non-neural terms (immune signaling via NOD2, telomere regulation), but the strongest cohesive theme centers on regulatory signaling in neural and sensory contexts. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0045736","count":3},{"id":"GO:0090501","count":2},{"id":"GO:0050966","count":2},{"id":"GO:0070431","count":2}]},{"hash":"1118088123913087684","title":"Translation and tRNA aminoacylation machinery","description":"This cluster is dominated by GO terms related to protein synthesis, including translation (GO:0006412), ribosomal small subunit assembly (GO:0000028), and various tRNA aminoacylation processes (e.g., prolyl-, glycyl-, threonyl-, and mitochondrial tRNA charging), suggesting a cohesive theme around translation machinery. A few single-term annotations (like blastocyst formation or cellulose catabolic process) appear incidental noise and do not override the central translation focus.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0000028","count":1},{"id":"GO:0001825","count":1},{"id":"GO:0006433","count":1}]},{"hash":"505001367760668390","title":"Neural development and synaptic vesicle trafficking","description":"The majority of top terms point to brain development, midbrain dopaminergic neuron differentiation, and regulation of synaptic vesicle exocytosis, suggesting a focus on neuronal differentiation and presynaptic transmission. Additional terms like Golgi-to-plasma membrane transport align with trafficking required for neurons, while a couple of peripheral terms (e.g., mating projection growth, mitotic spindle assembly) may be less related. Overall, a cohesive theme of neural development with vesicle trafficking.","confidence":"Medium","size":18,"edges":15,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0031384","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0010796","count":2},{"id":"GO:0045197","count":1}]},{"hash":"522355800405525779","title":"Neural signaling and synaptic plasticity","description":"The cluster is enriched for neurotransmitter secretion, long-term synaptic potentiation, and dendrite extension, indicating a core focus on neuronal signaling and synaptic plasticity. While additional terms touch on broader signaling pathways (PI-mediated signaling, VEGF receptor signaling) and apoptotic regulation, the predominant theme across the top terms is neural communication and synaptic development.","confidence":"Medium","size":18,"edges":8,"triangles":0,"max_degree":7,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0010796","count":4},{"id":"GO:0031384","count":4},{"id":"GO:0043065","count":4},{"id":"GO:0007269","count":4},{"id":"GO:1903861","count":4}]},{"hash":"1141594379221108887","title":"Embryonic Organogenesis and Differentiation","description":"This cluster\u2019s top GO terms center on embryonic development and organogenesis (pancreas, placenta, heart structures) with processes like EMT, differentiation, and tissue morphogenesis, plus regulatory steps in transcription and mRNA processing. The common theme is developmental differentiation and formation of multiple organs rather than a single biochemical function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0003323","count":3},{"id":"GO:0060806","count":3},{"id":"GO:0003198","count":3},{"id":"GO:0060707","count":3},{"id":"GO:0060536","count":3}]},{"hash":"1934756038536114447","title":"Transcriptional Regulation and Lineage Differentiation","description":"The cluster centers on transcriptional regulation (regulation of DNA-templated transcription) and contains multiple terms about positive regulation of differentiation across various lineages (megakaryocyte, erythrocyte) and even neuron development, suggesting a theme of transcription-driven lineage specification. Additional terms for apoptosis and defense responses may reflect stress-related aspects commonly linked to differentiation processes. Overall, it points to transcription control guiding multi-lineage differentiation rather than a single specific function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006355","count":4},{"id":"GO:0043046","count":4},{"id":"GO:0045654","count":4},{"id":"GO:0010976","count":4}]},{"hash":"661938322145208707","title":"Unknown","description":"Top GO terms are scattered across cytoskeletal remodeling, signaling via autophosphorylation, adhesion, stress responses, and cell death, with no single dominant function connecting the proteins. The lack of edges and the heterogeneous terms suggest no cohesive theme. Therefore Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031037","count":1},{"id":"GO:0010961","count":1},{"id":"GO:1990416","count":1},{"id":"GO:0071454","count":1},{"id":"GO:0051262","count":1}]},{"hash":"1448388738801360622","title":"Actin dynamics and Rho signaling","description":"This cluster is dominated by GO terms tied to actin cytoskeleton remodeling (Arp2/3-mediated nucleation, barbed-end actin capping) and regulation of Rho GTPase signaling, suggesting a core theme of actin dynamics and its signaling regulation, with supportive links to growth and TGF-beta\u2013responsive pathways.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050731","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0071560","count":3},{"id":"GO:0051016","count":3}]},{"hash":"2285270058661818027","title":"Mitochondrial respiration and protein import","description":"Based on the top GO terms, the proteins in this cluster cluster around mitochondrial function: electron transport (NADH to ubiquinone), assembly of respiratory chain components (complex II), and targeting/import/insertion of proteins into the mitochondrial inner membrane. Although a couple of terms touch on development, they are represented only once and do not define the group. The dominant signal is mitochondrial energy metabolism and protein handling, suggesting these proteins work together in respiration and mitochondrial biogenesis.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021536","count":1},{"id":"GO:0010923","count":1},{"id":"GO:0072321","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0045039","count":1}]},{"hash":"351814509248608328","title":"Proliferation, differentiation, and telomere regulation","description":"The top GO terms point to general cellular growth and differentiation processes (cell growth, fat cell differentiation, cell migration) along with regulation of the cell cycle (CDK activity) and genome maintenance (telomere capping/maintenance). This suggests the cluster reflects a proliferation/differentiation program with an emphasis on telomere maintenance, rather than a single signaling pathway. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":4},{"id":"GO:0035994","count":3},{"id":"GO:0045444","count":3},{"id":"GO:0045736","count":3},{"id":"GO:0016049","count":3}]},{"hash":"1683074698782669602","title":"Central carbon metabolism and biosynthetic pathways","description":"This cluster shows enrichment for glycolysis and the TCA cycle (central carbon metabolism) along with multiple biosynthetic processes (biotin, menaquinone, porphyrinogen IX) and even antibiotic biosynthesis, indicating coordinated energy production plus building blocks for cofactors and secondary metabolites.","confidence":"High","size":17,"edges":126,"triangles":554,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":7},{"id":"GO:0017000","count":6},{"id":"GO:0006096","count":6},{"id":"GO:0006782","count":5},{"id":"GO:0055114","count":5}]},{"hash":"1500105770419070144","title":"Unknown","description":"The top GO terms span diverse biological areas, including xenobiotic and cocaine response, regulatory processes (miRNA processing, tRNA locus\u2013related expression), hormone signaling, lipid A biosynthesis, and genome/mitochondrial maintenance, with no single cohesive function tying the proteins together. This suggests the cluster is heterogeneous rather than representing one specific pathway or process.","confidence":"","size":17,"edges":24,"triangles":8,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042220","count":5},{"id":"GO:0035690","count":5},{"id":"GO:0061587","count":5},{"id":"GO:0009245","count":5},{"id":"GO:0006196","count":4}]},{"hash":"1395828542422820286","title":"Hormone and retinoid metabolism","description":"The top GO terms point to vitamin A (retinal/retinol) metabolism, steroid hormone production (androgen and testosterone biosynthesis), and lipid-related processes (cholesterol catabolic), with supporting notes on hormone signaling (JAK-STAT) and thyroid hormone response, suggesting a cohesive theme of hormone and lipid/vitamin metabolism. ","confidence":"Medium","size":17,"edges":133,"triangles":637,"max_degree":16,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042574","count":8},{"id":"GO:0042572","count":8},{"id":"GO:0055114","count":6},{"id":"GO:0008209","count":5},{"id":"GO:0061370","count":5}]},{"hash":"2046633279334911194","title":"Mitochondrial metabolite and ion transport","description":"The top GO terms point to transport and regulation across mitochondrial membranes (CoA, citrate, deoxynucleotides, iron, magnesium, manganese) and to membrane permeability control, suggesting a cohesive module of mitochondrial transporters and regulators. A couple of broader metabolic terms (insulin response, liver regeneration) may reflect systemic metabolic context but do not outweigh the clear mitochondria-centered transport theme. ","confidence":"Medium","size":17,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":5},{"id":"GO:0000002","count":4},{"id":"GO:0035349","count":4},{"id":"GO:0006843","count":4},{"id":"GO:0046902","count":4}]},{"hash":"582467144075179823","title":"Actin Cytoskeleton Remodeling and Adhesion","description":"This cluster is dominated by GO terms pointing to actin cytoskeleton dynamics and cell\u2013substrate interactions: Rac signaling, filopodium and stress fiber assembly, and positive regulation of substrate adhesion-dependent cell spreading, all indicative of actin-driven remodeling and adhesion processes. Additional terms like mitotic spindle assembly support cytoskeletal roles in cell organization, while oxidative detoxification or NF-kappaB regulation appear more peripheral to the core theme.","confidence":"High","size":17,"edges":41,"triangles":58,"max_degree":7,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0098869","count":7},{"id":"GO:0043124","count":7},{"id":"GO:2000255","count":5},{"id":"GO:0032869","count":5},{"id":"GO:0051496","count":4}]},{"hash":"361337489355917476","title":"DNA replication and cell cycle machinery","description":"The cluster is enriched for core processes of genome duplication and mitosis, including DNA replication, DNA-templated transcription, cell division, and CENP-A\u2013mediated chromatin assembly, with supporting links to microtubule dynamics and ubiquitin-related regulation. These together point to a cohesive theme around DNA replication and the mitotic cell cycle, with some ancillary metabolic and RNA-stress related processes.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0019079","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0046034","count":3}]},{"hash":"2120459182383563204","title":"Ubiquitin-Driven Proteolysis and Cell Cycle Checkpoint Signaling","description":"The Top Terms cluster around ubiquitination processes (histone H2A K63-linked ubiquitination, K48-linked ubiquitination, ubiquitin-dependent ERAD, autoubiquitination, and general protein ubiquitination) with connections to proteasomal degradation, chromatin remodeling (histone catabolic process), and cell-cycle control (mitotic spindle assembly checkpoint signaling). Additionally, regulation of NF-kappaB and TNF signaling fits within ubiquitin-mediated signaling networks. This cohesive pattern supports a label focused on ubiquitin-driven proteolysis and associated cell-cycle signaling.","confidence":"High","size":17,"edges":14,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0070535","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0051865","count":4},{"id":"GO:1903265","count":4},{"id":"GO:1903833","count":3}]},{"hash":"1312574773987502424","title":"Unknown","description":"The GO terms are highly diverse, spanning antibiotic and biotin biosynthesis, detoxification, multiple catabolic pathways, lipid metabolism, signaling, and even plant development. There isn't a single cohesive function or theme that ties the proteins together, making a specific, intuitive label inappropriate.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0009102","count":7},{"id":"GO:0098869","count":6},{"id":"GO:0006212","count":5},{"id":"GO:0042952","count":5}]},{"hash":"256752665928598640","title":"Innate Immune and Stress Signaling","description":"These proteins are enriched for innate immune response, JNK cascade, Fc receptor signaling, and responses to toxic substances, suggesting a module of stress-induced immune signaling. Angiogenesis and cell-cycle terms may reflect inflammation-associated remodeling and proliferation, but the dominant theme points to immune-stress signaling.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001525","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0009636","count":4}]},{"hash":"1522911353060217988","title":"Cell Cycle Regulation and Developmental Growth Signaling","description":"The terms cluster around cell cycle control (DNA replication, centrosome cycle, G2/M transition), apoptosis, and growth-regulating pathways (Wnt, Hippo), with developmental processes (keratinocyte differentiation, embryonic cranial skeleton morphogenesis) and modulation of proliferation. This points to a cohesive program coordinating cell-cycle progression with developmental growth and lineage differentiation.","confidence":"High","size":17,"edges":39,"triangles":36,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010571","count":10},{"id":"GO:0007098","count":10},{"id":"GO:0006260","count":10},{"id":"GO:0048701","count":10},{"id":"GO:0060044","count":8}]},{"hash":"436093985448074080","title":"RNA processing and translation regulation","description":"The cluster is dominated by GO terms tied to RNA processing and post-transcriptional control: spliceosome-mediated splicing, splice-site recognition, alternative splicing, small-subunit processome assembly, translation initiation, and miRNA-mediated silencing of translation, plus regulation of mRNA stability under stress. Together these suggest a cohesive theme of post-transcriptional gene expression control rather than a single catalytic process.","confidence":"Medium","size":17,"edges":13,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006376","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0000380","count":1},{"id":"GO:1905663","count":1},{"id":"GO:1902625","count":1}]},{"hash":"707636524857491161","title":"Cellular Stress Signaling and Cell Cycle Control","description":"The top GO terms point to signaling and stress responses (cellular response to cAMP; response to xenobiotic stimulus) alongside regulators of gene expression (regulation of mRNA stability) and cell cycle progression (positive regulation of G1/S transition). This suggests a cohesive theme where signaling cues modulate transcriptional/post-transcriptional control and drive cell cycle decisions, despite some obsolete terms present. ","confidence":"Medium","size":17,"edges":10,"triangles":0,"max_degree":6,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0071320","count":6},{"id":"GO:0042493","count":5},{"id":"GO:2000327","count":4},{"id":"GO:0080111","count":4},{"id":"GO:1900087","count":4}]},{"hash":"1454286540839149090","title":"Neuronal synaptic plasticity and signaling","description":"The cluster is driven by GO terms related to synaptic function and signaling cascades, including long-term synaptic potentiation, synapse assembly, IP3 biosynthesis, and regulation of Rho/Ras pathways, pointing to neuron-specific communication and plasticity processes. While there are some neural development terms (substantia nigra development) and unrelated immune terms, the strongest and most representative theme is neuronal synaptic modulation and intracellular signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0002316","count":3},{"id":"GO:0009395","count":3},{"id":"GO:0035023","count":3}]},{"hash":"2160578485196099811","title":"DNA damage response and proteostasis","description":"The top GO terms point to genome maintenance activities (DNA-templated transcription, DNA replication, DNA recombination, SOS response) alongside protein quality control processes (aggresome assembly, proteasome regulatory particle assembly, ubiquitin-dependent ERAD). Translation appears as a general housekeeping term, suggesting these proteins participate in coordinating gene expression with genome integrity and protein turnover, especially under stress. Thus the cluster likely reflects a group involved in DNA damage response together with proteostasis mechanisms.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006310","count":2},{"id":"GO:0032508","count":2}]},{"hash":"548010713424495833","title":"Unknown","description":"The terms shown are highly heterogeneous, spanning digestion, protein autoprocessing, DNA replication, ERAD/ubiquitin pathways, regulation of APP biosynthesis, renin-angiotensin signaling, MHC II antigen processing, and mesonephros development. There is no single unifying function or pathway tying these proteins together, so a meaningful, specific label cannot be assigned. ","confidence":"","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007586","count":3},{"id":"GO:0016540","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0030433","count":2},{"id":"GO:1903071","count":2}]},{"hash":"127336772842069983","title":"Unknown","description":"The GO terms span RNA processing (mRNA capping, tRNA wobble modification), various protein post-translational/modification processes (tyrosine dephosphorylation, arginine hydroxylation), redox homeostasis, development, and even niche processes like antibiotic biosynthesis and cocaine response. This broad and scattered mix does not reveal a cohesive shared function or pathway for the cluster, so a meaningful, specific label cannot be confidently assigned.","confidence":"","size":17,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0045454","count":3},{"id":"GO:0035335","count":3},{"id":"GO:0021510","count":3}]},{"hash":"887093166446185681","title":"Unknown","description":"The top terms span multiple, seemingly unrelated biological areas (forebrain and mesoderm development, angiogenesis, keratinocyte differentiation, synaptic potentiation, innate immunity, muramyl dipeptide response, cell cycle, and cardiac progenitor proliferation), with no single dominant function or pathway tying them together. The absence of edges also suggests a lack of direct functional connections among proteins in the cluster, supporting an unknown, non-cohesive theme.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:2000811","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0045087","count":2}]},{"hash":"128803631711290272","title":"Polarity and Autophagy with Immune Regulation","description":"The top GO terms point to cellular organization (apical/basal polarity, cell-cell junctions, cell shape) and centrosome-related localization, plus macroautophagy. Additional terms reflect immune context (Th2 differentiation, chemokine regulation, endothelial apoptosis, glial proliferation), suggesting a cluster linking cell architecture and intracellular trafficking with immune signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016236","count":2},{"id":"GO:0060263","count":2},{"id":"GO:0045217","count":2},{"id":"GO:0045630","count":2},{"id":"GO:0035089","count":2}]},{"hash":"2119727791150945681","title":"Cell Migration and Polarity with Stress Responses","description":"The top GO terms cluster around dynamic cell behavior, notably cell migration and establishment of epithelial cell polarity. Additional terms reflect cellular stress responses (protein folding) and hypoxia detection, along with GTPase signaling that can drive cytoskeletal changes. Some terms touch on development and apoptosis, suggesting broader roles, but the strongest signals point to motility, polarity, and stress-related processes; hence this label captures the core theme while acknowledging broader functions.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0033028","count":2}]},{"hash":"1213503010429012559","title":"Regulatory signaling and transcription modifiers","description":"The top GO terms point to regulatory roles rather than core metabolism: protein ubiquitination; negative regulation of transcription by RNA Pol II; regulation of signaling pathways (NOD2, ephrin receptor signaling); sensory perception terms (thermoception, pain) and post-translational modification (poly-ADP-ribosylation). This pattern suggests proteins that modulate signaling and transcription in response to stress or stimuli, rather than enzymes driving a single metabolic process. Confidence: Medium","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0090501","count":2},{"id":"GO:0050966","count":2}]},{"hash":"855684910641232420","title":"Chromatin Remodeling and Transcription Regulation","description":"This cluster is enriched for chromatin- and transcription-related GO terms: DNA-templated transcription, nucleosome assembly, chromatin remodeling, and histone methylation, pointing to a shared role in regulating gene expression via chromatin state. Some terms about heart morphogenesis and IgA isotype switching appear incidental; they are less central to the core theme. Overall, the cluster is best characterized by chromatin-based transcription regulation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0003289","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0010452","count":2},{"id":"GO:0003290","count":2}]},{"hash":"1331213783602314300","title":"Transmembrane Ion and Sugar Transport","description":"Proteins in this cluster are linked to diverse transmembrane transport processes\u2014ions (sodium, potassium, phosphate, nitrate) and sugars/aromatic substrates\u2014and xenobiotic transport across membranes. The unifying theme is membrane transport of ions and simple metabolites, justifying a label centered on transmembrane transport.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070294","count":2},{"id":"GO:0071805","count":1},{"id":"GO:0042891","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0035435","count":1}]},{"hash":"852884667294747720","title":"Transmembrane Ion and Substrate Transporters","description":"The top GO terms are dominated by transmembrane transport activities for ions (potassium, sodium), vitamins, sugars, and xenobiotics, plus membrane hyperpolarization. This pattern points to a cluster of membrane transporter proteins with diverse substrates, rather than a single specific function.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0060081","count":2}]},{"hash":"1164004817235104847","title":"Host chromatin regulation and symbiont-responsive transcription","description":"The cluster's GO terms center on chromatin-level processes (nucleolar RNA Pol I transcription regulation, histone methylation regulation, dosage compensation) and also include host responses linked to symbionts (autophagy activation, ubiquitin-like modification, mRNA degradation). Together, these suggest a theme of chromatin regulation with symbiont-responsive host activity, rather than a single, isolated function.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901837","count":1},{"id":"GO:0007549","count":1},{"id":"GO:0061086","count":1},{"id":"GO:0051725","count":1},{"id":"GO:0039595","count":1}]},{"hash":"517256748503191409","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071800","count":2},{"id":"GO:1990314","count":2},{"id":"GO:0000147","count":2},{"id":"GO:1902951","count":2},{"id":"GO:0044379","count":2}]},{"hash":"948726853759328488","title":"Membrane trafficking and cell polarity","description":"The top terms cluster around membrane-related processes: phospholipid translocation (including its positive regulation), endocytosis, Golgi vesicle budding, establishment/maintenance of cell polarity, and regulation of microvillus assembly. These together suggest a function focused on membrane trafficking and cellular organization rather than a single signaling or immune pathway. A few terms (pre-B cell differentiation, vestibulocochlear nerve formation, response to auditory stimulus) appear more divergent, but the dominant theme is vesicle trafficking and polarity.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045332","count":1},{"id":"GO:0050884","count":1},{"id":"GO:0002329","count":1},{"id":"GO:0006897","count":1},{"id":"GO:0010996","count":1}]},{"hash":"1598186113148114513","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0000472","count":2}]},{"hash":"432946715442028965","title":"Transmembrane Transport of Sugars and Nutrients","description":"The GO terms cluster around transmembrane transport for a range of substrates\u2014sugars (galactose, arabinose, fucose), sialic acid, nitrate, phosphate, and xenobiotics\u2014pointing to a set of membrane transporter proteins with broad substrate specificity. While substrates vary, the shared function is moving molecules across membranes, supporting a transporter-centric cluster rather than a single substrate. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":3},{"id":"GO:0071805","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0035435","count":2}]},{"hash":"1751484446415085947","title":"Fat cell differentiation signaling","description":"This cluster is dominated by fat cell differentiation and intracellular signal transduction terms, with notable enrichment for positive regulation of GTPase activity and GPCR-related signaling, along with related processes like pinocytosis and cell migration. Together, these terms point to a module centered on adipocyte development and the signaling networks that control adipogenesis and adipocyte function, rather than a single enzymatic activity. Some GO terms are obsolete, but the core theme remains adipocyte differentiation signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":5},{"id":"GO:0035556","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0007205","count":4},{"id":"GO:2001275","count":4}]},{"hash":"846864537978885005","title":"Nuclear Transcription Regulation","description":"This cluster is dominated by transcription-related GO terms: DNA-templated transcription and negative regulation of transcription by RNA polymerase II, with a related chromatin modification term (H3-K4 demethylation). While there are a few trafficking and development terms, the strongest signal is transcriptional control in the nucleus, suggesting the proteins are mainly transcription regulators or chromatin modifiers with broader cellular roles.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0043547","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0010252","count":1}]},{"hash":"594223085968946991","title":"Embryonic Development and Organ Morphogenesis","description":"This cluster is enriched for GO terms related to embryonic development and tissue formation, including placenta and trophoblast differentiation, pancreatic cell development, EMT in heart cushion formation, cartilage morphogenesis, endocrine system development, left-right patterning, and palate (roof of mouth) development. The shared theme across these diverse processes is developmental differentiation and morphogenesis during embryogenesis, suggesting a broad but coherent developmental role for these proteins.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060806","count":2},{"id":"GO:0003323","count":2},{"id":"GO:0060707","count":2},{"id":"GO:0003198","count":2},{"id":"GO:0032298","count":2}]},{"hash":"1030153029433566405","title":"Transcription and Metabolic Processes","description":"Based on the GO terms, this cluster centers on gene expression machinery (DNA-templated transcription and spliceosome dynamics) together with metabolic pathways (heme A biosynthesis, tetrahydrofolate metabolism, anaerobic respiration). Additional signals point to development and stress/response processes (liver development, response to xenobiotic stimulus, brain-derived neurotrophic factor stimulus). This combination suggests a coherent module where transcriptional control is linked to metabolic state and environmental responses, justifying the label Transcription and Metabolic Processes.","confidence":"Medium","size":16,"edges":90,"triangles":269,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006784","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1990416","count":2},{"id":"GO:0000388","count":2},{"id":"GO:0046653","count":2}]},{"hash":"1646124040875899843","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":16,"triangles":7,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0070651","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0042254","count":1}]},{"hash":"638623318043342354","title":"Unknown","description":"The top terms cover RNA splicing (spliceosomal assembly and catalytic spliceosome) and a variety of metabolic biosynthetic/catabolic processes (purine base metabolism, allantoin assimilation, arginine/lysine pathways, diaminopimelate biosynthesis) along with proteolysis. Several terms are obsolete and there is no single cohesive biological function linking all proteins (no edges or clusters to indicate a shared pathway). Therefore, a precise, representative label cannot be confidently assigned.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030206","count":2},{"id":"GO:0000387","count":1},{"id":"GO:0000349","count":1},{"id":"GO:0010136","count":1},{"id":"GO:0006144","count":1}]},{"hash":"2182499971230966973","title":"Mitochondrial RNA Modification and Biosynthesis","description":"The cluster's strongest signals are mitochondrial-related processes (mitochondrial membrane fission) and RNA modification (rRNA modification, tRNA wobble uridine modification), complemented by several biosynthetic pathways (phosphatidylcholine, vitamin E, polyamine, antibiotic biosynthesis) that fit mitochondrial metabolism. Although two terms are obsolete and reduce clarity, the balance of mitochondrial dynamics, RNA modification, and biosynthesis suggests a mitochondria-centric biosynthetic/RNA-modifying role.","confidence":"Medium","size":16,"edges":10,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":4},{"id":"GO:0001300","count":3},{"id":"GO:0090149","count":3},{"id":"GO:0000154","count":2},{"id":"GO:0010189","count":2}]},{"hash":"118091068690344049","title":"RNA and protein methylation","description":"The top GO terms are dominated by methylation processes across RNA and proteins, including rRNA methylation, tRNA methylation (wobble uridine modification and general tRNA methylation), RNA guanine-N7 methylation, and protein methylation (peptidyl-arginine/asymmetrical-dimethylarginine and peptidyl-lysine dimethylation). This points to a cluster of proteins involved in methylation modifications rather than a single metabolic pathway, despite some incidental terms like antibiotic biosynthesis and nodulation. ","confidence":"High","size":16,"edges":118,"triangles":533,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031167","count":5},{"id":"GO:0002098","count":5},{"id":"GO:0017000","count":4},{"id":"GO:0019919","count":4},{"id":"GO:0009877","count":4}]},{"hash":"837974245577058296","title":"Ubiquitin-Dependent Proteolysis and Innate Immunity","description":"The cluster is dominated by ubiquitin-related processes (ubiquitin-dependent protein catabolic process and protein polyubiquitination) and immune defense terms (defense response to virus, innate immune response), suggesting a core role in targeted protein degradation tied to antiviral/immune stress. Additional terms point to circadian regulation and oxidative stress\u2013related apoptosis, indicating broader stress-response integration via ubiquitination. Confidence: High","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0071276","count":6},{"id":"GO:0051607","count":6},{"id":"GO:0045087","count":6},{"id":"GO:0000083","count":5}]},{"hash":"895693378509257334","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":111,"triangles":449,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006370","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0031047","count":3},{"id":"GO:1900363","count":3}]},{"hash":"702860763458601121","title":"Cell Cycle Regulation and Translational Initiation","description":"Top GO terms strongly link cell cycle progression and mitosis (mitotic cell cycle, cell division, anaphase-promoting complex-dependent catabolic process) with regulation of protein synthesis initiation (regulation of translational initiation, formation of translation preinitiation complex, IRES-dependent viral translational initiation). The presence of K11-linked ubiquitination suggests APC/C- or ubiquitin-mediated control of mitosis, while hypoxia-related response and proliferation signals provide a growth-context backdrop. This combination indicates a cohesive theme around coordinating cell division with translation control, hence the chosen label.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008284","count":3},{"id":"GO:0071456","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0001731","count":3}]},{"hash":"510067698802695456","title":"Differentiation and Cell Cycle Regulation","description":"The cluster centers on differentiation of cell types (fat, hepatocyte, sex differentiation) and cell-cycle control (regulation of the cell cycle, stem cell proliferation), with supporting signals like GTPase regulation and migration. While some terms reference broader cellular processes, the dominant theme is differentiation and cell-cycle regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007548","count":2},{"id":"GO:0007050","count":2},{"id":"GO:0070602","count":2},{"id":"GO:0016477","count":2}]},{"hash":"1038052772030245866","title":"Unknown","description":"The GO terms span diverse functions (glycerol catabolism, amino acid biosynthesis, peroxisomal protein import, transcription regulation, and dopamine metabolism) with several obsolete entries, showing no single cohesive function. Hence no specific, representative label can be assigned.","confidence":"","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0019563","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0016558","count":2}]},{"hash":"680683609284598271","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":74,"triangles":164,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":9},{"id":"GO:0048026","count":9},{"id":"GO:0000398","count":7},{"id":"GO:0010610","count":6},{"id":"GO:0071031","count":5}]},{"hash":"2240517299171681768","title":"Ribosome Biogenesis and Cell Cycle","description":"The top GO terms cluster around ribosome biogenesis (small/large subunit biogenesis and nuclear export) and core cell-cycle processes (cell division, cell cycle, and septum assembly, plus positive regulation of cell population proliferation). This suggests a cohesive module coordinating ribosome production with growth and division, hence the label. Peripheral terms like conjugation with cellular fusion and carnosine metabolism appear less central.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0035498","count":1}]},{"hash":"1992821013543362826","title":"Metal Ion Transport and Signaling","description":"Despite some metabolism-focused terms, the strongest signals are about metal ion transport (cadmium and copper) and cellular signaling/redox regulation (redox homeostasis, cAMP response, dephosphorylation, phospholipid dephosphorylation). Hormone and stilbene/antibiotic-related terms appear less central. This cluster is best characterized by metal transport intertwined with signaling and metabolic regulation.","confidence":"Medium","size":16,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:0071320","count":3},{"id":"GO:0017000","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0046839","count":2}]},{"hash":"805764819542855768","title":"Ribosome Biogenesis and Translation","description":"Based on the top GO terms, the cluster is dominated by ribosome-related processes: ribosome biogenesis, ribosomal subunit biogenesis, ribosomal large subunit export from nucleus, and cytoplasmic translation. While there are a few additional terms (cell cycle, septum assembly, iron transport) that hint at other cellular processes, the core theme across most proteins points to ribosome assembly and protein synthesis.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0055072","count":1},{"id":"GO:1903833","count":1}]},{"hash":"1948012955219471730","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":94,"triangles":298,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":13},{"id":"GO:0031047","count":12},{"id":"GO:0071051","count":11},{"id":"GO:0000467","count":11},{"id":"GO:0071035","count":11}]},{"hash":"1952104944236157733","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":2},{"id":"GO:0006376","count":1},{"id":"GO:0061158","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0000380","count":1}]},{"hash":"820037709888513660","title":"Unknown","description":"The top terms cover mitosis, multiple development processes (skeletal, forebrain, sperm-related), imprinting regulation, innate immunity, synaptic plasticity, a glucose-limitation\u2013driven invasion, and ER-stress\u2013induced apoptosis, which do not converge on a single cohesive function. With no clear shared theme and no network connectivity (Edges 0), a specific, representative label is not justifiable.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0001501","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0048240","count":2},{"id":"GO:0006349","count":2}]},{"hash":"769953762785267869","title":"Ubiquitin-Dependent Immune Signaling and Histone Turnover","description":"The top GO terms center on ubiquitin-related processes (ubiquitin-dependent protein catabolism, various ubiquitinations, autoubiquitination) and connect to histone ubiquitination, TNF signaling with I-kappaB phosphorylation, and apoptosis. This points to a cohesive theme of ubiquitin-driven regulation of immune signaling and histone/chromatin turnover, justifying the label.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0036205","count":5},{"id":"GO:1903265","count":5},{"id":"GO:0085020","count":5},{"id":"GO:0051865","count":5}]},{"hash":"2079375248176036938","title":"Vesicle trafficking and epithelial polarity in organ development","description":"The top GO terms point to intracellular trafficking (ER to Golgi, Golgi to plasma membrane), apical localization and epithelial polarity, alongside development of brain, liver, and kidney. This suggests a cohesive role in cargo sorting and membrane trafficking that supports tissue organization and organogenesis, with ER stress response reinforcing the connection to protein handling during development.","confidence":"High","size":16,"edges":41,"triangles":28,"max_degree":12,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:2000171","count":10},{"id":"GO:0001889","count":10},{"id":"GO:0001822","count":10},{"id":"GO:0006888","count":9},{"id":"GO:0006623","count":9}]},{"hash":"2170756810270697497","title":"Unknown","description":"The top GO terms span very different processes (cell cycle, GPCR signaling, pain and thermoception, immune signaling via NOD2, telomere maintenance, oligodendrocyte differentiation, etc.), with no clear single function tying the cluster together. This makes a cohesive, specific label inappropriate.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0007049","count":5},{"id":"GO:0007205","count":5},{"id":"GO:0090501","count":4},{"id":"GO:0050966","count":4}]},{"hash":"146928081175006585","title":"Regulated Kinase Signaling and GTPase Activity","description":"The cluster\u2019s top GO terms emphasize regulation of kinase activity (positive/negative), kinase autophosphorylation, and GTPase activity, pointing to a core theme of modulated intracellular signaling. Additional terms like hypoxia response and mitotic cell cycle suggest broader connections to cellular stress and division, but the shared thread appears to be control of signaling pathways through phosphorylation and GTPase regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0071456","count":5},{"id":"GO:0051028","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0007568","count":5}]},{"hash":"432849443040149476","title":"Immune signaling and mucosal epithelial development","description":"The terms cluster around innate/adaptive immune signaling (positive regulation of interferon-\u03b2 production, TLR4 signaling, dendritic cell differentiation, Th1 activation/differentiation) and also include mucosal/epithelial tissue development (trachea gland development, intrahepatic bile duct development) as well as endothelial proliferation. This pattern suggests a cohesive theme of immune response modulation in mucosal or epithelial contexts, with possible cross-talk to tissue development.","confidence":"Medium","size":16,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032728","count":1},{"id":"GO:0001935","count":1},{"id":"GO:0061153","count":1},{"id":"GO:2001200","count":1},{"id":"GO:0035711","count":1}]},{"hash":"2040337578476433850","title":"Actin dynamics and cell migration regulation","description":"Based on GO terms such as positive regulation of actin filament depolymerization, negative regulation of cell adhesion, and positive regulation of protein localization to the cell leading edge, the cluster seems centered on cytoskeletal remodeling and motility. Other terms (Golgi to plasma membrane transport, nuclear import) are related to trafficking but do not define a separate theme; overall, the shared theme is actin dynamics driving cell movement.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043001","count":1},{"id":"GO:0030307","count":1},{"id":"GO:0014823","count":1},{"id":"GO:0030836","count":1},{"id":"GO:0007162","count":1}]},{"hash":"1928997799779981179","title":"Unknown","description":"The top GO terms are highly diverse, spanning antibiotic and mercury responses, neuronal development, various transport processes, peptide export from mitochondria, cysteine transport, stem cell proliferation, bacteriocin-related immunity/transport, phospholipid translocation, and fatty acid catabolism. There is no single coherent function or pathway tying these terms together for this cluster, so a meaningful specific label cannot be assigned.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0031175","count":2},{"id":"GO:0046689","count":2},{"id":"GO:0090374","count":2},{"id":"GO:0042883","count":2}]},{"hash":"582337769035407957","title":"RNA transcription and translation regulation","description":"The top GO terms cluster around transcription initiation by RNA polymerase II, RNA-templated transcription, and both positive and negative regulation of translational initiation, indicating a cohesive theme of gene expression regulation at transcription and translation levels. Some outliers (e.g., isoprenoid biosynthesis, cytokinesis regulation) likely reflect annotation noise, but the core signal points to RNA-based regulatory processes.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050992","count":1},{"id":"GO:0097394","count":1},{"id":"GO:1905098","count":1},{"id":"GO:0010590","count":1},{"id":"GO:0006367","count":1}]},{"hash":"1804913489120028196","title":"Placental and Embryonic Development","description":"The top GO terms point to placental lineage and broader embryonic development\u2014trophoblast giant cell differentiation, placenta development, mesoderm formation, and palate roof development, with processes like EMT in heart formation. Although a couple terms pertain to transcription regulation and DNA replication, the shared theme centers on embryonic/placental tissue differentiation and early organogenesis. This supports labeling the cluster as placental and embryonic development-related.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060806","count":1},{"id":"GO:0003323","count":1},{"id":"GO:0060021","count":1},{"id":"GO:0060707","count":1},{"id":"GO:1903026","count":1}]},{"hash":"1337982330787294663","title":"Cardiac electrophysiology and ion transport","description":"The top GO terms cluster around cardiac electrical activity and ion homeostasis: membrane repolarization in atrial cardiac muscle, regulation of heart rate by cardiac conduction, action potential in cardiac muscle contraction, and potassium/sodium ion transport and membrane potential regulation, plus intracellular potassium homeostasis. This strongly suggests a module of ion channels and regulators governing cardiac excitability and conduction. A couple of terms (response to carbon monoxide, touch sensing) appear less central but do not override the main cardiac-focused theme.","confidence":"High","size":16,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0098914","count":13},{"id":"GO:0086091","count":11},{"id":"GO:0086002","count":11},{"id":"GO:1990573","count":11},{"id":"GO:0050976","count":11}]},{"hash":"904876463840964904","title":"Histone Modification and Chromatin Regulation","description":"This cluster is dominated by GO terms related to histone modifications and chromatin state (deacetylation and various histone acetylation/methylation events, regulation of heterochromatin, and regulation of transcription elongation by RNA Pol II). These themes point to epigenetic control of transcription as the primary function of this group, with a few ancillary terms like erythrocyte development appearing less central. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0016575","count":1},{"id":"GO:0080182","count":1},{"id":"GO:0032968","count":1},{"id":"GO:0051726","count":1}]},{"hash":"1138876996850167695","title":"Metabolic Biosynthesis and Detoxification","description":"The GO terms span biosynthetic processes (antibiotic, biotin), various catabolic pathways (beta-ketoadipate, uracil, triglyceride), detox-related responses (oxidant detoxification, response to toxic substance), and lipid/phospholipid remodeling, plus regulatory aspects of signaling. This points to a mixed set of metabolic and detoxification roles rather than a single, cohesive function, so the label reflects a broad metabolic-detox theme rather than a highly specific process.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0042952","count":3},{"id":"GO:0019433","count":3}]},{"hash":"1816013335548945995","title":"Unknown","description":"The GO terms span unrelated domains: spindle assembly and centrosome cycle (cell division), intra-Golgi vesicle transport (protein trafficking), and various biosynthetic processes (amino acids, serotonin, pyochelin) and transport, with no clear shared function across the cluster. This suggests no cohesive biological theme to name a specific function, hence Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":1},{"id":"GO:0007098","count":1},{"id":"GO:0006891","count":1},{"id":"GO:0006730","count":1},{"id":"GO:1903830","count":1}]},{"hash":"1403248856954312669","title":"Unknown","description":"The top GO terms are highly diverse (neural memory, morphine response, interferon signaling, male differentiation, chlorophyll biosynthesis, protein oligomerization, and protein isomerization) with no clear, common biological function tying the proteins together. The absence of edges reinforces the lack of a cohesive cluster theme, making a single representative label inappropriate.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007614","count":3},{"id":"GO:0071357","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0051348","count":2},{"id":"GO:0046661","count":2}]},{"hash":"998598261158000656","title":"Carbohydrate catabolism and glycolysis","description":"This cluster is characterized by GO terms focused on sugar processing and energy extraction, including lactose catabolism via tagatose-6-phosphate, D-ribose and 6-sulfoquinovose catabolism, glycolytic steps through fructose-6-phosphate, and related carbohydrate phosphorylation and salvage. While there are also broader metabolic terms (one-carbon metabolism, L-proline biosynthesis), the prominent theme is carbohydrate metabolism and glycolysis.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0055129","count":2},{"id":"GO:0006730","count":2},{"id":"GO:0019303","count":2},{"id":"GO:0009750","count":2}]},{"hash":"971609811212283478","title":"Bacterial carbon metabolism and vitamin B6 biosynthesis","description":"The cluster shows strong signals for central carbon metabolism (glycolysis, pyruvate biosynthesis, amino acid catabolism) and pyridoxine (vitamin B6) biosynthesis, plus antibiotic biosynthesis, with stress-related signals (response to starvation, cAMP) and transport. This suggests a bacterial metabolic and biosynthetic core, rather than a single, narrow function.","confidence":"Medium","size":15,"edges":97,"triangles":379,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0008615","count":6},{"id":"GO:0006096","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0051591","count":5},{"id":"GO:0042853","count":5}]},{"hash":"1093982641608432541","title":"Ribosome Biogenesis and Translation","description":"GO terms are dominated by translation and ribosome biogenesis, including cytoplasmic and mitochondrial translation (initiation, elongation, termination, and translational fidelity). A few terms relate to RNA decay and chromatin regulation, but the core signal is protein synthesis machinery.","confidence":"High","size":15,"edges":72,"triangles":175,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0046677","count":4},{"id":"GO:0042254","count":4},{"id":"GO:1902802","count":3},{"id":"GO:0006415","count":3}]},{"hash":"97621074606235283","title":"Growth, apoptosis, and differentiation signaling","description":"This cluster centers on apoptotic regulation alongside major signaling pathways (integrin, Wnt, Hippo) and processes like keratinocyte differentiation and angiogenesis, suggesting a cohesive theme of cell fate decisions, balance of survival/death, and tissue remodeling. Metabolic responsiveness and transcriptional regulation further support a broad growth/differentiation signaling program rather than a single pathway.","confidence":"High","size":15,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006915","count":5},{"id":"GO:0043065","count":4},{"id":"GO:0007229","count":4},{"id":"GO:0060044","count":4},{"id":"GO:0090263","count":4}]},{"hash":"1342539842040134863","title":"Unknown","description":"The Top Terms span transcription regulation, metal/iron and heme metabolism, APP biosynthesis regulation, ethanol and fructosamine metabolism, and mitochondrial ribosome assembly, with no single cohesive function linking the proteins. This suggests no clear, shared biological role for the cluster beyond broad cellular processes, so Unknown with None confidence.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006355","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0033212","count":1},{"id":"GO:0042167","count":1}]},{"hash":"529609579037783243","title":"Unknown","description":"GO terms are highly heterogeneous, including chromatin modification, RNA splicing, metabolism, and signaling, with only one edge and no cohesive functional theme, so no single representative function emerges.","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034720","count":4},{"id":"GO:0009228","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0016575","count":3}]},{"hash":"141681161093510031","title":"Lymphocyte development and signaling","description":"GO terms center on immune cell development (NK T cell differentiation, B cell affinity maturation, hemopoiesis) and signaling pathways common in lymphocytes (interleukin-4 production, cellular response to IL-7, Fc receptor signaling, JNK, and PI3K\u2013AKT). DNA replication suggests proliferative expansion during lymphopoiesis. Thus the cluster represents lymphocyte development and immune signaling.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032633","count":3},{"id":"GO:0046329","count":3},{"id":"GO:0001865","count":3},{"id":"GO:0098761","count":3},{"id":"GO:0043491","count":3}]},{"hash":"699563239440731397","title":"Cell cycle control and synaptic organization","description":"The cluster includes both classic cell cycle terms (apoptotic process, mitotic cell cycle, centrosome cycle, DNA replication, negative regulation of cell proliferation) and neuronal synapse\u2013related terms (dendritic spine morphogenesis, receptor clustering, protein localization to synapse, Rho signaling), suggesting proteins that link proliferation control with synaptic development and cytoskeletal dynamics.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006915","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0007098","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0008285","count":4}]},{"hash":"566319004965313304","title":"Unknown","description":"The top GO terms are scattered across autophagy, xenobiotic response, metabolism (including cobalamin biosynthesis and glycolysis-related regulation) and development, with several labeled obsolete. There is no single dominant function linking these proteins, and the zero edges/triangles indicate no cohesive interaction. This suggests the cluster does not represent a unified biological module, so Unknown is appropriate.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:0006914","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0045820","count":2}]},{"hash":"1160564918770016464","title":"Ribosome biogenesis and translation","description":"The top GO terms are dominated by translation, ribosome biogenesis and assembly, and rRNA processing, indicating a cluster centered on ribosome production and protein synthesis; additional signals for transcription termination/antitermination and stress responses accompany this core theme. This supports a coherent ribosome-centric function for the cluster.","confidence":"High","size":15,"edges":24,"triangles":31,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0007507","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0042594","count":2}]},{"hash":"23611677772460081","title":"Vascular remodeling and blood pressure regulation","description":"The cluster is dominated by terms tied to blood vessel biology\u2014angiogenesis in wound healing, regulation of endothelial cell migration, and the kallikrein-kinin cascade\u2014along with proteolysis, all of which point to vascular remodeling and blood pressure control. Additional terms on ROS metabolism and metabolic homeostasis (glucose, energy) can modulate vascular function, supporting a cohesive vascular/metabolic theme. Some items (symbiont entry into host cell, thyroid hormone signaling) are peripheral but may reflect broader signaling contexts.","confidence":"Medium","size":15,"edges":11,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":3},{"id":"GO:0046718","count":2},{"id":"GO:0003085","count":2},{"id":"GO:0043535","count":2},{"id":"GO:2000377","count":2}]},{"hash":"2166510155167043243","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":46,"triangles":39,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000462","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0006268","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006351","count":3}]},{"hash":"48358615134028917","title":"Stress-response signaling and DNA repair","description":"Based on the top GO terms, the cluster is enriched for responses to toxic substances, DNA repair, and stress-activated signaling such as the JNK cascade, plus related signaling pathways (PI3K/AKT, growth hormone). While some terms are broader or non-stress-specific, the dominant theme centers on cellular stress response and damage repair, suggesting a cohesive functional module.","confidence":"Medium","size":15,"edges":75,"triangles":218,"max_degree":13,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0009636","count":15},{"id":"GO:0006281","count":15},{"id":"GO:0038093","count":14},{"id":"GO:1990139","count":14},{"id":"GO:2000686","count":14}]},{"hash":"456165599476985586","title":"Histone demethylation and transcription in differentiation","description":"This cluster centers on histone modifications (H3K4/H3K36 demethylation and histone hydroxylation) and transcriptional regulation, with links to differentiation programs (myoblast/osteoblast) and signaling pathways such as Notch.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034720","count":7},{"id":"GO:0070544","count":7},{"id":"GO:0030961","count":6},{"id":"GO:0045668","count":6},{"id":"GO:2001214","count":4}]},{"hash":"2019723696530930208","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":37,"triangles":26,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007289","count":2},{"id":"GO:0006414","count":1},{"id":"GO:0061158","count":1},{"id":"GO:0001782","count":1},{"id":"GO:0038066","count":1}]},{"hash":"1690065404505376479","title":"Mitotic cell cycle and chromosome segregation","description":"The top GO terms are heavily weighted toward mitosis and cell division (mitotic cell cycle, cell division) and chromosome-related localization to kinetochores, pointing to a cluster focused on mitotic chromosome segregation machinery. A few terms like visual perception and pheromone response are less central but may reflect broader or pleiotropic roles; overall the dominant theme is cell-division-related processes.","confidence":"Medium","size":15,"edges":59,"triangles":96,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0007601","count":8},{"id":"GO:0051301","count":7},{"id":"GO:0006547","count":6},{"id":"GO:0019236","count":6}]},{"hash":"1091117915924692557","title":"Developmental gene regulation and tissue differentiation","description":"Primarily driven by gene-expression regulation (DNA-templated transcription, mRNA processing, and nuclear export) with concurrent roles in development (angiogenesis, fat cell differentiation, cell migration) and genome maintenance (telomere capping, CDK regulation). Calcium signaling adds a signaling layer, and the pain term may reflect tissue-specific expression but does not alter the core theme of transcriptional control guiding developmental differentiation and tissue remodeling.","confidence":"Medium","size":15,"edges":14,"triangles":2,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0050850","count":3},{"id":"GO:0019233","count":3},{"id":"GO:0045736","count":3},{"id":"GO:0001525","count":3}]},{"hash":"1737150077291260559","title":"Neuronal development and transcriptional regulation","description":"This cluster centers on neural development and gene expression control: cerebral cortex development, dopamine metabolism, regulation of transcription, alternative mRNA splicing, and histone demethylation point to neural differentiation and epigenetic/transcriptional regulation. Peripheral terms like sperm capacitation or thiamine biosynthesis are less explanatory, but do not override the core neuronal/gene expression theme.","confidence":"Medium","size":15,"edges":11,"triangles":2,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0048240","count":6},{"id":"GO:0045793","count":6},{"id":"GO:0021987","count":6},{"id":"GO:0034720","count":6},{"id":"GO:0000380","count":6}]},{"hash":"1748461500140835053","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0034476","count":2},{"id":"GO:0071042","count":2},{"id":"GO:0000467","count":2},{"id":"GO:0071038","count":2}]},{"hash":"246348433735791674","title":"Unknown","description":"The GO terms are highly diverse (mitotic cell cycle, GTPase signaling, skeletal/forebrain development, imprinting regulation, Gram-positive defense, hypoxia response, protein autophosphorylation/kinase activity, and mRNA transport) with no clear common function, and there are no edges among proteins, suggesting no cohesive pathway linkage. Therefore a specific label is not supported.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0001501","count":5},{"id":"GO:0030900","count":5},{"id":"GO:0006349","count":5}]},{"hash":"1052633580529711417","title":"Transcriptional Regulation and Histone Demethylation in Differentiation","description":"This cluster centers on DNA-templated transcription and epigenetic control via histone demethylation, with several terms for histone H3 demethylation and transcriptional regulation, plus differentiation-related processes (osteoblast and myoblast differentiation) and vascular development. The combination suggests a cohesive module where transcriptional control is linked to epigenetic histone modifications guiding differentiation programs.","confidence":"Medium","size":15,"edges":6,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0045668","count":3},{"id":"GO:0034720","count":3},{"id":"GO:2001214","count":2},{"id":"GO:0061428","count":2}]},{"hash":"2088474728902122300","title":"Glycosylation and glycoprotein biosynthesis","description":"The Top Terms are dominated by glycan biosynthesis and glycoprotein modification (arabinogalactan protein metabolism, O-linked glycosylation via hydroxyproline, Lewis a epitope, poly-N-acetyllactosamine), plus related cell-surface processes (cell adhesion, polarity) across plant and insect contexts. This suggests the cluster centers on glycosylation-related surface components affecting development, even though a few outliers are present. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015886","count":2},{"id":"GO:0075015","count":1},{"id":"GO:0010405","count":1},{"id":"GO:0018258","count":1},{"id":"GO:0042248","count":1}]},{"hash":"1616033996902109950","title":"Diverse biosynthesis and RNA modifications","description":"The top GO terms point to multiple biosynthetic pathways (menaquinone, vitamin E, phosphatidylcholine, chlorophyll) indicating lipid/pigment and related metabolite synthesis, while also including RNA and protein modification terms (rRNA methylation, tRNA wobble, peptidyl-lysine methylation, peptidyl-arginine hydroxylation). This combination suggests a cluster centered on various biosynthetic processes plus macromolecule modifications, rather than a single tightly connected function.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":2},{"id":"GO:1901407","count":2},{"id":"GO:0031167","count":2},{"id":"GO:0010189","count":2},{"id":"GO:0018026","count":2}]},{"hash":"1696507000658236061","title":"Ribosome biogenesis and translation","description":"The top terms are dominated by ribosome biogenesis, rRNA maturation (5.8S and LSU/SSU), ribosomal subunit export, and overall translation-related processes (translation and translational initiation). A few terms about fatty acid biosynthesis and glycolytic regulation are present but far less represented, so the cluster is best characterized by ribosome assembly and protein synthesis.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000466","count":2},{"id":"GO:0000054","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0042304","count":1}]},{"hash":"214181833832626673","title":"Zinc Ion Detoxification and Homeostasis","description":"The dominant GO terms point to detoxification of zinc ions, zinc and cadmium ion transport, and intracellular zinc ion homeostasis, indicating a coherent function in metal ion detoxification and regulation; the apoptotic term may reflect stress responses to metal imbalance.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010312","count":2},{"id":"GO:0070574","count":2},{"id":"GO:0006882","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0033081","count":2}]},{"hash":"1710337599352220022","title":"Developmental signaling and immune modulation","description":"The GO terms point to both developmental processes (oligodendrocyte differentiation, trachea gland development, endothelial proliferation) and immune/regulatory functions (neutrophil clearance, interferon-beta production, dendritic cell differentiation, regulation of Wnt/TGF-beta signaling). This suggests a cluster aligned with signaling that coordinates development with immune responses, rather than a single uniform pathway. Edges are zero, indicating no direct interactions captured, but the thematic overlap supports a developmental-immune regulatory theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048709","count":2},{"id":"GO:0097350","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0090090","count":2},{"id":"GO:0071560","count":2}]},{"hash":"578408332690854","title":"Ubiquitin-Mediated Protein Turnover","description":"The cluster is dominated by GO terms related to ubiquitination and ubiquitin-dependent protein degradation (protein ubiquitination, ubiquitin-dependent protein catabolic process, and protein deubiquitination involved in ubiquitin-dependent protein catabolic process). This points to a core theme of regulating protein stability via the ubiquitin system, with secondary connections to transcriptional regulation through ubiquitin-mediated control and occasional RNA processing or cytoskeletal terms. Overall, the strongest shared function ties to ubiquitin pathways governing protein turnover. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0000921","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0043547","count":2}]},{"hash":"422954055143505294","title":"Broad-substrate membrane transporters","description":"The top GO terms are dominated by transport across membranes for a variety of substrates (potassium, sialic acid, xenobiotics, 4-hydroxyphenylacetate) and related osmotic stress response, pointing to a coherent theme of broad substrate membrane transport proteins. While a few terms touch on other processes (cell division, conjugation), the strongest signal is membrane transport, supporting a broad-substrate transporter cluster. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":3},{"id":"GO:0000747","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0006004","count":2}]},{"hash":"147013356414465171","title":"Unknown","description":"The GO terms cover plant metabolism (cellulose catabolic, raffinose biosynthetic, gibberellin signaling), stress and xenobiotic responses, receptor internalization, and even cholesterol transport, with no single unifying function across all proteins. The lack of edges or clusters suggests no coherent module, so a meaningful label cannot be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0085014","count":2},{"id":"GO:0006950","count":2},{"id":"GO:0042136","count":2}]},{"hash":"69573383226825970","title":"Cardiac Muscle Development and Myofibril Assembly","description":"The top GO terms are dominated by heart-related processes: cardiac myofibril assembly and heart development, plus potassium ion transmembrane transport, which is critical for cardiac electrophysiology. Regulation of cell shape and actin cytoskeleton remodeling further points to structural organization of cardiac muscle fibers, supporting a theme of cardiac muscle development and assembly.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":2},{"id":"GO:0007118","count":2},{"id":"GO:0008360","count":2},{"id":"GO:2000251","count":2},{"id":"GO:0055003","count":2}]},{"hash":"946241707784450934","title":"Vacuolar trafficking and ion homeostasis","description":"This cluster shows strong enrichment for vacuolar-related processes (protein targeting to vacuole, vacuole organization, vacuolar acidification) along with ion transport and energy-related terms (proton transmembrane transport, proton motive force-driven ATP synthesis, sodium and copper ion homeostasis). The combination suggests a functional module centered on vacuolar trafficking plus membrane ion/homeostasis dynamics, with some antibiotic-related terms possibly reflecting ancillary stress responses. ","confidence":"Medium","size":14,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0006623","count":2},{"id":"GO:0006878","count":2},{"id":"GO:0042777","count":2},{"id":"GO:0007033","count":2}]},{"hash":"172764620112351563","title":"Brain Energy Metabolism and Neuronal Development","description":"The cluster is enriched in central metabolic processes (glycolysis, TCA cycle, branched-chain amino acid catabolism, glyoxylate metabolism, and regulation of pyruvate decarboxylation to acetyl-CoA) alongside neural development terms (pyramidal neuron development, cerebellar cortex development, tangential migration to the olfactory bulb), suggesting proteins involved in brain energy metabolism linked to neuronal maturation and migration.","confidence":"Medium","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006099","count":2},{"id":"GO:0021860","count":2},{"id":"GO:0009083","count":2},{"id":"GO:0021695","count":2}]},{"hash":"135684650930299429","title":"Monoaminergic neurotransmitter synthesis and packaging","description":"This cluster centers on biogenic amine production (serotonin and epinephrine) and dopaminergic synaptic transmission, plus loading of aminergic neurotransmitters into synaptic vesicles, pointing to monoaminergic synthesis and vesicular packaging as the core function. A few outlier terms (adipogenesis, mammary development) are present but do not define the primary theme.","confidence":"High","size":14,"edges":86,"triangles":308,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0045600","count":2},{"id":"GO:0042136","count":1},{"id":"GO:0006587","count":1},{"id":"GO:0042418","count":1},{"id":"GO:0001963","count":1}]},{"hash":"1371473562835437228","title":"Metabolism and Protein Modification","description":"The enriched terms cluster around core metabolic pathways (glycolysis, carbohydrate phosphorylation, fatty acid and glutamine metabolism) with supporting protein-level regulation processes (proteolysis, depalmitoylation) and a trafficking regulation term, suggesting a group of metabolic enzymes linked to post-translational regulation rather than a single, uniform pathway.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":3},{"id":"GO:0006631","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0002084","count":2},{"id":"GO:0042997","count":2}]},{"hash":"443035749820221965","title":"Ribosome biogenesis and translation regulation","description":"The top terms point to ribosome biogenesis, ribosomal subunit assembly, translation, and cell cycle, indicating a cluster of proteins involved in ribosome production and protein synthesis control during cell growth. Stress-related terms (amino acid starvation response, UV-regulated translation) further support a theme of linking translation to nutrient and environmental cues, with a few broader terms (heart morphogenesis, one-carbon metabolism) likely reflecting peripheral associations rather than core function.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0042254","count":2},{"id":"GO:1903833","count":2},{"id":"GO:0006412","count":2}]},{"hash":"783986169841486091","title":"Unknown","description":"The Top Terms cover neural signaling, endocrine/metabolic functions (insulin secretion, glucose response), stress and proteostasis (oxidative response, amyloid formation, sumoylation, folding), and even development and cell proliferation, with little cohesive functional theme. This diversity makes it hard to assign a single, high-confidence label that represents the cluster\u2019s core biology.","confidence":"","size":14,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019227","count":3},{"id":"GO:0042542","count":3},{"id":"GO:1990000","count":3},{"id":"GO:0009749","count":3},{"id":"GO:0046661","count":3}]},{"hash":"591788082498044029","title":"Steroid, lipid, and alkaloid biosynthesis","description":"The cluster\u2019s top GO terms cluster around biosynthetic processes for steroids (glucocorticoids, androgens), lipids (sphingolipids, very long-chain fatty acids), and alkaloids (tropane alkaloids), with additional general transcription regulation terms suggesting coordinated control of these pathways. This points to a common theme of diverse metabolite biosynthesis rather than a single protein function.","confidence":"Medium","size":14,"edges":6,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0006706","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0009710","count":3}]},{"hash":"512554150268685701","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":50,"triangles":86,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":10},{"id":"GO:0048026","count":10},{"id":"GO:0071031","count":6},{"id":"GO:0000716","count":6},{"id":"GO:0042766","count":6}]},{"hash":"1319249237501936011","title":"Endothelial Barrier Regulation and Junction Signaling","description":"The dominant GO terms point to endothelial barrier function and tight junction assembly (bicellular tight junction assembly; establishment of endothelial intestinal barrier) along with Rho-mediated signaling that governs cytoskeletal dynamics and cell junctions, suggesting a vascular barrier/regulatory role. Immune signaling (CD40 pathway) and stress-related apoptotic signaling also appear, implying cross-talk between endothelial cells and immune responses. Additional terms related to transcription, chromatin maintenance, DNA repair, and adipose development may reflect broader shared cellular regulation or pleiotropy within the cluster.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0035023","count":3},{"id":"GO:1902237","count":2},{"id":"GO:1904179","count":2},{"id":"GO:1990414","count":2}]},{"hash":"782171598886505812","title":"Zinc Homeostasis and ER Stress Response","description":"The cluster shows strong representation of zinc ion import/detoxification and zinc starvation responses, along with ER-stress\u2013related processes (unfolded protein response, translation initiation regulation, and chaperone-assisted refolding). This points to a cohesive module managing zinc homeostasis together with protein quality control under stress, despite a few outlier terms like limb development. ","confidence":"Medium","size":14,"edges":12,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":3},{"id":"GO:0036494","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006986","count":2}]},{"hash":"1195927947302023435","title":"Bacterial Biosynthesis Pathways","description":"The cluster\u2019s top GO terms are dominated by biosynthetic processes such as antibiotic biosynthesis, lipopolysaccharide biosynthesis, and poly-hydroxybutyrate biosynthesis, which points to a bacterial metabolism module. Other terms like transcription or histone demethylation and vasculogenesis are less coherent with the core theme, likely reflecting annotation noise or broad background associations. Overall, the common thread is bacterial biosynthetic activity.","confidence":"Medium","size":14,"edges":12,"triangles":2,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0042619","count":3},{"id":"GO:0055114","count":3}]},{"hash":"2217652162182941447","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0007275","count":5},{"id":"GO:0051028","count":4},{"id":"GO:0001501","count":4},{"id":"GO:0000278","count":4}]},{"hash":"110553742455077196","title":"Neural development and cell cycle control","description":"This cluster is dominated by terms tied to neural development, notably forebrain development and axonogenesis, suggesting a primary role in neural differentiation and connectivity. It also prominently features mitotic cell cycle activity (mitotic cell cycle and G2/M transition), along with mRNA processing and ribosomal RNA maturation, indicating coordinated cell proliferation and gene expression control that often accompanies developmental programs. Some terms (skeletal development, immune defense) appear less central and may reflect broader functional pleiotropy or dataset noise, but the neural development and cell cycle themes are the strongest link.","confidence":"Medium","size":14,"edges":9,"triangles":2,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0000462","count":3},{"id":"GO:0001501","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0000086","count":3}]},{"hash":"2050226378306461107","title":"Transcriptional Regulation and Chromatin Modification","description":"Top terms point to transcription by RNA polymerase II and histone acetylation (chromatin modification) and also cell-cycle related processes (cell division, negative regulation of G0 to G1). While some terms (pigmentation, osteoblast differentiation, SREBP signaling) are more distant, the dominant signal is nuclear transcription control and chromatin state, with a cell-cycle tie-in.","confidence":"Medium","size":14,"edges":11,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0032933","count":2},{"id":"GO:0016573","count":2},{"id":"GO:0006366","count":2},{"id":"GO:0070317","count":2}]},{"hash":"1463894069563709547","title":"Diverse biosynthetic processes","description":"The set of top GO terms centers on biosynthetic processes producing various metabolites and macromolecules (anthocyanin-containing compounds, phenylpropanoids, PHB, colanic acid), plus some general metabolic biosynthesis like galactose and L-glutamine. This pattern suggests the proteins participate in multiple biosynthetic steps across different pathways rather than a single pathway, so a label focused on \"biosynthesis\" is most representative.","confidence":"Medium","size":14,"edges":25,"triangles":9,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009718","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0097171","count":3}]},{"hash":"502846996970887642","title":"Cell signaling and cytoskeleton organization","description":"The top terms point to receptor signaling (T cell receptor, ephrin signaling) coupled with cytoskeletal dynamics (actin filament branching, cell polarity/shape maintenance) and membrane trafficking (endocytosis, lipid tube assembly), suggesting a core theme of signaling interfaces with actin remodeling and membrane remodeling. Some terms are unrelated (transcription, spermatid development), but the prevalent pattern supports a signaling-cytoskeleton axis.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0090135","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0006897","count":2}]},{"hash":"590988290601773460","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":58,"triangles":114,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000472","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0000398","count":3}]},{"hash":"1426957634281909499","title":"Cardiac Development and Cardiomyocyte Signaling","description":"This cluster centers on heart development and cardiac muscle function, with frequent GO terms for heart development, cardiac muscle contraction, Rho signaling, integrin activation, and PI3K/AKT signaling, suggesting a cohesive cardiomyocyte signaling network. Some terms (e.g., response to food, retinal apoptosis) are less clearly related and may reflect broader or incidental associations, but the heart-centric terms provide a strong core theme. ","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0007507","count":4},{"id":"GO:0032094","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0060048","count":4}]},{"hash":"2074668947777048364","title":"Ion Transport and Cyclic Nucleotide Signaling","description":"This cluster is dominated by terms related to ion movement across membranes (sodium import, potassium export/transport, potassium homeostasis) and by cellular responses to cyclic nucleotides (cAMP, cGMP), suggesting a theme of ion-based signaling. Peripheral terms like sensory perception of pain, development, and aerotaxis are less central to the core function of these proteins.","confidence":"Medium","size":14,"edges":11,"triangles":3,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098719","count":8},{"id":"GO:0019233","count":7},{"id":"GO:0007275","count":7},{"id":"GO:0071321","count":7},{"id":"GO:0071320","count":7}]},{"hash":"2081635095619518935","title":"Neuronal signaling and brain development","description":"The top GO terms cluster around signaling cascades and neural function, including JNK and PI3K/AKT signaling, growth hormone receptor signaling, and glutamatergic synaptic transmission, along with cerebellar cortex formation. Some terms, like Fc receptor signaling, broaden to general signaling contexts, and a couple (DNA replication, nuclear periphery localization) appear as noise or outliers. Overall, the dominant theme ties to neuronal signaling and brain development.","confidence":"Medium","size":14,"edges":14,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0038093","count":3},{"id":"GO:1990139","count":3},{"id":"GO:2000686","count":3},{"id":"GO:0007254","count":3}]},{"hash":"497470341776233955","title":"Ribosome Biogenesis and Translation Initiation","description":"This cluster centers on RNA processing and ribosome assembly, featuring ribosome biogenesis, SSU-rRNA maturation, formation of the translation preinitiation complex, translation reinitiation, and related GTPase regulation, indicating proteins involved in ribosome production and initiation of protein synthesis. A few non-translation terms (transcription-related and embryo sac development) are present but do not dominate, suggesting the core signal is translation machinery.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0009553","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0043547","count":2}]},{"hash":"2121183211903297280","title":"Unknown","description":"The top GO terms pull in several unrelated processes (DNA-templated transcription, histone acetylation/catabolic processes, Arp2/3-mediated actin nucleation/depolymerization, ubiquitin-related pathways, and TNF signaling) with several marked as obsolete, and there are no network connections (Edges 0, Triangles 0). This mix suggests no single coherent biological function for the cluster, so it\u2019s not possible to assign a representative, specific label beyond Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0034314","count":3},{"id":"GO:0043981","count":3},{"id":"GO:0043982","count":3},{"id":"GO:0030042","count":3}]},{"hash":"2186020562644832133","title":"Bacterial LPS and O-antigen biosynthesis","description":"The top GO terms cluster around cell wall organization and lipopolysaccharide biosynthesis, especially O-antigen, with sugar-nucleotide biosynthesis (UDP-N-acetylglucosamine, GDP-mannose) supporting polysaccharide assembly for the bacterial outer membrane. Some metabolism terms are auxiliary, but the dominant theme is envelope biosynthesis and glycan construction.","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":5},{"id":"GO:0009243","count":4},{"id":"GO:0019388","count":4},{"id":"GO:0009103","count":4},{"id":"GO:0055114","count":3}]},{"hash":"679658032879551606","title":"Unknown","description":"The top GO terms are a scattered mix of metabolic pathways (fatty acid metabolism, ectoine biosynthesis/catabolism, alpha-oxidation) and unrelated processes (verruculogen biosynthesis, cell cycle regulation, mRNA stability, cAMP response) with no interactions among proteins (Edges 0, Max Degree 0). There is no clear common function tying the cluster together, so a cohesive label cannot be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097089","count":1},{"id":"GO:0019491","count":1},{"id":"GO:0001561","count":1},{"id":"GO:1902181","count":1},{"id":"GO:0042400","count":1}]},{"hash":"786421647232817813","title":"Potassium Ion Transport and Homeostasis","description":"The top GO terms are dominated by potassium ion export/import across the plasma membrane and intracellular potassium ion homeostasis, pointing to proteins involved in potassium handling. Additional terms about protein oligomerization and regulation of kinase/GTPase activity suggest these proteins may function as membrane-associated transporters or channel-forming units that also participate in signaling and developmental processes. Overall, the theme centers on potassium transport/homeostasis with related regulatory roles.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097623","count":4},{"id":"GO:1990573","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0030007","count":3},{"id":"GO:1903244","count":3}]},{"hash":"841515401038581361","title":"Mitotic Cell Cycle and DNA Repair","description":"The cluster is dominated by mitosis- and DNA repair-related GO terms (mitotic cell cycle, G2/M transition, DNA repair, telomere regulation), suggesting a core theme of cell-cycle progression and genome maintenance; other terms like axonogenesis and innate immunity are present but less represented.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0000902","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0051973","count":3}]},{"hash":"1558633413475353384","title":"Cell signaling and remodeling","description":"The top GO terms include JNK cascade (signaling), regulation of cell-matrix adhesion, and proteasomal ubiquitin-dependent protein catabolic process, along with processes like apoptotic clearance and tissue-specific development (retina vasculature) and smooth muscle contraction. This mix suggests a cluster centered on signaling pathways and structural/dynamic cellular remodeling rather than a single focused function.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007254","count":2},{"id":"GO:0048240","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0001954","count":2}]},{"hash":"1090074269177179874","title":"Unknown","description":"The terms span diverse regulatory processes\u2014from transcription elongation and RNA processing to autophagy, differentiation, dendrite outgrowth, and lipid biosynthesis\u2014without a single dominant shared function. Therefore, there isn\u2019t a cohesive theme tying all terms, so the cluster is labeled Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":3},{"id":"GO:2000232","count":2},{"id":"GO:0071211","count":1},{"id":"GO:0060242","count":1},{"id":"GO:0060575","count":1}]},{"hash":"1095028285543668160","title":"Developmental signaling and cell adhesion","description":"The top GO terms cluster around signaling and cell interactions that guide development: ephrin receptor signaling, regulation of integrin-mediated cell adhesion, retinal ganglion cell axon guidance, and myotube differentiation. These point to developmental signaling and adhesion processes. There are also related terms like activated T cell proliferation and DNA-templated transcription, which are more general, and telomere maintenance terms that seem less connected to the main theme, suggesting a mixed but core signal/adhesion developmental pattern. Overall, the dominant theme appears to be signaling and adhesion in development rather than a single cohesive enzymatic or metabolic function.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904355","count":3},{"id":"GO:0032212","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0031290","count":2},{"id":"GO:0060044","count":2}]},{"hash":"59320002269342408","title":"RNA and histone methyltransferases","description":"This cluster centers on enzymes involved in RNA methylation (rRNA, tRNA modifications) and histone/peptide methylation, plus chromatin-related processes like rDNA heterochromatin formation and transcriptional regulation by RNA Pol II, indicating a cohesive methylation-driven role in RNA processing and chromatin state.","confidence":"Medium","size":14,"edges":28,"triangles":20,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":4},{"id":"GO:0018013","count":4},{"id":"GO:0018027","count":4},{"id":"GO:0000183","count":3},{"id":"GO:0018023","count":3}]},{"hash":"1499792013072059456","title":"Developmental signaling and cell-cycle regulation","description":"The cluster mixes signals related to development (Wnt pathway) with core cell-cycle processes (mitotic checkpoint signaling, cytokinesis) and genome maintenance/modification (DNA ligation/repair, ubiquitination, poly-ADP-ribosylation). This suggests a broad theme of coordinating development with cell division and protein regulation, rather than a single narrow function.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006288","count":2},{"id":"GO:0051102","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0051103","count":2},{"id":"GO:0033314","count":2}]},{"hash":"862510278721487667","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0009190","count":2}]},{"hash":"1135846386451924224","title":"Photoreceptor Outer Segment Organization","description":"The cluster is enriched for GO terms tied to photoreceptor biology, including photoreceptor outer segment organization, localization to photoreceptor outer segment, and retinal rod cell development. This points to proteins involved in photoreceptor cilia/outer segment formation and maintenance. A few GPCR signaling terms are present but likely reflect general signaling roles rather than core function of this cluster.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903526","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0070493","count":2},{"id":"GO:1903646","count":1},{"id":"GO:0035845","count":1}]},{"hash":"1957613307679683012","title":"Developmental Proteostasis","description":"This cluster centers on developmental processes (brain and multicellular development, muscle differentiation) and protein turnover (ubiquitin-dependent and SCF-proteasomal proteolysis). The combination suggests a theme of development regulated by proteostasis, with microtubule-based movement reflecting cytoskeletal dynamics during growth and differentiation; other terms like Pol III transcription and stress responses may be supportive by enabling cellular growth and adaptation. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007018","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0031146","count":2}]},{"hash":"1834374690632466088","title":"Translation initiation and ribosome assembly","description":"The top terms are dominated by translation-related processes: translation (GO:0006412), initiation and preinitiation complex formation (GO:0006413, GO:0001731, GO:0001732), cytosolic ribosome assembly (GO:0042256) and regulation of translational initiation (GO:0045947). This pattern points to a cluster of proteins involved in the protein synthesis machinery and its initiation steps. A few terms (germ cell proliferation, photoreceptor guidance, oocyte microtubule polarization) are unrelated to translation and may reflect multifunctional proteins or annotation noise, but they do not override the main translation-centric signal.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045947","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0006413","count":1},{"id":"GO:0002176","count":1}]},{"hash":"1169002481103467614","title":"Cytoskeletal remodeling and ER-Golgi vesicle trafficking","description":"This cluster is dominated by terms related to the cytoskeleton and its dynamics (mitotic spindle assembly, microtubule-based movement, actin filament depolymerization, and Arp2/3-mediated actin nucleation) as well as vesicle trafficking between the ER and Golgi (ER-Golgi and Golgi-to-ER transport). This points to a cohesive theme of cytoskeletal remodeling coordinating intracellular transport; the development and pigmentation terms are broader or context-dependent and do not override the core signal.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090307","count":5},{"id":"GO:0021510","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0007018","count":4},{"id":"GO:0030042","count":4}]},{"hash":"1938461376159369162","title":"Unknown","description":"The GO terms listed are highly diverse (glycolytic regulation, dephosphorylation, autophagy, development, xenobiotic response, respiratory burst, mitophagy regulation, cardiac apoptosis, cobalt ion response), with no single shared function or pathway tying the proteins together. This makes it unclear what specific theme defines the cluster, so a precise, concise label isn\u2019t justifiable beyond Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045820","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0006914","count":1},{"id":"GO:0060576","count":1},{"id":"GO:0009410","count":1}]},{"hash":"2034654082782173797","title":"Neuronal signaling and calcium response","description":"The top GO terms strongly point to neuronal signaling and calcium-dependent processes, including phosphatidylinositol-mediated signaling, neurotransmitter secretion, calcium ion response, and long-term synaptic potentiation, suggesting a cluster tied to synaptic signaling and calcium-driven plasticity. Some terms relate to broader cellular processes (mitotic cell cycle, prospore membrane formation, RNA polymerase III transcription, etc.), indicating heterogeneity, but the core signals align with neuronal communication and calcium signaling.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":3},{"id":"GO:0032120","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0043065","count":2},{"id":"GO:0007269","count":2}]},{"hash":"557575195362652452","title":"Neuronal signaling and membrane dynamics","description":"Top GO terms cluster around neuron-related functions: neurotransmitter secretion, dendrite growth, and neuropeptide signaling indicate a neuronal context. Supporting membrane-related processes (ER membrane organization and plasma membrane repair) and protein turnover (K48-linked ubiquitination) suggest roles in maintaining membrane integrity and regulated signaling in neurons. The combination points to a functional cluster centered on neuronal signaling with membrane maintenance, rather than a single narrowly defined process.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070936","count":1},{"id":"GO:0043065","count":1},{"id":"GO:0007269","count":1},{"id":"GO:0019433","count":1},{"id":"GO:0090038","count":1}]},{"hash":"833503910119551189","title":"Ribosome biogenesis and cytoplasmic translation","description":"The top terms are centered on translation and ribosome biogenesis (cytoplasmic translation, ribosome biogenesis, ribosomal small subunit biogenesis) and include SRP-dependent cotranslational targeting to membranes, indicating a cluster of proteins involved in protein synthesis and ribosome assembly, with related membrane targeting of nascent chains. A few cell cycle terms appear, but the predominant signal ties to ribosome function and translation.","confidence":"High","size":13,"edges":51,"triangles":127,"max_degree":11,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0051301","count":4},{"id":"GO:0002181","count":4},{"id":"GO:0007049","count":3},{"id":"GO:0042254","count":3}]},{"hash":"2217257661602865037","title":"Central carbon metabolism and amino acid biosynthesis","description":"This cluster shows strong signals for core metabolism: glycolytic and TCA cycle processes, along with several amino acid biosynthetic/catabolic pathways (lysine, glutamate, aspartate, phenylalanine, kynurenic acid). The DNA-templated transcription term is present but appears peripheral to the dominant metabolic theme, suggesting a group of proteins involved in carbon flux and amino acid metabolism, possibly including regulatory roles.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0033512","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0019551","count":2}]},{"hash":"2068838931940454457","title":"Potassium Ion Homeostasis and Membrane Potential","description":"This cluster centers on potassium ion homeostasis, potassium transport, and regulation of membrane potential, including membrane stabilization and repolarization. These terms strongly suggest a core function in ion transport and electrical excitability, with a few peripheral terms (touch perception, cAMP response, sperm capacitation, ER-stress signaling) that appear secondary to the main theme.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":4},{"id":"GO:0030322","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0098914","count":3},{"id":"GO:0050976","count":3}]},{"hash":"483530596571400221","title":"Fungal sterol and sphingolipid metabolism","description":"The cluster is driven by lipid-related processes: ergosterol (sterol) biosynthesis and regulation, sphingolipid metabolism (mannosyl-inositol phosphorylceramide), and unsaturated fatty acid biosynthesis, all characteristic of fungal lipid metabolism. Oxidative detoxification terms suggest a redox-linked aspect to lipid processing, supporting a cohesive lipid-metabolism theme rather than unrelated functions, though some outlier terms appear.","confidence":"Medium","size":13,"edges":21,"triangles":12,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0042128","count":2},{"id":"GO:0006809","count":2},{"id":"GO:0032443","count":2}]},{"hash":"73496768353655465","title":"Unknown","description":"The GO terms span metabolism, bacterial lipopolysaccharide biosynthesis, immune signaling, and reproductive development, with no clear single function tying the proteins together. This diversity makes it hard to assign a specific, cohesive label.","confidence":"","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0046661","count":3},{"id":"GO:0030850","count":3},{"id":"GO:0006463","count":3},{"id":"GO:0071357","count":3}]},{"hash":"1752342980107551557","title":"Unknown","description":"The GO terms span photosynthesis, ubiquitin-related processes, multiple acetylation reactions, and various biosynthetic pathways, with only a couple of connections and a very sparse network. There isn\u2019t a single cohesive biological theme uniting the cluster, so a confident specific label isn\u2019t supported.","confidence":"","size":13,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051865","count":2},{"id":"GO:1903265","count":2},{"id":"GO:0030187","count":2}]},{"hash":"1979755134896136551","title":"Unknown","description":"The cluster mixes terms from xenobiotic metabolism (carbazole catabolic process), lipid/retinoid/vitamin D pathways (cholesterol catabolic process, oxylipin biosynthetic process, 9-cis-retinoic acid biosynthesis, response to vitamin D), epigenetic methylation, inflammatory regulation, eye development, and cell cycle signaling. There is no single dominant biological process or pathway linking all terms, and the network has no edges, suggesting a heterogeneous set. Therefore, Unknown with None confidence. ","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046232","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0002677","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0006707","count":2}]},{"hash":"1695888730152225252","title":"Chromatin Remodeling and Transcription Regulation","description":"The strongest signals are chromatin remodeling, rDNA heterochromatin formation, transcription by RNA Pol II, and DNA-templated transcription, indicating a nuclear module that governs chromatin state and transcription control. Additional terms for RNA modification and metabolism exist but are less central to the cluster\u2019s main theme. Overall, the cluster appears to represent chromatin dynamics and transcription regulation with supporting RNA processing signals.","confidence":"Medium","size":13,"edges":17,"triangles":12,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0002098","count":4},{"id":"GO:0006744","count":4},{"id":"GO:0043044","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0006351","count":3}]},{"hash":"2276684199319708309","title":"Retinoid and Steroid Metabolism","description":"This cluster shows strong representation of retinol and retinal metabolic processes, along with prostaglandin, androgen, and testosterone biosynthesis, indicating a core theme of lipid-derived metabolite production and vitamin-A\u2013related metabolism. Additional terms touch on calcium signaling and JAK-STAT\u2013related receptor signaling, but the dominant signal is metabolic biosynthesis of lipid- and vitamin-related compounds.","confidence":"Medium","size":13,"edges":17,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0042572","count":5},{"id":"GO:0001516","count":5},{"id":"GO:0042574","count":4},{"id":"GO:0008209","count":4}]},{"hash":"772870799709412172","title":"Ribosome biogenesis, translation, and growth signaling","description":"GO terms indicate a strong focus on ribosome biogenesis and translation, with supporting roles for RNA methylation and mRNA transport, suggesting active protein synthesis. Additional signals from TORC1 signaling and Wnt pathway regulation, alongside cell division and phosphorylation-related regulation, point to a broader growth-control context linking translation to proliferation.","confidence":"High","size":13,"edges":16,"triangles":9,"max_degree":5,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0036265","count":2},{"id":"GO:0043065","count":2}]},{"hash":"1859578951885279495","title":"Neural and brain development","description":"The top GO terms skew toward neural development (neural tube closure, forebrain development, hippocampus development) with some broader developmental terms (skeletal system development). While there are a few unrelated terms (cell cycle, immune response), the dominant signal is brain/neural development, justifying this label with medium confidence.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001843","count":3},{"id":"GO:0001501","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0006349","count":2}]},{"hash":"170958439888811422","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by GO terms related to translation, cytosolic ribosome assembly, and ribosome biogenesis, with additional ties to mitochondrial translation and translational elongation/termination. This points to a cohesive group of proteins involved in ribosome production and the protein synthesis machinery, spanning both cytosolic and mitochondrial contexts; a few outlier terms (e.g., differentiation and chromatin regulation) are present but do not override the core signal.","confidence":"High","size":13,"edges":11,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042256","count":2},{"id":"GO:0042254","count":2},{"id":"GO:1902802","count":1},{"id":"GO:0002244","count":1}]},{"hash":"1360992196756763390","title":"Diverse Biosynthetic Pathways","description":"The top GO terms cluster around synthesis and biosynthetic processes across different metabolite types (antibiotics, polyhydroxybutyrate, UDP-L-arabinose, SAM, anthocyanin) as well as related metabolic and regulatory processes (L-glutamine metabolism, sporulation, transcription regulation). This points to a broad set of biosynthetic/metabolic roles rather than a single specific function, justifying a label centered on biosynthesis diversity.","confidence":"Medium","size":13,"edges":5,"triangles":1,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006541","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0042619","count":4}]},{"hash":"218801679094245531","title":"Ribosome biogenesis and RNA processing","description":"The top GO terms center on rRNA maturation (SSU/LSU/5.8S) and translation, with additional signals for RNA processing, splicing regulation, RNA surveillance, regulatory ncRNA silencing, and mRNA tail regulation, indicating a cluster of proteins involved in ribosome assembly and broader RNA metabolism. This combination points to a cohesive theme of ribosome biogenesis coupled with RNA processing and quality control.","confidence":"High","size":13,"edges":15,"triangles":5,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000462","count":4},{"id":"GO:0000463","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0060213","count":3}]},{"hash":"1209810051275503289","title":"Diverse signaling and transcriptional regulation","description":"The top GO terms span transcriptional control (DNA-templated transcription) and multiple signaling pathways (Wnt, PI3K), along with processes like angiogenesis, apoptosis, chemotaxis, differentiation, and immune defense. This suggests proteins that coordinate transcriptional programs with broad signaling networks across development, immunity, and stress responses, rather than a single specific function.","confidence":"Medium","size":13,"edges":27,"triangles":21,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0071333","count":10},{"id":"GO:0006935","count":10},{"id":"GO:0060044","count":10},{"id":"GO:0090263","count":10}]},{"hash":"789275471142029108","title":"RNA Splicing and Silencing Regulators","description":"These proteins cluster around RNA processing and post-transcriptional control: spliceosome assembly and alternative splicing, mRNA splice site recognition, regulatory ncRNA\u2013mediated gene silencing (including miRNA-driven translation inhibition), formation of the translation preinitiation complex, and small-subunit processome assembly. Together, they point to roles in RNA biogenesis and gene expression regulation at the RNA level.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0006376","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0000380","count":3},{"id":"GO:1905663","count":3}]},{"hash":"1596197118824977170","title":"RNA Processing and Translational Regulation","description":"This cluster is dominated by GO terms related to RNA processing and control of translation, including regulatory ncRNA-mediated gene silencing, assembly of translation initiation complexes, regulation of translational initiation, and viral translation initiation/reinitiation, as well as splicing regulation. A couple of terms (gastric acid secretion and intracellular pH elevation) appear as outliers, suggesting some annotation noise or multifunctional proteins. Overall, the shared theme is post-transcriptional gene expression regulation at the RNA level and during translation.","confidence":"Medium","size":13,"edges":15,"triangles":4,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0001731","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0075522","count":3},{"id":"GO:0006446","count":3}]},{"hash":"256634997687415680","title":"Redox Homeostasis and Transcription Regulation","description":"This cluster centers on redox-related processes (oxidant detoxification, redox homeostasis, removal of superoxide radicals, and deglutathionylation) alongside negative regulation of transcription by RNA polymerase II, suggesting a link between oxidative stress responses and transcriptional repression. Some terms (ubiquitin recycling, specific hydroxylation) may reflect related post-translational or metabolic processes or annotation noise, but the dominant signal ties redox balance to transcriptional control.","confidence":"Medium","size":13,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0019430","count":2}]},{"hash":"742676985573251435","title":"LPS core and heptose biosynthesis","description":"Most of the top GO terms point to lipopolysaccharide biosynthesis, especially the LPS core and the ADP-L-glycero-beta-D-manno-heptose biosynthetic step. While a few terms (stilbene catabolic process, cytolysis) seem unrelated, the core pattern suggests a bacterial LPS biosynthesis function for this cluster. Confidence is moderate due to some noise in the term set but strong signal around LPS core/heptose biosynthesis. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046839","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0097171","count":2},{"id":"GO:0046272","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1893514567831327298","title":"Unknown","description":"The terms span diverse biological themes (DNA base-excision repair, protein heterotetramerization, neuromuscular junction development, cytokine response, plus several obsolete terms), with no single, coherent function tying all proteins together. Without a clear common theme, a specific label is not justified.","confidence":"","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051290","count":2},{"id":"GO:0006284","count":2},{"id":"GO:0045213","count":1},{"id":"GO:0007528","count":1},{"id":"GO:0014070","count":1}]},{"hash":"770875879880751309","title":"Developmental signaling and transcription regulation","description":"The cluster shows strong signals for developmental processes (blastocyst and multicellular organism development, and branching morphogenesis of blood vessels) together with regulation of signaling and transcription (kinase activity, GTPase activity, and transcription regulation). While a few terms relate to xenobiotic response or protein autoprocessing, the dominant theme is developmental signaling and transcription control.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042993","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006469","count":2},{"id":"GO:1901896","count":2},{"id":"GO:0001824","count":2}]},{"hash":"1723622365551233226","title":"RNA Modification and Ribosome Biogenesis","description":"The cluster is dominated by RNA modification and ribosome-related terms, including RNA (guanine-N7)-methylation, rRNA methylation, rRNA modification, and ribosomal small subunit export, indicating roles in RNA processing and ribosome biogenesis. Some antibiotic-related terms and a few other processes appear, but they are secondary to the main RNA/ribosome theme.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0008284","count":2},{"id":"GO:0035948","count":2},{"id":"GO:0000056","count":2}]},{"hash":"894500927233690983","title":"Unknown","description":"The GO terms cover a highly diverse set of functions (heart rhythm regulation, prostate development, hormone secretion, various sensory and immune signaling, RNA stability, telomere maintenance, and stress responses), with no clear shared theme or tightly connected biological process. The lack of a unifying function and no internal network edges suggest there isn't a coherent single concept to name the cluster.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":3},{"id":"GO:0060743","count":2},{"id":"GO:0071446","count":2},{"id":"GO:0030103","count":2},{"id":"GO:0050966","count":2}]},{"hash":"1206050850134133432","title":"Wnt signaling and apoptosis regulation","description":"The top terms converge on regulation of Wnt signaling (including negative regulation of canonical Wnt and Wnt-related EMT) and regulation of apoptotic signaling, suggesting a theme of balancing cell fate decisions. Additional terms on deubiquitination and intracellular transport hint at broader signal regulation and protein turnover within this context, potentially linked to development processes like inner cell mass morphogenesis. Overall, the cluster seems centered on modulating growth factor signaling and cell death pathways rather than a single, narrowly defined process.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902042","count":2},{"id":"GO:0001828","count":2},{"id":"GO:0010909","count":2},{"id":"GO:0044334","count":2},{"id":"GO:0090090","count":2}]},{"hash":"1838190122385437635","title":"Nuclear transcription and cell cycle regulation in cardiac development","description":"The top GO terms center on RNA Pol II transcription and CDK-regulated cell cycle, with heart- and ventricular-development terms, suggesting a nuclear regulatory module linked to transcription and cell-cycle control in a cardiac context.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0032088","count":2},{"id":"GO:1901409","count":1},{"id":"GO:0007512","count":1},{"id":"GO:0051592","count":1}]},{"hash":"1756129388364307104","title":"Chromosome segregation and septin/cytoskeleton dynamics","description":"The top terms cluster around chromosome management during cell division (mitotic spindle orientation checkpoint, establishment of protein localization to chromosomes, meiotic sister chromatid cohesion) and septin-based cytoskeletal organization/disassembly, suggesting a shared theme of chromosome dynamics and cytokinetic architecture. Some terms (e.g., P granule assembly, certain signaling terms) are less tightly connected and may reflect annotation noise, but the dominant signal points to cell-division\u2013related chromosome and cytoskeleton processes.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031578","count":1},{"id":"GO:0032186","count":1},{"id":"GO:0090005","count":1},{"id":"GO:0090219","count":1},{"id":"GO:0007165","count":1}]},{"hash":"867089452450150288","title":"Ubiquitination-driven TNF-NF-kB signaling","description":"The top GO terms point to ubiquitin-related processes (ubiquitination, autoubiquitination, ubiquitin-dependent ERAD, and specific ubiquitin linkages) and TNF pathway regulation (TNF-mediated signaling, I-kappaB phosphorylation, and regulation of TNF signaling), with an additional histone ubiquitination term. This suggests the cluster comprises proteins involved in ubiquitin-mediated control of inflammatory signaling and protein turnover.","confidence":"High","size":13,"edges":19,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0085020","count":6},{"id":"GO:0036205","count":5},{"id":"GO:0033209","count":5}]},{"hash":"1707889441946446826","title":"Vesicle trafficking and membrane transport regulation","description":"This cluster shows enrichment for ER-to-Golgi transport, COPII-coated vesicle loading, and plasma membrane to endosome transport, indicating a core theme of intracellular vesicle trafficking and the secretory pathway, with accompanying regulatory signaling terms that may modulate trafficking or cell cycle processes.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900026","count":2},{"id":"GO:0045737","count":2},{"id":"GO:0051534","count":2},{"id":"GO:0031030","count":2},{"id":"GO:0044829","count":2}]},{"hash":"1819172334699623149","title":"Cell division and mitotic spindle assembly","description":"Top GO terms indicate a focus on cell division, mitotic spindle assembly, and actin cytoskeleton dynamics (e.g., Arp2/3 complex\u2013mediated actin nucleation), suggesting the proteins participate in mitosis and related cytoskeletal reorganization. While some terms are obsolete or peripheral, the central pattern points to a mitotic/cytoskeletal function cluster.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0034314","count":1},{"id":"GO:0060770","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0060733","count":1}]},{"hash":"673800746207799843","title":"Cell cycle control and kinase signaling","description":"The top terms point to regulation of the mitotic cell cycle and kinase signaling (including positive/negative regulation of protein kinase activity and serine/threonine kinase activity), with supporting notes on GTPase activity and broader transcription-related processes. This pattern suggests a cohesive theme around cell cycle control and signaling pathways governing proliferation. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0051028","count":2}]},{"hash":"153688337946212953","title":"Ubiquitin-Driven Proteostasis and Stress Signaling","description":"The top GO terms cluster around ubiquitination processes (K63-linked, monoubiquitination, autoubiquitination) and ubiquitin-dependent proteolysis pathways such as ERAD, alongside notes on chaperone-assisted complex assembly and transcriptional regulation. The inclusion of stress-related terms like responses to chitin and ethanol, and ABA-related regulation, points to a broader ubiquitin-mediated proteostasis and stress-signaling program. Some terms are plant- or obsolete-specific, but the common thread is ubiquitin-driven protein quality control and transcriptional influence under stress. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010200","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006513","count":2}]},{"hash":"19486516680281124","title":"Unknown","description":"The terms span differentiation, hormone signaling, stress responses, RNA regulation, and ubiquitination with no shared function or pathway evident, and the protein set shows no interaction structure, so there isn't a cohesive theme to label.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":2},{"id":"GO:0060743","count":1},{"id":"GO:0071446","count":1},{"id":"GO:0070936","count":1},{"id":"GO:0030103","count":1}]},{"hash":"2063944481907244823","title":"Unknown","description":"The top GO terms cover cartilage and kidney development, immune activation, platelet regulation, stress responses, and fungal sensing, with no single coherent function dominating the cluster. This diversity makes it hard to assign a specific biological theme.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001502","count":2},{"id":"GO:0001867","count":2},{"id":"GO:0010572","count":2},{"id":"GO:0072218","count":2},{"id":"GO:0051873","count":2}]},{"hash":"1928653989803843749","title":"Cellular stress response and detoxification","description":"The top GO terms cluster around oxidative stress/detoxification, response to toxic substances, autophagy, and metabolic regulation (glycolysis, dephosphorylation), which together point to cellular stress response and detox pathways. Some developmental terms (brain and intestinal epithelial development) appear but do not define a single cohesive pathway; overall, the shared theme is cellular stress adaptation and detoxification. Confidence: Medium","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0007585","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0009636","count":2}]},{"hash":"470528558046706254","title":"Heat-Responsive Proteolysis and Autophagy Regulation","description":"The cluster features GO terms for proteolysis, negative regulation of macroautophagy, and response to heat, suggesting a shared theme of proteostasis under thermal stress, where heat triggers protein turnover and autophagy control. An obsolete term is present but does not alter the overall interpretation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":1},{"id":"GO:0070584","count":1},{"id":"GO:0016242","count":1},{"id":"GO:0009408","count":1}]},{"hash":"990231992369953220","title":"Mating-associated fungal metabolism and sterol biosynthesis","description":"The top terms point to a fungal-specific context: karyogamy involved in conjugation with cellular fusion and ergosterol biosynthetic process/regulation, alongside amino acid (leucine/valine) and fatty acid catabolism and gluconeogenesis regulation, plus stress responses (cold, starvation). This combination strongly suggests a cluster centered on fungal metabolism coupled with sterol biosynthesis and mating-related processes, hence the chosen label.","confidence":"High","size":12,"edges":16,"triangles":12,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006552","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0000742","count":2},{"id":"GO:0042594","count":1},{"id":"GO:0009791","count":1}]},{"hash":"250553051359676278","title":"Ribosome Biogenesis and Translation","description":"This cluster is enriched for GO terms centered on translation, ribosome assembly, and rRNA processing, suggesting a core role in ribosome biogenesis and protein synthesis; accompanying terms like protein retention in Golgi and protein homooligomerization likely reflect broader protein maturation processes tied to ribosomal machinery.","confidence":"High","size":12,"edges":57,"triangles":151,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0045053","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1868897214543518243","title":"Mitochondrial redox and sterol lipid biosynthesis","description":"The GO terms cluster around redox balance (oxidant detoxification, redox homeostasis), mitochondrial components (cytochrome complex assembly, mitochondrion inheritance), and lipid/sterol biosynthesis (ergosterol biosynthetic process, ether lipid metabolism, fatty acid biosynthetic process). This combination points to mitochondrial oxidative metabolism intertwined with sterol and lipid biosynthesis, particularly in fungi (ergosterol). Some terms like anther development seem incidental/noise.","confidence":"Medium","size":12,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0017004","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006696","count":1}]},{"hash":"735737255556456631","title":"Olfactory GPCR-cAMP/cGMP Signaling","description":"The top GO terms center on olfactory perception and cyclic nucleotide signaling (cellular responses to cAMP/cGMP and regulation of adenylate cyclase), complemented by ion transport consistent with olfactory transduction.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071321","count":1},{"id":"GO:0098719","count":1},{"id":"GO:0007608","count":1},{"id":"GO:0045762","count":1},{"id":"GO:0071320","count":1}]},{"hash":"1652492057944386777","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031119","count":2},{"id":"GO:0031120","count":2},{"id":"GO:1990481","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0034553","count":1}]},{"hash":"1502095638075709482","title":"Antibiotic Response and Biosynthesis","description":"The top GO terms are dominated by antibiotic-related processes (response to antibiotic, antibiotic biosynthetic process), with supporting secondary metabolism terms such as tropane alkaloid and steroid catabolic processes. This points to a theme centered on antibiotic response and secondary metabolite biosynthesis, with some regulatory and general metabolism signals. The scattered auxiliary terms and low connectivity suggest a broad association rather than a tight, single-function module, but the antibiotic/metabolic theme is clear enough for labeling.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0042208","count":3}]},{"hash":"1037406344574248406","title":"Nucleocytoplasmic transport and translation with stress signaling","description":"This cluster centers on RNA processing and protein synthesis, with GO terms for mRNA export from the nucleus, protein export from the nucleus, ribosome biogenesis, and translation, plus splicing regulation. The presence of stress-related pathways (JNK cascade, nitric oxide response) and apoptosis suggests these proteins link RNA metabolism and translation to cellular stress responses, consistent with an overarching theme of nucleocytoplasmic transport and ribosome function under stress.","confidence":"Medium","size":12,"edges":60,"triangles":169,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006406","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0034501","count":3},{"id":"GO:0046330","count":2},{"id":"GO:0048025","count":2}]},{"hash":"1697856738432167858","title":"Rac-Mediated Cytoskeleton, Polarity, and Division","description":"Top terms center on Rac protein signal transduction, epithelial cell polarity, vesicle transport, and mitotic processes like spindle assembly and exit from mitosis, along with cell migration. This suggests a cohesive theme around Rac-driven cytoskeletal dynamics that govern cell shape, polarity, intracellular trafficking, and progression through division. Some terms (neural differentiation, sporulation) may reflect broader annotations rather than a core cluster function, but the dominant signals align with cytoskeleton organization, polarity, and mitosis.","confidence":"Medium","size":12,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016601","count":3},{"id":"GO:0045197","count":2},{"id":"GO:0006893","count":2},{"id":"GO:0035264","count":2},{"id":"GO:1904948","count":2}]},{"hash":"1793201112524211828","title":"Xenobiotic Detoxification and Oxidative DNA Repair","description":"Top GO terms indicate detoxification of oxidants, cellular redox homeostasis, and responses to xenobiotics (ethanol, estradiol, L-ascorbic acid), along with nucleotide-excision repair. Together these suggest a functional module focused on managing chemical stress and repairing oxidative DNA damage, justifying a label centered on detoxification and DNA repair under oxidative stress.","confidence":"Medium","size":12,"edges":14,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0045471","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0032355","count":3}]},{"hash":"1913734421231176470","title":"Chromatin Remodeling in Hormone-Driven Differentiation","description":"The cluster is enriched for epigenetic processes (nucleosome assembly, heterochromatin formation, histone methylation) and transcriptional regulation, together with differentiation in hormone-responsive tissues (estradiol stimulus, skeletal muscle, osteoblast, endocrine pancreas). This suggests a theme of chromatin-based regulation guiding hormone-driven developmental differentiation.","confidence":"Medium","size":12,"edges":39,"triangles":73,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0071392","count":6},{"id":"GO:0000122","count":4},{"id":"GO:0035914","count":4},{"id":"GO:0031018","count":4},{"id":"GO:0006334","count":4}]},{"hash":"537625122943022105","title":"Neuronal vesicle trafficking and synaptic signaling","description":"The cluster shows strong representation of brain development, synaptic vesicle budding, calcium-dependent exocytosis, and dendritic spine development, pointing to neuronal vesicle trafficking and synaptic function. The presence of ER-to-Golgi transport and small GTPase signaling further supports a cohesive trafficking/signaling theme in neurons, despite a few outlier terms.","confidence":"High","size":12,"edges":19,"triangles":12,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":6},{"id":"GO:0070142","count":6},{"id":"GO:1902307","count":6},{"id":"GO:0060999","count":6},{"id":"GO:0033028","count":6}]},{"hash":"1030120801933728839","title":"Cell Growth, Differentiation, and Apoptosis Regulation","description":"This cluster includes terms for gene expression and DNA replication (transcription, replication), developmental differentiation (cranial skeleton morphogenesis, myotube differentiation), immune activation (activated T cell proliferation), chemotaxis, telomere maintenance, osmosensory signaling, and apoptosis. The mixture suggests a broad regulatory program governing growth, lineage specification, stress responses, and cell survival, rather than a single cohesive pathway.","confidence":"Medium","size":12,"edges":20,"triangles":8,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0048701","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0006935","count":4},{"id":"GO:0060044","count":3}]},{"hash":"288785344727287517","title":"Transcriptional and Differentiation Regulators","description":"This cluster centers on transcriptional control (DNA-templated transcription and related regulatory processes) and the regulation of differentiation in tissues like muscle, bone, and vasculature, suggesting proteins that modulate gene expression to influence lineage outcomes. Some GO terms are obsolete, but the recurring themes of transcription regulation and differentiation support a cohesive functional group.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":2},{"id":"GO:2001214","count":2},{"id":"GO:0061428","count":2},{"id":"GO:0045668","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1756243965452046894","title":"Unknown","description":"The GO terms cover a wide range of distinct processes\u2014from transcription coactivator regulation and estrogen signaling to mRNA deadenylation, ncRNA-mediated silencing, cytokine signaling, glycolysis regulation, autophagy, and intestinal development\u2014without a clear single function tying these proteins together. This lack of a cohesive theme makes it inappropriate to assign a specific, representative label.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000327","count":1},{"id":"GO:0007548","count":1},{"id":"GO:0033147","count":1},{"id":"GO:0000289","count":1},{"id":"GO:0031047","count":1}]},{"hash":"1186237805368786335","title":"Hippo-Wnt driven epithelial growth control","description":"The terms show strong emphasis on growth control pathways (hippo signaling, positive regulation of canonical Wnt signaling) together with epithelial-specific processes (keratinocyte differentiation, regulation of bicellular tight junction assembly). Also included are DNA replication and apoptotic processes, indicating coordination of proliferation, differentiation, and cell fate with survival decisions in epithelial contexts. This suggests a coherent module regulating epithelial growth and differentiation via Hippo/Wnt signaling.","confidence":"High","size":12,"edges":9,"triangles":4,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0060044","count":10},{"id":"GO:0030216","count":10},{"id":"GO:0006915","count":10},{"id":"GO:0035329","count":10},{"id":"GO:0006260","count":9}]},{"hash":"1621646212327493655","title":"Neuronal signaling and cerebellar development","description":"The top GO terms center on neural signaling (JNK cascade, PI3K/AKT signaling, synaptic transmission) and cerebellar development (cerebellar cortex formation, glutamatergic transmission), suggesting a theme of neuronal signal transduction linked to cerebellar formation. Although some terms are more general or include immune signaling, the core appears neuronal. ","confidence":"Medium","size":12,"edges":24,"triangles":13,"max_degree":7,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0046827","count":12},{"id":"GO:0038093","count":11},{"id":"GO:1990139","count":11},{"id":"GO:2000686","count":11},{"id":"GO:0007254","count":11}]},{"hash":"2113675356505509523","title":"Immune signaling and neuronal plasticity","description":"The cluster's top GO terms span innate immune response and Fc receptor signaling, alongside major signaling pathways like JNK cascade and PI3K/AKT regulation, plus a neuronal plasticity term (long-term synaptic potentiation) and apoptosis. This suggests a cohesive theme of signaling cross-talk between immune responses and neural function, with possible links to cell fate decisions. Confidence: Medium","confidence":"","size":12,"edges":22,"triangles":18,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0071375","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0038093","count":1}]},{"hash":"2149151002851497412","title":"Signaling Pathways in Immune and Neural Development","description":"The top GO terms cluster around core signal transduction pathways (Fc receptor signaling, JNK cascade, PI3K/AKT signaling, growth hormone receptor signaling) and include neural-development related terms (cerebellar cortex formation, glutamatergic synaptic transmission) as well as placental development. This suggests a cohesive theme of proteins involved in fundamental signaling processes that influence both immune signaling and neural development, with some terms reflecting broader developmental contexts. Given the mix of immune-related and neural/developmental terms, a label centered on \"signaling pathways\" with a developmental emphasis fits best, even though the set spans multiple tissues.","confidence":"Medium","size":12,"edges":7,"triangles":2,"max_degree":4,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0038093","count":8},{"id":"GO:1990139","count":8},{"id":"GO:2000686","count":8},{"id":"GO:0007254","count":8},{"id":"GO:0033129","count":8}]},{"hash":"1223376363179529995","title":"Neuronal synapse assembly and signaling regulation","description":"This cluster is defined by postsynaptic density assembly and associations with synaptic vesicle clustering and cerebellar cortex formation, pointing to neuronal synapse organization and brain development. The presence of terms about regulation of major signaling pathways (ERK, PI3K/AKT) and phosphatase activity suggests tight modulation of synaptic signaling and plasticity, while TRAIL-related apoptotic signaling hints at neuronal survival/pruning processes. Overall, the proteins cohere around synapse formation and control of neuronal signaling in the cerebellum.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0097107","count":8},{"id":"GO:0051895","count":8},{"id":"GO:1903984","count":8},{"id":"GO:2000808","count":8},{"id":"GO:0051898","count":8}]},{"hash":"1999137312113292092","title":"Neuronal-immune signaling with transcription regulation","description":"Enrichment centers on signaling pathways (JNK cascade, T cell receptor signaling) and transcription-related processes (DNA-templated transcription, nuclear export regulation), with ties to neuron development and synapse assembly. This points to a theme of transcriptional regulation driven by signaling in neural and immune contexts, rather than a single cohesive pathway; cell-cycle terms are present but less central.","confidence":"Medium","size":12,"edges":12,"triangles":1,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007254","count":2},{"id":"GO:0000722","count":2},{"id":"GO:0050852","count":2}]},{"hash":"2072177200282344141","title":"Developmental Growth and Cell Proliferation","description":"Enrichment centers on developmental processes (angiogenesis, brain development, multicellular organism growth) and cell division (mitotic spindle assembly, mitotic cell cycle), suggesting a developmental growth program tied to proliferation. Additional terms for ER-to-Golgi vesicle transport and cellular response to hypoxia imply coordination of intracellular trafficking and stress signaling during development. Together these terms indicate a cluster focused on developmental growth and regulation of cell proliferation, rather than a single specialized pathway.","confidence":"Medium","size":12,"edges":8,"triangles":4,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0001525","count":4},{"id":"GO:0035264","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0007420","count":3}]},{"hash":"1971131958517737411","title":"Ubiquitin-Proteostasis and ERAD","description":"The Top Terms are dominated by ubiquitin-related processes (protein deubiquitination, protein autoubiquitination) and ER-associated degradation (ERAD) pathways, suggesting a core theme of protein quality control. Additional terms indicate stress- and toxin-related responses (toxic substances, insecticide) and autophagy regulation, which commonly intersect with ubiquitin-mediated degradation and proteostasis. Together, these point to a cohesive cluster of ubiquitin cycling, ERAD, and proteostasis functions.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":6},{"id":"GO:0034140","count":4},{"id":"GO:0017085","count":4},{"id":"GO:0045648","count":4},{"id":"GO:1901097","count":4}]},{"hash":"960871605636279883","title":"Protein post-translational modification and autophagy","description":"This cluster centers on multiple protein modification pathways (sumoylation, neddylation, C-terminal lipidation) and autophagy-related processes (macroautophagy, nucleophagy), pointing to a core theme of proteostasis and cellular remodeling. Additional linked terms for tRNA wobble thiolation and molybdenum cofactor biosynthesis suggest broader metabolic and RNA-level regulation connected to growth and transcriptional control (e.g., cell cycle regulation). The mix supports a cohesive label around PTMs and autophagy with growth-regulatory context, hence a Medium confidence. ","confidence":"Medium","size":12,"edges":47,"triangles":102,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":9},{"id":"GO:0016236","count":7},{"id":"GO:0006777","count":7},{"id":"GO:0045116","count":7},{"id":"GO:0002143","count":7}]},{"hash":"1340873879478799815","title":"Chromatin regulation and one-carbon metabolism","description":"This cluster is anchored by GO terms for rDNA heterochromatin formation and negative regulation of transcription by RNA polymerase II, pointing to chromatin-mediated transcriptional silencing. The inclusion of one-carbon metabolic processes and NADPH regeneration suggests metabolic support for epigenetic modification (e.g., methylation) and redox balance that fuels chromatin regulation. Although some terms are obsolete, the dominant theme links chromatin state to transcriptional control with metabolic context.","confidence":"High","size":12,"edges":29,"triangles":30,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0006730","count":2},{"id":"GO:1903758","count":2},{"id":"GO:0001666","count":2}]},{"hash":"484901122868310402","title":"Unknown","description":"The top terms cover a broad mix of processes (NF-kappaB regulation, Golgi trafficking, drug response, miRNA export, mitochondrial inheritance, neuron differentiation, and immune cytotoxicity) with no single dominant function, and the absence of edges or connections suggests no cohesive pathway linking the proteins. So a specific, representative label cannot be confidently assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043124","count":3},{"id":"GO:0006893","count":2},{"id":"GO:0097327","count":2},{"id":"GO:0048211","count":2},{"id":"GO:0035264","count":2}]},{"hash":"1722377111709625931","title":"Chromatin remodeling and cell division","description":"The cluster\u2019s top GO terms emphasize chromatin state regulation (histone H3-K4 demethylation, positive regulation of chromatin binding) and mitotic processes (spindle assembly, cell division), pointing to proteins involved in chromatin remodeling coordinated with the cell cycle. While a few terms are obsolete or reflect unrelated metabolic salvage pathways, the core signal centers on epigenetic regulation linked to mitosis. ","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034720","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0035563","count":2},{"id":"GO:0034356","count":2},{"id":"GO:0019358","count":2}]},{"hash":"1010733712308698013","title":"Embryonic development and signaling regulation","description":"This cluster is dominated by developmental processes (skeletal system development, forebrain development, mesoderm formation) and signaling/growth control (negative regulation of SHH signaling in neural tube patterning, mitotic cell cycle). While other terms touch on stress responses (ER stress\u2013related apoptosis) and immune defense, these appear ancillary to the core theme of embryonic growth and patterning, suggesting proteins involved in development and its accompanying signaling pathways. Hence a label around embryogenesis and signaling regulation fits best, with some caveats due to the miscellaneous terms.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001501","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0060044","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006349","count":3}]},{"hash":"1779370250293108325","title":"Lipid-derived signaling and metabolism","description":"Top terms center on lipid-derived signaling: prostaglandin and oxylipin biosynthesis, retinoic acid biosynthesis, cholesterol catabolism, and vitamin D response, accompanied by redox homeostasis and regulation of inflammation, with an additional hint toward eye biology (retina vasculature) and photoregulatory signaling.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":3},{"id":"GO:0046232","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0002677","count":2},{"id":"GO:0033280","count":2}]},{"hash":"680485139377555343","title":"Bacterial cell wall biosynthesis and glycosylation","description":"The cluster is dominated by GO terms related to cell wall organization and envelope components (cell wall organization, teichoic acid biosynthetic process) plus sugar metabolism and protein glycosylation (UDP-glucose metabolic process, glycogen biosynthetic process, protein O-linked glycosylation via mannose and via GalNAc), pointing to cell wall biogenesis and glycosylation as the shared theme. Immune signaling terms (Fc receptor signaling) and apoptotic process appear less central, likely as outliers. ","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0071375","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0006011","count":2}]},{"hash":"1238651032585111072","title":"GTPase signaling in neural development and axon guidance","description":"The cluster is dominated by small GTPase-mediated signal transduction and includes multiple neural development terms (nervous system development, hippocampus development) as well as axon extension, indicating a core theme of GTPase-driven signaling that governs neural differentiation and axon growth. Other enriched terms (ephrin receptor, Wnt, JNK cascades) point to broader signaling interactions supporting neural development, making the label representative of the cluster\u2019s function.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007264","count":5},{"id":"GO:0050852","count":4},{"id":"GO:0048013","count":4},{"id":"GO:0046330","count":4},{"id":"GO:0090263","count":4}]},{"hash":"1033756337352035736","title":"Mitosis and Vesicle Trafficking","description":"The top GO terms cluster around mitotic events (spindle assembly, exit from mitosis) and intracellular transport between organelles (Golgi to plasma membrane, plasma membrane to endosome, ribosomal subunit export), indicating a theme of coordinating cell division with membrane trafficking and secretion, with additional notes of growth/differentiation. This supports a concise label that emphasizes the dominant processes found in the cluster.","confidence":"Medium","size":12,"edges":13,"triangles":5,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":4},{"id":"GO:0048227","count":4},{"id":"GO:0006893","count":3},{"id":"GO:0035264","count":3},{"id":"GO:1904948","count":3}]},{"hash":"39387957376485830","title":"Dendritic Spine Development and Actin Dynamics","description":"The cluster is enriched for GO terms related to neuronal synapse formation and actin-driven membrane protrusions, including regulation of dendritic spine morphogenesis and development, lamellipodium/ruffle assembly, and Rac signaling, all pointing to actin remodeling that shapes dendritic spines in hippocampal neurons. While a few terms touch on cell cycle and ubiquitination, the dominant theme is spine development and cytoskeletal dynamics.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071260","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0016601","count":4},{"id":"GO:0097178","count":4}]},{"hash":"128316364036624334","title":"Genome maintenance and protein quality control","description":"These terms cluster around genome maintenance (CENP-A chromatin assembly; cell division; microtubule dynamics) as well as protein quality control and trafficking (ERAD, vesicle formation, ER-Golgi transport, translation initiation regulation, nonfunctional rRNA decay, and translesion synthesis). The combination suggests a broad theme of maintaining cell viability by coordinating chromosome biology with proteostasis and intracellular transport.","confidence":"Medium","size":12,"edges":51,"triangles":105,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0051013","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0070651","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0030433","count":2}]},{"hash":"187334827028615035","title":"Nucleocytoplasmic transport and transcription regulation","description":"This cluster centers on nucleocytoplasmic transport (mRNA export, NLS-bearing protein import) and transcriptional control (DNA-templated transcription and its regulation). The inclusion of NFAT signaling and GTPase activity regulation suggests links between signaling, trafficking, and gene expression, with a broader intracellular transport component (Golgi-to-lysosome). ","confidence":"Medium","size":12,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0090160","count":2},{"id":"GO:0051533","count":2}]},{"hash":"1922990142514458480","title":"Spliceosome-driven mRNA processing and apoptosis regulation","description":"Most terms center on mRNA splicing and spliceosome activity (regulation of alternative splicing, cis splicing), indicating a core role in RNA processing. Several terms point to apoptosis and its negative regulation, suggesting the proteins may modulate cell death in the context of splicing or stress. A few terms (iron-sulfur cluster assembly, development, hematopoiesis) appear incidental or reflect broader roles of some members. Overall, the theme is RNA splicing machinery with associated apoptotic regulation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0006915","count":1},{"id":"GO:0016226","count":1}]},{"hash":"2252472328215118812","title":"Nuclear transcription and chromatin regulation","description":"Reasoning: The dominant terms describe nuclear gene expression control\u2014DNA-templated transcription and its regulation, histone modifications (methylation and deubiquitination), and RNA processing/surveillance in the nuclear context. A few peripheral terms (protein transport, insulin signaling) are less central.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0016578","count":1},{"id":"GO:0071033","count":1},{"id":"GO:0061179","count":1},{"id":"GO:0034729","count":1}]},{"hash":"1680751099890348781","title":"Translation Regulation and ER Stress Response","description":"This cluster centers on GO terms related to translation initiation, preinitiation complex formation, reinitiation, and termination, plus a cellular response to unfolded protein, pointing to a shared function in controlling protein synthesis and managing ER stress; other terms appear incidental noise from developmental annotations.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0006415","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0075525","count":1}]},{"hash":"287958881380475423","title":"ER stress response and proteostasis","description":"The cluster is dominated by GO terms tied to endoplasmic reticulum stress response, unfolded protein response, chaperone-assisted refolding, and ubiquitin-proteasome\u2013mediated ERAD, indicating coordination of protein folding and degradation in the ER. Some terms like DNA replication and cytokinin signaling are less coherent with ER proteostasis, but the predominant pattern supports ER stress proteostasis as the cluster theme.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036494","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1903070","count":2}]},{"hash":"1270304191718438012","title":"Unknown","description":"The top terms include antibiotic biosynthesis, multiple developmental terms (forebrain and skeletal development), cell division and mitotic cycle, defense response to Gram-positive bacteria, invasive growth under glucose limitation, and ER-stress\u2013related apoptotic signaling. The mixture lacks a single coherent function or pathway, so a single, intuitive label cannot be confidently assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0030900","count":2}]},{"hash":"239937684500202","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061158","count":1},{"id":"GO:1903883","count":1},{"id":"GO:0035278","count":1},{"id":"GO:0010586","count":1},{"id":"GO:1903265","count":1}]},{"hash":"339583462180773090","title":"Cardiac Development and Function","description":"Based on the GO terms, there is a clear emphasis on heart development and cardiac muscle contraction (GO:0007507, GO:0060048), with supportive signals from embryonic development and signaling pathways (GO:0001701, GO:0022400, GO:0071320, GO:0007205). While a couple terms appear peripheral (selenium ion response, granulocyte differentiation), the dominant pattern centers on cardiac development and function, suggesting these proteins collectively contribute to heart development and signaling. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010269","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0030851","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0051412","count":2}]},{"hash":"822803230344621541","title":"Neuronal signaling and synaptic plasticity","description":"The Top Terms are dominated by neural-related processes: neurotransmitter secretion, regulation of long-term synaptic potentiation, neural crest formation, and calcium-related mitochondrial activity, which together suggest neuron-centered signaling and synaptic modulation. There are a few outliers (kidney development, miRNA processing) that are less central to this theme, but the core pattern points to neural communication and plasticity as the cluster\u2019s function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014029","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0043065","count":1},{"id":"GO:0008016","count":1},{"id":"GO:0007269","count":1}]},{"hash":"1933015590566519698","title":"Cell cycle control and telomere maintenance","description":"The top GO terms are strongly centered on cell cycle processes (GO:0007049) and regulation of CDK activity (GO:0045736), along with telomere maintenance/capping (GO:0032212, GO:1904355). This suggests a core theme of cellular proliferation control and genome stability. Additional terms like mRNA processing (GO:0006397) indicate broader nuclear regulation, while fat cell differentiation and muscle stretch response hint at ancillary differentiation or mechanotransduction signals that are less central to the cluster. Overall, the dominant pattern aligns with cell cycle regulation and telomere maintenance, with peripheral associations to transcriptional processing and differentiation signals.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007049","count":6},{"id":"GO:0045736","count":6},{"id":"GO:0006397","count":6},{"id":"GO:0016477","count":6},{"id":"GO:0045444","count":6}]},{"hash":"755405893212179633","title":"Photosynthesis Light Harvesting and Light Response","description":"This cluster is dominated by GO terms tied to photosynthesis and light interactions, including light harvesting in photosystems I and II, photosynthesis in general, and cellular responses to various light stimuli (UV-A, red, far red) as well as high or low light. The presence of multiple chlorophyll/phytol-related processes (phytol biosynthesis regulation) further supports a chloroplast/light-absorbing function. Together, these terms point to proteins involved in photosynthesis and light-responsive regulation, making a concise label along the lines of photosynthesis and light response appropriate.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018298","count":2},{"id":"GO:0009768","count":2},{"id":"GO:0071492","count":2},{"id":"GO:0010114","count":2},{"id":"GO:0071486","count":2}]},{"hash":"2021646140869587441","title":"Unknown","description":"This cluster's GO terms span chlorophyll catabolic, heme biosynthesis, various catabolic pathways, lipid and nucleotide catabolism, and some cell-cycle/stress terms, with no single shared pathway dominating, so no cohesive functional label can be assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015996","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0006782","count":1},{"id":"GO:0018160","count":1}]},{"hash":"1523868226242591703","title":"Membrane trafficking and actin dynamics","description":"This cluster centers on Golgi to plasma membrane transport and regulation of the actin cytoskeleton, with recurrent themes of protein localization to the cell edge, adhesion modulation, and signaling responses. The presence of GO terms for Golgi-to-plasma-membrane transport, positive regulation of actin depolymerization, and protein localization to the leading edge suggests a cohesive theme around membrane trafficking coupled with cytoskeletal remodeling, despite no observed physical interactions in the graph. Overall, the label captures the dominant functional threads tying these terms together.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043001","count":2},{"id":"GO:0030307","count":2},{"id":"GO:0014823","count":2},{"id":"GO:0030836","count":2},{"id":"GO:0007162","count":2}]},{"hash":"1821466428539877656","title":"Epigenetic regulation and transcription","description":"Top terms cluster around DNA-templated transcription and histone modifications (H3K4/H3K79 methylation, H2B deubiquitination), indicating an epigenetic regulation theme driving transcription. Other terms appear more general or context-specific, so the core label reflects chromatin regulation of transcription.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0051568","count":3},{"id":"GO:0034729","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0045444","count":2}]},{"hash":"584667564791766064","title":"Vitamin/antibiotic biosynthesis and RNA methylation","description":"The cluster is dominated by biosynthetic processes for vitamins and antibiotics (biotin, menaquinone, vitamin E, antibiotic biosynthesis) and includes a tRNA methylation term, implying a link between metabolism and RNA modification or regulation. Transcription-related GO terms also appear, suggesting a broader coupling to gene expression. While the presence of some obsolete histone modification terms muddies the signal, the core theme centers on biosynthesis with RNA-level regulation. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":4},{"id":"GO:0009234","count":3},{"id":"GO:0030488","count":3},{"id":"GO:0010189","count":3},{"id":"GO:0017000","count":3}]},{"hash":"1001385685616583088","title":"Unknown","description":"The top GO terms span a wide range of unrelated processes (metabolism, development, signaling, DNA repair, neural function, and muscle biology) with no single dominant theme linking them, and there are no edges within the cluster to suggest a common pathway or function. Therefore, a cohesive, specific label cannot be assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034638","count":2},{"id":"GO:0003315","count":2},{"id":"GO:0032423","count":2},{"id":"GO:0035414","count":2},{"id":"GO:0021881","count":2}]},{"hash":"1511353474050972405","title":"Mitochondrial Metabolism and Neural Detoxification","description":"The cluster\u2019s terms center on mitochondrial biology (mitochondrion inheritance; mitochondrial electron transport) and detoxification/oxidant handling (cellular oxidant detoxification; mercury detoxification), with several neural-related terms (dopamine metabolism regulation, CNS myelin maintenance). This suggests proteins involved in mitochondrial energy production and redox balance that support neural metabolism and detoxification processes, despite the presence of an outlier immune-related term (response to lipopolysaccharide). Confidence: Medium","confidence":"","size":11,"edges":15,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":2},{"id":"GO:0000001","count":1},{"id":"GO:0045964","count":1},{"id":"GO:1902114","count":1},{"id":"GO:0098869","count":1}]},{"hash":"1307133004097635385","title":"Actin Cytoskeleton Remodeling and Cell Motility","description":"The terms cluster strongly around actin dynamics (polymerization, lamellipodium assembly, actin-based movement) and morphogenesis (dendritic spine morphogenesis, collateral sprouting), with neuronal signaling themes supporting neurite outgrowth; a few outliers relate to immune processes or mitochondrial fission but do not dominate. This points to a cohesive theme of actin-driven remodeling and movement across cell types.","confidence":"High","size":11,"edges":30,"triangles":30,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051497","count":4},{"id":"GO:0060997","count":4},{"id":"GO:0007121","count":4},{"id":"GO:0030041","count":3},{"id":"GO:0002625","count":3}]},{"hash":"79357991093220601","title":"Unknown","description":"The top GO terms span detoxification, gene regulation, chromatin remodeling, various biosynthetic pathways, and stress responses, with no clear shared function tying all 11 proteins together. Some terms are obsolete, suggesting annotation noise. Therefore there isn\u2019t a cohesive theme to name the cluster.","confidence":"","size":11,"edges":18,"triangles":4,"max_degree":5,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0046294","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0019518","count":3},{"id":"GO:0006069","count":3}]},{"hash":"1988530068313766167","title":"Genome replication and chromatin maintenance","description":"The top terms cluster around DNA replication, centromere/chromatin assembly (CENP-A), and DNA damage tolerance (translesion synthesis), with related processes in cell division (microtubule severing) and chromatin maintenance. Additional signals for protein regulation and stress responses fit under a broader genome- and chromatin-centric cellular context, supporting a label focused on genome replication and chromatin maintenance rather than a single housekeeping pathway.","confidence":"Medium","size":11,"edges":18,"triangles":13,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051260","count":5},{"id":"GO:0070987","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0046034","count":4}]},{"hash":"1502661613091301101","title":"RNA splicing and ribosome biogenesis","description":"This cluster is dominated by GO terms related to RNA processing, especially spliceosome-mediated mRNA splicing (including regulation and splice site recognition) and small-subunit processome assembly, with an additional hint of translation initiation. Together these point to RNA metabolism and ribosome biogenesis as the core theme of the proteins in this group.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006376","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0000380","count":1}]},{"hash":"777540323837038588","title":"Proteolysis and peptide processing","description":"GO terms cluster around proteolysis and peptide processing (proteolysis, digestion, APP processing/amyloid-beta metabolism, angiotensin maturation and regulation, antigen presentation via MHC II), suggesting a shared function in generating or regulating peptide fragments across systems (neurodegeneration, cardiovascular signaling, immune surveillance); a few terms (mesonephros development, xylan catabolic process) are looser fits but may reflect broader degradative roles.","confidence":"High","size":11,"edges":23,"triangles":20,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":3},{"id":"GO:0007586","count":2},{"id":"GO:0042985","count":2},{"id":"GO:0002016","count":2},{"id":"GO:0002018","count":2}]},{"hash":"1395505544501201314","title":"RNA modification and translation machinery","description":"The cluster is dominated by translation-related terms (initiation, translation, termination) and pseudouridine synthesis across tRNA, mRNA, and snRNA, pointing to RNA modification integral to protein synthesis. Additional terms for ribosomal subunit export and mRNA decay fit within RNA processing and translation pathways, with a minor note on salt-stress response. Overall, these proteins appear to function together in RNA modification and ribosome-based translation processes.","confidence":"High","size":11,"edges":15,"triangles":7,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0031119","count":1},{"id":"GO:1990481","count":1},{"id":"GO:0031120","count":1},{"id":"GO:0090529","count":1}]},{"hash":"189262042764279774","title":"RNA metabolism and genome maintenance","description":"Proteins in this cluster are linked to RNA-related processes (translation, tRNA aminoacylation, tRNA wobble modification, mitochondrial tRNA charging) as well as genome stability functions (DNA recombination, DNA repair, telomere capping and telomere maintenance, mitotic cell cycle checkpoint signaling), suggesting a theme that connects RNA biology with genome maintenance.","confidence":"Medium","size":11,"edges":15,"triangles":1,"max_degree":5,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006310","count":5},{"id":"GO:0070154","count":5},{"id":"GO:0016233","count":5},{"id":"GO:0006412","count":5},{"id":"GO:0010833","count":5}]},{"hash":"2128566827536356199","title":"Neurodevelopment and cell cycle regulation","description":"The cluster\u2019s top GO terms center on nervous system development (forebrain and general neural development) alongside multiple cell cycle processes (mitotic and meiotic cycles, G1/S transition, kinetochore localization, and nuclear export regulation). This suggests a cohesive theme where genes drive neural development while coordinating cell division. A couple of terms (defense response to Gram-positive bacteria, imprinting regulation) appear less central and may reflect multifunctionality or annotation noise, but the core signal supports a link between neurodevelopment and cell-cycle control.","confidence":"High","size":11,"edges":6,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001501","count":5},{"id":"GO:0030900","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0007399","count":5},{"id":"GO:0006349","count":5}]},{"hash":"878612632571616502","title":"Meiosis-linked DNA replication and repair","description":"Most prominent terms cluster around DNA replication, meiotic recombination repair, and meiotic cell cycle, suggesting a focus on genome maintenance during meiosis. Other terms (ER-Golgi transport, protein oligomerization, hormone signaling, and metabolism) appear ancillary but do not define the cluster's core function. ","confidence":"Medium","size":11,"edges":20,"triangles":8,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:1990918","count":5},{"id":"GO:0006888","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0006196","count":3}]},{"hash":"1172354532521813816","title":"Centromeric chromatin assembly and mitotic chromosome dynamics","description":"These proteins show a strong signal for chromosome-centromere related processes (CENP-A chromatin assembly) and mitotic/spindle dynamics (microtubule severing, cell division), suggesting a role in chromosome segregation during cell division. Additional terms for transcription, RNA methylation, and ribosome biogenesis point to broader cell-cycle\u2013related biosynthesis and gene expression that accompany division, though the core theme remains centromeric assembly and chromosome maintenance.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0051260","count":4},{"id":"GO:0051013","count":3},{"id":"GO:0061641","count":3},{"id":"GO:0030433","count":3}]},{"hash":"499219173044276529","title":"Steroid, lipid, and retinoid biosynthesis","description":"The top GO terms cluster around biosynthetic processes for steroids, lipids, and retinoids (retinol and retinoic acid), plus related lipid pathways like sphingolipid and very long-chain fatty acid biosynthesis, indicating a cohesive theme of metabolite biosynthesis. Some terms point to secondary metabolite production (tropane alkaloids, antibiotics), but the dominant pattern is biosynthetic pathways for lipids and hormone-like compounds.","confidence":"Medium","size":11,"edges":16,"triangles":10,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042572","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0009710","count":3}]},{"hash":"358186087976862495","title":"Microtubule-Driven Spindle and Cytoskeleton Dynamics","description":"The top GO terms point to microtubule-based processes: spindle assembly/elongation, plus-end\u2013directed sliding, and maintenance of microtubule polarity, along with nuclear migration along microtubules and related cytoskeletal organization. The inclusion of stress granule disassembly and cerebellar layer organization suggests broader cytoskeletal and cellular architecture roles, not just mitosis. Together, these terms indicate a coherent theme of microtubule-dependent spindle dynamics and cytoskeleton organization across mitotic and neuronal contexts.","confidence":"High","size":11,"edges":29,"triangles":27,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":6},{"id":"GO:0090307","count":6},{"id":"GO:0000022","count":5},{"id":"GO:0035617","count":5},{"id":"GO:0030473","count":5}]},{"hash":"595069437533403053","title":"Chromatin remodeling and histone modifications","description":"The proteins cluster around chromatin structure and histone regulation, including CENP-A chromatin assembly, histone H2B ubiquitination, H3-K27 methylation regulation, nucleosome mobilization, and heterochromatin formation, as well as transcriptional repression by RNA polymerase II. These terms point to a cohesive theme of chromatin organization and epigenetic control of gene expression, with a few minor peripheral GO terms (like peroxisome import) not altering the overall pattern. ","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0042766","count":4},{"id":"GO:0071894","count":4},{"id":"GO:0061641","count":3},{"id":"GO:0061086","count":3}]},{"hash":"1209538567298681188","title":"Vascular and Cardiac Smooth Muscle Differentiation","description":"Most of the top GO terms point to regulation and differentiation of smooth muscle cells, especially vascular smooth muscle cells and cardiac smooth muscle. Terms like positive regulation of smooth muscle cell differentiation, positive regulation of cardiac muscle cell differentiation, and vascular-associated smooth muscle cell differentiation support a cohesive theme around smooth muscle development and signaling (including TGF-beta receptor signaling). A few other annotations (telomere maintenance, histone mRNA catabolic process, double-strand break repair) appear less connected to this core theme, likely reflecting broader cellular processes annotated to these proteins. Overall, the cluster best fits a smooth muscle differentiation/growth signaling group.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051152","count":1},{"id":"GO:0010667","count":1},{"id":"GO:0071475","count":1},{"id":"GO:2000727","count":1},{"id":"GO:0035886","count":1}]},{"hash":"817263972479514927","title":"Golgi\u2013ER and Endosome Trafficking","description":"The top GO terms cluster around vesicle transport and Golgi dynamics (Golgi to plasma membrane transport, Golgi organization, retrograde Golgi\u2013ER transport, early endosome to Golgi transport), with an autophagy-related Cvt pathway note; translation-related terms appear but are secondary. This pattern points to intracellular trafficking involving Golgi/ER/endosomes as the core function of the cluster.","confidence":"Medium","size":11,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0006893","count":2},{"id":"GO:0007030","count":2}]},{"hash":"1865295975722764913","title":"ER stress\u2013lipid metabolism\u2013APP regulation","description":"This cluster centers on endoplasmic reticulum stress responses and lipid metabolism pathways (sphingolipid and phosphatidylserine metabolism, myelination) with a specific link to amyloid precursor protein biosynthesis regulation. There are some additional terms related to xenobiotic response and redox/iron turnover, but the strongest cohesive signals point to ER stress-lipid-APP\u2013related functions. Confidence: Medium","confidence":"","size":11,"edges":21,"triangles":17,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042493","count":2},{"id":"GO:0033212","count":1},{"id":"GO:0042167","count":1},{"id":"GO:0042984","count":1}]},{"hash":"1657871749318849804","title":"Cell cycle progression and kinetochore localization","description":"Top terms cluster around DNA replication and mitotic control: DNA replication, meiotic cell cycle, G1/S and G2/M transitions, and protein localization to the kinetochore, indicating a cohesive group of proteins involved in chromosome replication and mitotic progression. Several other terms (response to cocaine, Schwann cell development, excitatory postsynaptic potential, Wnt signaling, and cardiac muscle regulation) appear but are less central and may reflect broader signaling or annotation noise. Overall, the core theme is cell cycle regulation and chromosome segregation.","confidence":"High","size":11,"edges":12,"triangles":5,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0051321","count":8},{"id":"GO:0000082","count":8},{"id":"GO:0034501","count":8},{"id":"GO:0042220","count":8}]},{"hash":"1087667009940421984","title":"Central Metabolism and Energy Regulation","description":"The cluster shows strong representation of carbon and sulfur metabolism (serine catabolism, transsulfuration, gluconeogenesis, carbohydrate metabolism, fatty acid biosynthesis, H2S biosynthesis) and energy-related responses such as glucose starvation; magnesium transport supports metal-dependent enzyme activity. An outlier term on mitotic regulation exists, but overall the terms converge on metabolism and energy homeostasis.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0006565","count":9},{"id":"GO:0051289","count":9},{"id":"GO:1903830","count":9},{"id":"GO:0019346","count":9},{"id":"GO:0045722","count":9}]},{"hash":"1315792457459785733","title":"Cell cycle and telomere regulation","description":"The cluster centers on mitotic cell cycle and telomere maintenance/capping, with terms for positive regulation of telomere maintenance via telomerase and negative regulation of CDK activity, suggesting a core theme of cell cycle control linked to telomere integrity. While additional terms (mRNA processing, differentiation, migration, defense responses) appear, they seem secondary to the dominant cell cycle\u2013telomere signal.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0045736","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0016477","count":3}]},{"hash":"1122167657028903675","title":"Viral entry, replication, and latency","description":"The Top Terms include symbiont entry into host, uncoating of virus, host-mediated activation of viral genome replication, establishment of integrated proviral latency, and viral release from host cell, all pointing to different stages of a viral infection cycle within host cells. A couple of general terms (protein folding, multicellular development) are present but do not outweigh the clear viral lifecycle signal, so the name reflects virus-host infection processes.","confidence":"High","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0030260","count":2},{"id":"GO:0071492","count":2},{"id":"GO:0019061","count":2}]},{"hash":"143944250397669429","title":"RNA Splicing and Processing","description":"Most of the top GO terms cluster around RNA processing and mRNA splicing (spliceosome-mediated splicing, splice-site recognition, alternative splicing, and general RNA processing). A smaller subset includes translation initiation/reinitiation terms, which may reflect dual-function proteins or annotation noise. Overall, the shared theme appears to be RNA maturation and post-transcriptional regulation.","confidence":"Medium","size":11,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0042766","count":2},{"id":"GO:0016584","count":2}]},{"hash":"1802361804670314817","title":"Spliceosome-driven RNA processing and translation initiation","description":"This cluster centers on RNA processing and splicing machinery (alternative mRNA splicing regulation via the spliceosome, splice-site recognition, small-subunit processome assembly) and also includes factors involved in forming the translation preinitiation complex and post-transcriptional regulation (miRNA-mediated silencing). The shared theme is RNA maturation and preparation for translation, linking splicing/processing with initiation of translation.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0006376","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0000380","count":1},{"id":"GO:1905663","count":1}]},{"hash":"2234799403310614797","title":"Transcription Regulation and Phosphorylation","description":"Top GO terms indicate transcriptional control (DNA-templated transcription, RNA Pol II CTD phosphorylation) and regulation of phosphorylation/kinase activity, alongside developmental processes (mesoderm formation, cerebellar cortex development, neural patterning). Even without edges, these terms consistently point to a theme where gene expression is modulated by phosphorylation in developmental contexts, supporting this label.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":2},{"id":"GO:0001707","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1567666686586649911","title":"Skeletal muscle development and sarcomere assembly","description":"Dominant GO terms point to skeletal muscle fiber development, sarcomere organization, and actin filament bundle assembly, with calcium-responsive signaling, suggesting a core role in muscle structure and contraction. Some non-muscle terms (xenobiotic/amine responses and substantia nigra development) may reflect broader signaling connections or annotation noise, but the muscle-centric terms provide a coherent theme for the cluster.","confidence":"Medium","size":11,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0014075","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0001300","count":2}]},{"hash":"1050347327180259399","title":"Chromatin remodeling and transcriptional regulation","description":"This cluster is dominated by GO terms tied to chromatin state and transcription control, including histone modification (H2B ubiquitination), nucleosome density and mobilization, nucleosome remodeling, and positive regulation of transcription by RNA polymerase II, plus related transcriptional processes (even RNA Pol I rRNA transcription). Together these terms point to a set of proteins functioning to regulate gene expression via chromatin dynamics and chromatin-associated transcription regulation.","confidence":"High","size":11,"edges":40,"triangles":70,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":2},{"id":"GO:1900050","count":2},{"id":"GO:0060303","count":2},{"id":"GO:0071894","count":2},{"id":"GO:1902661","count":2}]},{"hash":"137778783592557707","title":"Actin remodeling and cell division regulation","description":"This cluster centers on cytoskeletal dynamics and cell division. It features Arp2/3-mediated actin nucleation and regulation of GTPase activity, both core to actin remodeling, along with mitotic spindle assembly indicating cell division. The presence of growth and epithelial proliferation terms suggests broader involvement in cell-cycle control. Taken together, the proteins seem to participate in coordinating cytoskeletal remodeling with cellular proliferation.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0034314","count":2},{"id":"GO:0060770","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0060733","count":2}]},{"hash":"1046149119826581608","title":"Embryonic development and organogenesis","description":"The cluster shows multiple developmental and morphogenesis terms, including roof of mouth development, pancreatic cell development, trophoblast differentiation, EMT in heart cushion formation, cartilage morphogenesis, endocrine system development, and left-right patterning, suggesting a cohesive role in embryogenesis and organ formation. The presence of a single non-developmental term (ADP-L-glycero-beta-D-manno-heptose biosynthetic process) appears incidental to the dominant developmental theme. ","confidence":"High","size":11,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0097171","count":2},{"id":"GO:0060021","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0060806","count":2},{"id":"GO:0003323","count":2}]},{"hash":"1361719058155802075","title":"Interferon-Driven Antiviral Innate Immunity","description":"The strongest signals in this cluster are innate antiviral responses: cellular response to type I interferon, innate immune response, and cellular response to exogenous dsRNA, which together point to an interferon-driven antiviral state. Additional terms like unfolded protein response and cell-cycle-related processes appear but do not define the main theme. Therefore, the label reflects the core function of interferon-mediated antiviral innate immunity.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071357","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0050689","count":3},{"id":"GO:0071360","count":3},{"id":"GO:0008277","count":3}]},{"hash":"1963729198567713402","title":"Diverse Biosynthetic Enzymes","description":"Based on the GO terms, the proteins are linked to many biosynthetic processes (sterol, SAM, anthocyanin-containing compounds, UDP-rhamnose, O antigen, galactose, poly-hydroxybutyrate, ubiquinone, heptose) with only one direct interaction. This pattern points to a collection of enzymes involved in different biosynthetic pathways rather than a single shared function, so a broad \"diverse biosynthesis\" label best captures the cluster.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016126","count":2},{"id":"GO:0006556","count":1},{"id":"GO:0009718","count":1},{"id":"GO:0010253","count":1},{"id":"GO:0009243","count":1}]},{"hash":"102453803856979336","title":"Hormone signaling and genome maintenance","description":"The cluster centers on peptide hormone-responsive signaling (including insulin-related pathways and angiogenesis) and also includes DNA repair and telomere regulation terms, suggesting a link between hormonal signaling and genome integrity/stress responses.","confidence":"Medium","size":11,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071375","count":2},{"id":"GO:0046856","count":2},{"id":"GO:0006915","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0006281","count":2}]},{"hash":"2094378065680380685","title":"Neuronal calcium signaling and synaptic plasticity","description":"The cluster centers on calcium dynamics and synaptic strengthening, with terms like long-term potentiation and regulation of calcium release from the sarcoplasmic reticulum via ryanodine receptors (including negative regulation). Additional terms about mitochondrial membrane potential and Golgi organization fit calcium signaling and trafficking roles that support neuronal activity. While a couple terms are obsolete or less specific, the dominant theme is calcium signaling in neurons and synaptic plasticity.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0046232","count":2},{"id":"GO:0060291","count":2},{"id":"GO:1903358","count":2},{"id":"GO:0097274","count":2}]},{"hash":"580704521474571575","title":"ER Stress and Redox Homeostasis","description":"The cluster\u2019s top GO terms cluster around transcriptional regulation and oxidative stress management, including DNA-templated transcription, cellular oxidant detoxification, ER stress response, and redox homeostasis. This suggests a common theme of coordinating transcription with cellular defense against oxidative and protein-folding stress, even though some terms (e.g., mitochondrial fission, endocytosis) are less central to the apparent theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0098869","count":2},{"id":"GO:0034976","count":2},{"id":"GO:0045454","count":2},{"id":"GO:1903206","count":2}]},{"hash":"1844487208435007261","title":"Membrane Transporters for Xenobiotics and Nutrients","description":"The top GO terms point to transmembrane transport of diverse substrates\u2014xenobiotics, sialic acid, urate, potassium ions, and related compounds\u2014suggesting these proteins function as membrane transporters. A few terms relate to metabolism or stress response, but transport is the dominant theme.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042891","count":2},{"id":"GO:0006004","count":2},{"id":"GO:1904728","count":2},{"id":"GO:0015739","count":2},{"id":"GO:0042908","count":2}]},{"hash":"572470684568642117","title":"Brain, retina, and gonad development","description":"The top GO terms are largely developmental, with multiple entries for brain/forebrain and retina development, plus a multicellular organism development and male gonad development, indicating a theme of developmental programs across tissues, especially neural ones. Auxiliary terms like actin depolymerization and RNA methylation likely reflect broader regulatory processes accompanying development.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016575","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0007420","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0030900","count":3}]},{"hash":"108014705803047500","title":"Unknown","description":"The GO terms are spread across many unrelated processes (cytoskeletal regulation, neuronal migration, dendritic spine modification, various signaling pathways, vascular permeability, and Golgi maintenance). There\u2019s no single cohesive function or pathway tying the proteins together, and there are no edges to suggest a defined module, so a specific, confident label isn\u2019t evident.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051497","count":1},{"id":"GO:0035024","count":1},{"id":"GO:0043114","count":1},{"id":"GO:0021816","count":1},{"id":"GO:0098886","count":1}]},{"hash":"1582878467564485292","title":"Pollen Tube Growth Guidance Signaling","description":"The GO terms point to pollen tube growth regulation and guidance in plants, with intracellular signal transduction linking these signals. This suggests a coherent module of signaling components that direct pollen tube growth toward the ovule, a central step in plant fertilization. The proteins likely function as receptors or signaling mediators in this pathway.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080092","count":1},{"id":"GO:0035556","count":1},{"id":"GO:0010183","count":1}]},{"hash":"394408712088523910","title":"DNA Repair and Chromatin Maintenance","description":"This cluster is dominated by GO terms related to genome stability: double-strand break repair via homologous recombination, maintenance of mitotic sister chromatid cohesion, and rDNA chromatin condensation, which together point to DNA repair and chromatin dynamics. Some terms (lipid metabolism and transport) appear as outliers, likely annotation noise, but the core signals support a DNA damage response/chromatin maintenance theme.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0072089","count":3},{"id":"GO:0070550","count":3},{"id":"GO:0000733","count":3},{"id":"GO:0042760","count":3},{"id":"GO:0031460","count":3}]},{"hash":"1592598849734918718","title":"Transmembrane transport of diverse substrates","description":"The top GO terms indicate transport across membranes for a range of substrates, including ions (potassium, phosphate, nitrate), sugars (fucose, arabinose, galactose), folate, and xenobiotics, as well as related metabolic processes. This cohesive theme points to membrane transporter activity handling diverse substrates.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0006855","count":2}]},{"hash":"1425413515854934842","title":"Secretory vesicle trafficking and GABAergic transmission","description":"This cluster centers on vesicle transport from the Golgi to the plasma membrane, COPII budding, and synaptic vesicle exocytosis, with several GO terms pointing to GABAergic signaling. The presence of filopodium assembly and small GTPase\u2013mediated signaling suggests coordinated cytoskeletal dynamics underpinning vesicle trafficking and synaptic release.","confidence":"High","size":11,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006893","count":3},{"id":"GO:0045792","count":3},{"id":"GO:0031384","count":3},{"id":"GO:1903206","count":3},{"id":"GO:1900026","count":3}]},{"hash":"859992183375102583","title":"Embryonic Development and Organ Morphogenesis","description":"These GO terms cluster around developmental and morphogenetic processes across multiple tissues (placenta, pancreas, heart, cartilage) and stages (EMT, left-right patterning, organ formation). The common theme is embryonic development and organ morphogenesis, rather than a single specific function, so this label captures the shared theme.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060806","count":2},{"id":"GO:0003323","count":2},{"id":"GO:0060707","count":2},{"id":"GO:0003198","count":2},{"id":"GO:0060536","count":2}]},{"hash":"376926761282652231","title":"Calcium-regulated macrophage inflammatory signaling","description":"Reasoning: The GO terms converge on calcium signaling (ER Ca2+ homeostasis, Ca2+ transport, regulation of calcium-mediated signaling) and immune activation (TNF and IL-6 production, chemokine production, macrophage foam cell differentiation, respiratory burst, T cell proliferation), with a note on protein palmitoylation. Together these suggest a cohesive theme of calcium-dependent inflammatory signaling in macrophages that can modulate broader immune responses.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032760","count":2},{"id":"GO:0032469","count":1},{"id":"GO:0006816","count":1},{"id":"GO:2000778","count":1},{"id":"GO:0010742","count":1}]},{"hash":"1295091476696270465","title":"Autophagy Regulation and Cellular Stress Response","description":"The GO terms converge on autophagy and its regulation (including mitophagy), with supporting signals from cellular stress responses (xenobiotic response, cobalt ion exposure, respiratory burst) and metabolic regulation (dephosphorylation, glycolytic modulation). While a few terms touch on development or apoptosis, the strongest coherent theme is autophagy/mitophagy control within a stress-response context, suggesting a cluster focused on autophagy regulation under stress.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045820","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0006914","count":1},{"id":"GO:0060576","count":1},{"id":"GO:0009410","count":1}]},{"hash":"424424097542358987","title":"Notch signaling and receptor proteolysis in development","description":"The terms strongly point to Notch pathway activity and its activation mechanism via receptor processing and proteolysis (Notch signaling pathway, Notch receptor processing, membrane protein ectodomain and intracellular domain proteolysis). Developmental terms (pharynx development, in utero embryonic development, neuroepithelial cell differentiation) suggest a broader embryonic developmental context. The presence of cilium assembly and smoothened signaling further hints at a developmental signaling network that can intersect with Notch. Overall, the cluster seems best described as Notch signaling and receptor proteolysis in development.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007219","count":1},{"id":"GO:0034205","count":1},{"id":"GO:0060465","count":1},{"id":"GO:0007220","count":1},{"id":"GO:0006509","count":1}]},{"hash":"1793190405997142656","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019546","count":1},{"id":"GO:0044210","count":1},{"id":"GO:0006526","count":1},{"id":"GO:0009088","count":1},{"id":"GO:0035975","count":1}]},{"hash":"2128404310254899505","title":"Carbohydrate metabolism and osmotic stress response","description":"This cluster is enriched for carbohydrate-related processes (glucose, sucrose, starch biosynthesis) and osmotic stress responses (response to water deprivation, response to mannitol), suggesting a theme around sugar metabolism and osmotic adaptation. Some terms (e.g., GPI anchor biosynthesis) are tangential but fit within cell-surface glycosylation contexts linked to carbohydrate biology.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006006","count":2},{"id":"GO:0006506","count":1},{"id":"GO:0007631","count":1},{"id":"GO:0010125","count":1},{"id":"GO:0005985","count":1}]},{"hash":"2212669194248990861","title":"Phosphatidylinositol and inositol biosynthesis during stress signaling","description":"This cluster centers on phosphatidylinositol and inositol biosynthetic processes (PI and inositol biosynthesis) and related signaling, with links to stress signaling pathways such as ABA response and osmotic stress. The combination suggests a cohesive role in lipid-based signaling under stress, though a few terms are less directly connected, so confidence is Medium.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903204","count":1},{"id":"GO:0071447","count":1},{"id":"GO:1902083","count":1},{"id":"GO:0042538","count":1},{"id":"GO:0046855","count":1}]},{"hash":"1852028520556647104","title":"Vacuolar amino acid and ion transport","description":"Most top GO terms point to transmembrane transport into or out of the vacuole for various amino acids (lysine, arginine, tyrosine, histidine, proline) and ions (lithium, potassium). This pattern suggests a cluster of vacuolar transporters handling amino acid and ion flux, reflecting a shared function in vacuolar transport and ion/nutrient homeostasis. The lack of edges does not negate this interpretation, as functional similarity and localization can prevail without direct interactions in this dataset.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0090517","count":2},{"id":"GO:1990818","count":2},{"id":"GO:0090518","count":2},{"id":"GO:0090452","count":2}]},{"hash":"412468111662566789","title":"Unknown","description":"The top GO terms span transcription initiation, preinitiation complex assembly, nuclear membrane reassembly, autophagosome and ubiquitin-dependent degradation processes, Golgi organization, and even sporulation and chromatid biorientation. The terms cover a wide range of distinct cellular roles with no clear single function tying the cluster together, so a cohesive, specific label is not supported.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006352","count":1},{"id":"GO:2000648","count":1},{"id":"GO:0051123","count":1},{"id":"GO:0007030","count":1},{"id":"GO:0000045","count":1}]},{"hash":"1964163018006513407","title":"DNA recombination and immunoglobulin diversification","description":"The proteins in this cluster are enriched for processes involving DNA recombination and genome stability (meiotic gene conversion, gene conversion at mating-type loci, mismatch repair, maintenance of DNA repeats) as well as immunoglobulin diversification mechanisms (somatic hypermutation and isotype switching to IgA). There is also a DNA damage response component (p53-mediated apoptotic signaling), tying these processes to genome integrity and controlled variation. This combination suggests a theme of genetic variation generation alongside genome maintenance.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045910","count":2},{"id":"GO:0007534","count":2},{"id":"GO:0010777","count":2},{"id":"GO:0043570","count":2},{"id":"GO:0006311","count":2}]},{"hash":"1564822612724032339","title":"Amino acid metabolism: catabolism and biosynthesis","description":"The cluster is enriched for GO terms covering several amino acid catabolic (alanine, kynurenine) and biosynthetic (serine, aspartate) processes, plus related lysine pathways, suggesting a common theme of amino acid metabolism; the presence of Notch signaling appears to be an outlier rather than the defining function. ","confidence":"Medium","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033512","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0007219","count":4},{"id":"GO:0097053","count":4},{"id":"GO:0006564","count":4}]},{"hash":"453202612494119999","title":"Ribosome Biogenesis and Translation Machinery","description":"This cluster is characterized by strong enrichment for translation and cytoplasmic translation, along with ribosome biogenesis, ribosomal subunit export from the nucleus, and ribosome assembly, pointing to components of the protein-synthesis machinery. The presence of antibiotic response and amino acid starvation regulation terms suggests links to growth control and stress-responsive regulation of ribosome function.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0002181","count":5},{"id":"GO:0046677","count":4},{"id":"GO:0090529","count":3},{"id":"GO:1901001","count":3}]},{"hash":"389128635942494199","title":"Unknown","description":"The GO terms are highly diverse, covering multiple biosynthetic and catabolic pathways, transcription, and development, with no clear shared function or pathway linking the proteins (0 edges; several terms are obsolete). This lack of a coherent theme means a meaningful, specific cluster label cannot be assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042619","count":2},{"id":"GO:0030324","count":2},{"id":"GO:1902128","count":1},{"id":"GO:0009718","count":1}]},{"hash":"1918034413406083500","title":"Diverse metabolite biosynthesis","description":"Top GO terms cluster around biosynthesis of diverse metabolites, including alkaloids, steroids, retinoids, sphingolipids, very long-chain fatty acids, phylloquinone, and antibiotics, with minor involvement in transcription regulation and oxidation\u2013reduction. This pattern suggests the proteins participate in multiple biosynthetic pathways rather than a single specific function, supporting a label of broad metabolite biosynthesis.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0006355","count":5},{"id":"GO:0009710","count":5},{"id":"GO:0006704","count":5},{"id":"GO:0002138","count":5}]},{"hash":"2179056797266274405","title":"Bacterial cell division and genome segregation","description":"The top GO terms point to core processes of bacterial division and genome handling, notably chromosome segregation, cell cycle, and plasmid partitioning. Other terms appear more as general biosynthetic processes, but the strongest signals are about genome maintenance during cell division, suggesting this as the cluster\u2019s representative function.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007059","count":1},{"id":"GO:0002098","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0055114","count":1}]},{"hash":"446467777949341750","title":"Gene expression regulation and stress response","description":"Based on the GO terms, the proteins touch on regulation of transcription/coactivator activity, mRNA stability, cell-cycle regulation, and responses to cellular signals and xenobiotics. Although several terms are obsolete and there are no reported edges, the common theme appears to be regulation of gene expression and cellular stress/detox signaling, suggesting a regulatory/stress-response cluster.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000327","count":1},{"id":"GO:0080111","count":1},{"id":"GO:1900087","count":1},{"id":"GO:0043488","count":1},{"id":"GO:0071320","count":1}]},{"hash":"1670022735871436435","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0010043","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0071266","count":1}]},{"hash":"308582683552225591","title":"Steroid and Retinoid Metabolism","description":"Based on the top GO terms, the cluster shows enrichment for retinal and retinol metabolism as well as androgen and testosterone biosynthesis, suggesting a shared theme around retinoid and steroid metabolism. Some other terms (e.g., mitochondrial translation, embryonic development) are less cohesive with this theme and may reflect broader cellular processes or noise. Overall, the strongest signal points to metabolism of retinoids and steroids, hence this label.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042574","count":2},{"id":"GO:0008209","count":2},{"id":"GO:0042572","count":2},{"id":"GO:0061370","count":2}]},{"hash":"671401905688156077","title":"Kinase-Regulated Signaling and Cytoskeletal Dynamics","description":"The cluster is dominated by GO terms related to regulation of phosphorylation (peptidyl-tyrosine, serine/threonine, autophosphorylation), regulation of GTPase activity, and Arp2/3-mediated actin nucleation, pointing to signaling pathways that control cytoskeletal dynamics and cell cycle processes; supporting terms include hypoxia response and RNA processing, suggesting broader regulatory roles but the central theme remains signaling-linked cytoskeletal regulation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071456","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0050731","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1493788329464876826","title":"Growth signaling and cytoskeletal dynamics","description":"The terms cluster around growth and signaling (TGF-\u03b2 response, nutrient response, multicellular growth, epithelial proliferation), cell division (mitotic spindle assembly), and cytoskeletal remodeling (Arp2/3-mediated actin nucleation), with a stress/nutrient sensing angle (GCN2 signaling). Together they point to coordination between growth signals, cytoskeletal dynamics, and cell cycle processes, making this an integrated growth-cytoskeleton cluster. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0071560","count":5},{"id":"GO:0007584","count":4},{"id":"GO:0034314","count":3},{"id":"GO:0060770","count":3},{"id":"GO:0035264","count":3}]},{"hash":"900164068153694622","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035278","count":3},{"id":"GO:0010610","count":3},{"id":"GO:0033129","count":3},{"id":"GO:0032435","count":3},{"id":"GO:0070059","count":3}]},{"hash":"506128196401088421","title":"Translation and ribosome biogenesis","description":"Based on the GO terms, the cluster is dominated by translation and ribosome biogenesis (translation, ribosome biogenesis, ribosomal small subunit biogenesis; including mitochondrial translation termination), with additional chromatin/nuclear organization terms appearing but secondary. This suggests a primary theme around protein synthesis machinery, with some linkage to chromatin-related processes. ","confidence":"High","size":10,"edges":37,"triangles":71,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0070126","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0006334","count":2}]},{"hash":"960210119569270630","title":"Developmental morphogenesis and differentiation","description":"This cluster is driven by multiple GO terms tied to developmental processes and tissue formation\u2014osteoblast development/proliferation, ring gland development, eyelid formation, outflow tract morphogenesis, and regulation of cell fate and differentiation. Calcium signaling and growth factor/TGF-beta related terms further suggest signaling that guides development. Taken together, the proteins likely participate in broad developmental programs rather than a single pathway.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0031063","count":3},{"id":"GO:0071277","count":3},{"id":"GO:0045669","count":3},{"id":"GO:0035271","count":3},{"id":"GO:0051124","count":3}]},{"hash":"1844321785104972849","title":"Epithelial Differentiation and Proliferation Signaling","description":"The GO terms point to epithelial differentiation (keratinocyte and lung epithelial differentiation) and key proliferation/signaling pathways (Wnt and Hippo) alongside processes tied to the cell cycle (DNA replication, cytokinesis) and transcription regulation. This suggests a cohesive theme of how epithelial cells differentiate and regulate proliferation via conserved signaling networks, with apoptosis as a balancing process. ","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045944","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0060044","count":3}]},{"hash":"1150307167722064121","title":"Cardiac and neural development","description":"Based on the top GO terms, the cluster centers on development and signaling in muscle/heart and neural systems, with terms for heart development, myoblast fusion, cardiac proliferation regulation, axonogenesis, and long-term synaptic potentiation. While there are also cell cycle and signaling terms (mitotic processes, T cell signaling, phosphorylation regulation), the cohesive theme is neuro-muscular development and associated signaling pathways.","confidence":"Medium","size":10,"edges":20,"triangles":16,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060291","count":9},{"id":"GO:0014850","count":9},{"id":"GO:0007507","count":9},{"id":"GO:0050852","count":8},{"id":"GO:0000086","count":8}]},{"hash":"24388226695860530","title":"DNA replication and cell cycle regulation","description":"The cluster is enriched for DNA replication (GO:0006260) and DNA-templated transcription (GO:0006351), along with cell-cycle related terms such as G1/S transition (GO:0000082), meiotic cell cycle (GO:0051321), and kinetochore localization (GO:0034501), pointing to proteins involved in DNA replication and cell-cycle control. There are additional terms like innate immune response and blastocyst development, but they are less represented and likely reflect multifunctionality or annotation spillover. Overall, the dominant theme is cell cycle and DNA replication machinery.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0045087","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0001824","count":3},{"id":"GO:0006915","count":3}]},{"hash":"81007521559471048","title":"Angiogenesis and Growth Factor Signaling","description":"The top GO term is angiogenesis, supported by multiple growth-related pathways (PI3K/AKT, JNK, growth hormone receptor signaling) and vascular-associated terms like smooth muscle contraction, suggesting a signaling network driving vascular development and growth; immune signaling (Fc receptor) and axon regeneration references reflect broader interconnected signaling in this cluster.","confidence":"Medium","size":10,"edges":10,"triangles":3,"max_degree":5,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0001525","count":6},{"id":"GO:0006939","count":5},{"id":"GO:0048680","count":5},{"id":"GO:0038093","count":4},{"id":"GO:1990139","count":4}]},{"hash":"2000617624410839145","title":"ER stress and RNA processing network","description":"This cluster centers on protein quality control in the ER (protein folding, unfolded protein response, ERAD-related pathway) alongside nuclear RNA processing/transport terms (ncRNA silencing, tRNA import, regulation of nucleocytoplasmic transport). The combination suggests a broader proteostasis and RNA metabolism network spanning ER and nuclear compartments, rather than a single narrow function.","confidence":"Medium","size":10,"edges":29,"triangles":32,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0034975","count":3},{"id":"GO:0006452","count":3},{"id":"GO:0006986","count":3}]},{"hash":"543072415108098724","title":"RNA Splicing and Translation Regulation","description":"This cluster centers on RNA processing and ribosome biogenesis, with GO terms for mRNA splicing, spliceosome assembly, and preinitiation complex formation, plus small-subunit processome assembly. It also includes post-transcriptional regulatory links to translation, such as miRNA-mediated translational repression and mRNA stability regulation during stress. Together, these terms point to a module of proteins involved in RNA processing and control of translation, representing a coherent RNA-centric post-transcriptional regulation cluster.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006376","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0000380","count":2},{"id":"GO:1905663","count":2},{"id":"GO:1902625","count":2}]},{"hash":"1696801836499439157","title":"RNA modification and methylation","description":"This cluster\u2019s top GO terms are strongly centered on RNA modification, including RNA (guanine-N7)-methylation, rRNA methylation/modification, and tRNA wobble uridine modification, suggesting a core function in RNA chemical modification. A few other terms appear (protein methylation, metabolism), but the RNA-related signals are the dominant theme.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":3},{"id":"GO:0060041","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0031167","count":2},{"id":"GO:0010189","count":2}]},{"hash":"126008600686515952","title":"Developmental signaling and transcription regulation","description":"The GO terms point to multiple signaling pathways (Wnt, ephrin, JNK) that govern development and cell communication, paired with transcriptional control and nervous system development. The presence of stem cell maintenance and cell cycle regulation suggests a cluster of proteins that modulate developmental signals and downstream transcription rather than a single pathway, justifying a label focused on developmental signaling and transcriptional regulation.","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":3},{"id":"GO:1902459","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0060044","count":2}]},{"hash":"395595661368725837","title":"Angiogenesis and endothelial cell polarity","description":"Based on the top GO terms, the cluster is enriched for negative regulation of sprouting angiogenesis, endothelial tube lumen extension, and establishment/maintenance of epithelial cell apical/basal polarity, suggesting a cohesive theme around vascular development and cell polarity. While other terms (DNA replication, virion attachment, xenobiotic response) are broader, the strongest signal centers on endothelial morphogenesis and polarity.","confidence":"Medium","size":10,"edges":11,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0090051","count":2},{"id":"GO:0097498","count":2},{"id":"GO:0019062","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0051259","count":2}]},{"hash":"761039514751976831","title":"Pain and Temperature Sensation","description":"The strongest shared theme among the terms is sensing physical stimuli: detection of mechanical stimulus involved in pain, thermoception, and response to cold, which together point to sensory and temperature-related perception pathways. Other terms (vasopressin secretion, epithelial maturation, telomere capping, mRNA stability, NOD2 signaling) appear less connected and likely reflect background noise. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":4},{"id":"GO:0060743","count":3},{"id":"GO:0071446","count":3},{"id":"GO:0030103","count":3},{"id":"GO:0050966","count":3}]},{"hash":"1034777815005994387","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060027","count":1},{"id":"GO:0061351","count":1},{"id":"GO:0007608","count":1},{"id":"GO:0009566","count":1},{"id":"GO:1905515","count":1}]},{"hash":"1528210351560986175","title":"Developmental Epigenetics","description":"The cluster centers on epigenetic regulation events (histone modifications, DNA methylation) that broadly influence developmental programs across diverse tissues, including heart, cerebellum, gliogenesis, immune differentiation, and uterine development; while some terms are obsolete, the shared theme is epigenetic control of development.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003289","count":1},{"id":"GO:0080182","count":1},{"id":"GO:0033082","count":1},{"id":"GO:0014013","count":1},{"id":"GO:0021695","count":1}]},{"hash":"158843628741268416","title":"Ubiquitin-regulated transcription and NF-\u03baB signaling","description":"The top terms emphasize transcriptional regulation by RNA Pol II, histone turnover, and protein ubiquitination, including autoubiquitination. They are complemented by indications of TNF-mediated signaling and I\u03baB phosphorylation, pointing to NF-\u03baB\u2013related regulatory processes. The cluster likely represents nuclear regulators that integrate ubiquitin signaling with control of gene expression, cell cycle, and apoptotic decisions in the context of TNF/NF-\u03baB pathways.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0051865","count":4},{"id":"GO:0071157","count":4},{"id":"GO:0043066","count":4},{"id":"GO:0036205","count":3}]},{"hash":"1289061980167649667","title":"Unknown","description":"The top GO terms are very diverse, spanning tissue-specific cerebellar layer structural organization (Purkinje/granular layers) and broad intracellular processes (TNF and Wnt signaling, DNA replication initiation, mitotic checkpoint, transcription regulation, chromatin modification). There isn\u2019t a single cohesive biological theme tying these functions together, so a concise, representative label cannot be assigned beyond Unknown.","confidence":"","size":10,"edges":25,"triangles":23,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0033209","count":3},{"id":"GO:0010950","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0021693","count":3},{"id":"GO:0021685","count":3}]},{"hash":"209481587024779106","title":"CDK and G1/S Cell Cycle Regulation","description":"The GO terms cluster around control points of the cell cycle, especially CDK activity and the G1/S transition, with regulation via phosphorylation/dephosphorylation and links to protein turnover and stress responses (e.g., proteasome regulation and mitophagy). While translation and viral process terms are present, the dominant theme is regulation of cell-cycle progression and associated post-translational control.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0016032","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0006281","count":1}]},{"hash":"2056870086257249007","title":"Plant chromatin regulation and hormone responses","description":"This cluster centers on chromatin-related GO terms (nucleosome assembly, histone deubiquitination) and plant developmental/hormone response processes (leaf formation, jasmonic acid, ethylene, abscisic acid, chlorophyll biosynthesis regulation), suggesting a theme of gene regulation in plant development modulated by hormonal signals. Telomere/RNA localization terms and D-loop disassembly provide some epigenetic/genome maintenance context, but the dominant signal is chromatin organization linked to hormone-responsive development.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010338","count":1},{"id":"GO:0035522","count":1},{"id":"GO:1904911","count":1},{"id":"GO:1905778","count":1},{"id":"GO:0061820","count":1}]},{"hash":"790957671264038992","title":"ER protein folding and quality control","description":"This cluster centers on endoplasmic reticulum\u2013related protein handling: folding and maturation in the ER, ER-associated degradation via the ubiquitin-proteasome system, and translation upregulation in response to ER stress, indicating ER stress response and quality control mechanisms.","confidence":"High","size":10,"edges":12,"triangles":3,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0009408","count":3},{"id":"GO:0071630","count":3},{"id":"GO:0036494","count":3},{"id":"GO:0070389","count":3}]},{"hash":"2105053553877049489","title":"Ubiquitin-Mediated TNF/NF-kB Signaling","description":"The top terms are dominated by ubiquitination processes (protein ubiquitination, autoubiquitination, K6-linked ubiquitination) and TNF-mediated signaling with I-kappaB phosphorylation, indicating a cohesive theme of ubiquitin-regulated inflammatory signaling and NF-kB activation; a few terms relate to histone turnover and vitamin D response, likely serving as peripheral associations.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0070535","count":4},{"id":"GO:0016567","count":3},{"id":"GO:0033280","count":3},{"id":"GO:0036205","count":3}]},{"hash":"1875499848154673481","title":"T cell activation and cytokine production","description":"This cluster is driven by immune-related GO terms: T cell cytokine production, IL-2 and IL-3 production, and dendritic cell antigen processing/presentation, indicating adaptive immune activation. Additional terms like regulation of Rho signaling and respiratory burst align with cytoskeletal changes and effector functions in activated immune cells. While there are some transport-related terms, the dominant signal points to a module coordinating T cell\u2013mediated cytokine output and antigen presentation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0035176","count":2},{"id":"GO:0002606","count":1},{"id":"GO:0002369","count":1},{"id":"GO:0032623","count":1}]},{"hash":"837557768447974751","title":"Unknown","description":"Top GO terms span energy metabolism, cytoskeleton remodeling, chromatin assembly, ubiquitin regulation, stress response, and organelle dynamics, with no clear single shared function tying them together. Because of this lack of a coherent theme, a specific label cannot be assigned beyond Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046034","count":1},{"id":"GO:0051013","count":1},{"id":"GO:0061641","count":1},{"id":"GO:2000158","count":1},{"id":"GO:2001171","count":1}]},{"hash":"1387071003791745008","title":"Embryonic development and tissue morphogenesis","description":"These terms cluster around broad embryonic development and tissue formation across multiple lineages (placental development, pancreatic cell development, trophoblast differentiation, EMT in heart formation, cartilage morphogenesis and development, endocrine system development, left-right patterning, neural crest migration, forebrain proliferation). The common theme is morphogenesis and differentiation during embryogenesis rather than a single pathway or cell type.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060806","count":3},{"id":"GO:0003323","count":3},{"id":"GO:0060707","count":3},{"id":"GO:0003198","count":3},{"id":"GO:0060536","count":3}]},{"hash":"2087120919549566968","title":"Proteostasis and Stress Response","description":"This cluster centers on protein quality control and stress-induced remodeling: proteasome regulatory particle assembly, positive regulation of ubiquitin-specific protease activity, and components linked to misfolded protein handling (stress granule disassembly, inclusion body assembly). It also includes energy-related GO terms (ATP metabolism, ATP biosynthetic process) indicating the energy demand of proteostasis, plus microtubule severing and chromatin assembly as broader cellular remodeling under stress. Overall, the common theme is a proteostasis/stress-response module.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070682","count":2},{"id":"GO:0046034","count":1},{"id":"GO:0051013","count":1},{"id":"GO:0061641","count":1},{"id":"GO:2000158","count":1}]},{"hash":"2030868588214127661","title":"Unknown","description":"The top GO terms are scattered across neural synapse-related activity (PSD-95 clustering, neuromuscular posture, GPCR signaling) and lipid metabolism/secretion (phospholipid metabolism, arachidonate secretion), with many terms being singletons or obsolete. There is no single cohesive function or pathway that ties these proteins together, so a specific, representative label cannot be reliably assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902897","count":1},{"id":"GO:0035372","count":1},{"id":"GO:0050482","count":1},{"id":"GO:0006644","count":1},{"id":"GO:0016042","count":1}]},{"hash":"1127747985377678515","title":"Cell Cycle and Division Proteins","description":"The top GO terms are dominated by cell cycle and cell division (each appears twice), suggesting a core theme around cell cycle-related functions. The other terms show a diverse mix of metabolic processes and enzymatic activities, and the cluster has no reported edges, which implies weak or no functional connectivity. Given the strongest shared signal is cell cycle/division, this label is the most representative, though not strongly reinforced by the rest of the terms. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006212","count":1},{"id":"GO:0042952","count":1},{"id":"GO:0046839","count":1}]},{"hash":"915809135238452137","title":"RNA processing and translation control","description":"The terms cluster around mRNA splicing and spliceosome components, formation of the translation preinitiation complex, miRNA-mediated translational silencing, and regulation of mRNA stability under stress, indicating a coherent theme of post-transcriptional gene expression control via RNA processing and translation regulation.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006376","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0000380","count":1},{"id":"GO:1905663","count":1},{"id":"GO:1902625","count":1}]},{"hash":"410762066720217275","title":"Inflammation and oxidative stress response","description":"The cluster\u2019s GO terms consistently point to inflammatory signaling (acute inflammatory response, response to cytokine) and redox/metabolic lipid signaling (lipoxygenase pathway, lipid hydroperoxide response, cellular oxidant detoxification), with related signaling processes (calcium response; retinoic acid response). This suggests proteins participating in coordinating inflammation alongside oxidative stress responses.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032526","count":1},{"id":"GO:0071277","count":1},{"id":"GO:0002526","count":1},{"id":"GO:0071449","count":1},{"id":"GO:0019372","count":1}]},{"hash":"895295144971634924","title":"ER Stress and Oxidative Stress Response","description":"GO terms show robust signals for unfolded protein response and ER stress (response to unfolded protein, translation initiation upregulation during ER stress, ERAD-related pathway) as well as detoxification and catabolic processes for reactive oxygen species (oxidative stress, cellular oxidant detoxification, hydrogen peroxide catabolism). This suggests a cluster enriched for proteins involved in managing ER stress and oxidative stress. A couple of plant-specific terms appear (cell wall organization, lignin catabolism), which may reflect broader annotations. Net effect: the proteins likely function together in stress-induced protein folding and redox defense.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0030433","count":2}]},{"hash":"2097729587663169322","title":"NF-kB and Growth Factor Signaling Regulators","description":"The proteins here show enrichment in signaling-related terms: I-kappaB phosphorylation (NF-kB pathway), cellular response to PDGF, and regulation of GTPase activity, along with negative regulation of VEGF signaling and angiogenesis. Innate immune response and developmental terms (bone development, mammary gland epithelial cell proliferation) suggest roles in signaling dynamics during immune responses and tissue development. Collectively, this cluster appears to consist of regulators of NF-kB\u2013 and growth factor\u2013driven signaling in immunity, angiogenesis, and development.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007252","count":2},{"id":"GO:0036120","count":2},{"id":"GO:0043547","count":2},{"id":"GO:1900747","count":2},{"id":"GO:0016525","count":2}]},{"hash":"968455600340224624","title":"Unknown","description":"The top GO terms include rRNA maturation, cell-cycle re-entry, liver and renal development, N-glycan processing (to lysosome), rhamnose catabolic process, carbohydrate phosphorylation, TLR2 signaling, and neuron projection development regulation. These reflect diverse, seemingly unrelated processes with no single cohesive function linking the proteins, so a meaningful cluster label cannot be assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0000321","count":1},{"id":"GO:0001889","count":1},{"id":"GO:0046835","count":1},{"id":"GO:0010977","count":1}]},{"hash":"1245399599309765915","title":"Amino acid catabolism and vitamin biosynthesis","description":"The top GO terms cluster around amino acid catabolic processes (valine, serine, homocysteine; D-serine biosynthesis) together with biosynthesis of vitamins/quinones (menaquinone, phylloquinone), plus energy-related pathways (fatty acid beta-oxidation, TCA cycle). This pattern points to a general metabolic cluster focused on amino-acid turnover and cofactor/vitamin biosynthesis rather than a single, narrow function.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0006574","count":3},{"id":"GO:0010124","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0042372","count":3}]},{"hash":"366427368551237187","title":"Unknown","description":"The top GO terms are very heterogeneous, including mitochondrial complex assembly/import, plant development (seedling development, auxin signaling), carbohydrate transport/secretion (sucrose/fructose, nectar), and a ribosome-associated ubiquitin-dependent protein catabolic process, with little overlap. There isn\u2019t a single clear function tying these proteins together, so a coherent label isn\u2019t warranted. ","confidence":"","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0032981","count":1},{"id":"GO:0090351","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0010930","count":1}]},{"hash":"1634168893501338226","title":"Dopaminergic neuron development and vesicle transport","description":"This cluster combines intracellular transport processes (ER\u2013Golgi and Golgi\u2013plasma membrane trafficking, and intracellular protein transport) with neuronal development and synaptic regulation signals (midbrain dopaminergic neuron differentiation; learning; regulation of excitatory postsynaptic potentials). The shared theme is how vesicle trafficking supports maturation and synaptic function in dopaminergic neurons.","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":3},{"id":"GO:0043001","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0090316","count":3},{"id":"GO:0007612","count":3}]},{"hash":"2183153284518153158","title":"Steroid and Retinoid Hormone Metabolism","description":"GO terms cluster around retinal/retinol and androgen/cholesterol metabolism, plus hormone signaling responses, suggesting a shared theme of steroid/retinoid metabolism and related hormone signaling.","confidence":"Medium","size":9,"edges":27,"triangles":37,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042574","count":6},{"id":"GO:0008209","count":6},{"id":"GO:0042572","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0061370","count":6}]},{"hash":"1220958276023959297","title":"Antibiotic and toxin stress response with growth regulation","description":"This cluster centers on responses to antibiotics and toxic substances (and to cycloheximide) and includes translation and cell cycle processes, suggesting a theme where stress response interfaces with protein synthesis and cell growth; it also contains biosynthetic-related terms (antibiotic biosynthetic process, poly-hydroxybutyrate biosynthesis) that fit with metabolic adjustments during stress.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0000083","count":2}]},{"hash":"1877166163745776244","title":"ER Stress and Protein Quality Control","description":"Top terms indicate a core theme of endoplasmic reticulum protein folding, ER-associated degradation/ubiquitin-proteasome quality control, and translation regulation in response to ER stress, with some heat-shock and unrelated developmental terms likely representing noise. This supports a label focusing on ER protein folding and quality control under stress.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0071630","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0030433","count":2}]},{"hash":"77507883944906326","title":"Arp2/3-driven actin polymerization and endocytosis regulation","description":"The cluster is dominated by GO terms tied to actin cytoskeleton remodeling, notably Arp2/3 complex\u2013mediated actin nucleation and actin filament polymerization, along with regulation of endocytosis. Although there are some miscellaneous terms (e.g., deubiquitination, chromatin-related processes), the strongest and most cohesive signal is actin dynamics and membrane trafficking, suggesting a cytoskeletal regulation module.","confidence":"Medium","size":9,"edges":23,"triangles":26,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":5},{"id":"GO:0034314","count":4},{"id":"GO:0030041","count":4},{"id":"GO:0042766","count":4},{"id":"GO:1904623","count":4}]},{"hash":"203748220707678057","title":"Ribosome biogenesis and translation","description":"The top GO terms are dominated by ribosome-related processes: ribosome biogenesis (GO:0042254), ribosomal subunit export from the nucleus (GO:0000055), ribosomal small/large subunit biogenesis (GO:0042274, GO:0009236), and cytoplasmic translation (GO:0015684). This points to a cluster of proteins involved in assembling and functioning of the ribosome and protein synthesis. A few other terms (cobalamin biosynthesis, iron transport, cell septum assembly, stress response regulation) are present but appear peripheral to the central ribosome-related theme, likely reflecting broader or overlapping roles or annotation overlap. Overall, the ribosome biogenesis/translation theme best reconciles the data. ","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0006461","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0090529","count":2},{"id":"GO:1901001","count":2}]},{"hash":"1079106614130758119","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0044208","count":1},{"id":"GO:0014850","count":1},{"id":"GO:0042594","count":1},{"id":"GO:0071257","count":1},{"id":"GO:0071276","count":1}]},{"hash":"821371290425475187","title":"Zinc Ion Homeostasis and Detoxification","description":"The majority of top GO terms point to zinc handling\u2014zinc ion transport, detoxification, and homeostasis\u2014with a cadmium detox note, while unrelated RNA-processing terms are incidental. This suggests the cluster centers on zinc (and broader metal) homeostasis and detox functions.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006432","count":1},{"id":"GO:0070475","count":1},{"id":"GO:0017196","count":1},{"id":"GO:0061090","count":1},{"id":"GO:0006877","count":1}]},{"hash":"89288647985485533","title":"Epigenetic Methylation & Chromatin Remodeling","description":"Dominated by methylation-related processes (DNA, rRNA, protein methylation) and chromatin remodeling, with links to transcriptional regulation. This suggests the cluster contains methyltransferases and chromatin modifiers shaping epigenetic states. The cobalamin-related term hints at methylation chemistry; overall it points to epigenetic regulation rather than metabolic flux.","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032259","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0045654","count":3},{"id":"GO:0043046","count":3}]},{"hash":"2297932296132280049","title":"RNA processing, export, and translation regulation under stress","description":"The cluster centers on RNA maturation and export (tRNA processing, spliceosome-mediated splicing, mRNA export) and post-transcriptional control of translation (deadenylation-dependent decapping, regulation of translation initiation), with accompanying stress-response signals (abscisic acid and water deprivation). This suggests a cohesive role in adjusting gene expression at the RNA level during stress.","confidence":"Medium","size":9,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0010610","count":2},{"id":"GO:1901407","count":2},{"id":"GO:0006406","count":2}]},{"hash":"1138719309918825691","title":"Viral entry, uncoating, and replication in host","description":"The cluster prominently features GO terms tied to viruses interacting with host cells, including entry into the host, uncoating, proviral latency, activation of viral genome replication, and viral release, suggesting a cohesive viral lifecycle within a host. Protein folding and peptidyl-prolyl isomerization terms may reflect chaperone involvement in maturation of viral proteins, reinforcing a virus-centric functional theme.","confidence":"High","size":9,"edges":31,"triangles":54,"max_degree":8,"top_function":"protein folding","top_go_terms":[{"id":"GO:0000413","count":4},{"id":"GO:1901407","count":4},{"id":"GO:0006457","count":3},{"id":"GO:0030260","count":3},{"id":"GO:0071492","count":3}]},{"hash":"258988747579031995","title":"Ribosome biogenesis and mitotic cell cycle","description":"This cluster is driven by strong signals for ribosome biogenesis and translation (ribosomal subunit biogenesis, translation, ribosome biogenesis) along with mitotic cell cycle processes (cell division, mitotic cell cycle, APC-dependent catabolic process), suggesting coordination between protein synthesis capacity and cell division machinery. Other terms like mRNA splicing and vesicle transport appear secondary, and a coagulation term is likely incidental. ","confidence":"High","size":9,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0031145","count":2},{"id":"GO:2001162","count":2}]},{"hash":"1612904204467035174","title":"Acetylation-Related Modifications","description":"The cluster centers on acetylation events, including N-terminal acetylation, peptidyl-lysine and histone H4 acetylation, and related acetylation processes (spermine acetylation, N-acetylglucosamine metabolism). This suggests a cohesive theme around acetyl group transfer/modification affecting proteins and metabolites, with some associated biosynthetic pathways (melatonin and mycothiol) that tie into acetyl chemistry. Confidence: Medium","confidence":"","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030187","count":2},{"id":"GO:0017196","count":2},{"id":"GO:0043967","count":2},{"id":"GO:0010125","count":2},{"id":"GO:0018002","count":2}]},{"hash":"259440540728399999","title":"Spliceosome-mediated RNA processing and translation initiation","description":"This cluster centers on mRNA processing with spliceosome-mediated splicing, splice-site recognition, and alternative splicing, plus small-subunit processome assembly and formation of the translation preinitiation complex, indicating a role in RNA maturation and translation readiness.","confidence":"High","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":7},{"id":"GO:0006378","count":6},{"id":"GO:0006376","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0000380","count":5}]},{"hash":"2301693370144970106","title":"Unknown","description":"The Top Terms are diverse (muscle contraction, neural regeneration, placenta development, immune signaling, reproduction, apoptosis, and cytoskeletal reorganization) with no clear shared function or strong connectivity (no edges/triangles), so there isn\u2019t a coherent biological theme to name the cluster beyond Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006939","count":4},{"id":"GO:0048680","count":4},{"id":"GO:0001893","count":3},{"id":"GO:0032633","count":3},{"id":"GO:0048240","count":3}]},{"hash":"1914413729572074971","title":"H/ACA snoRNPs and telomerase biogenesis","description":"This cluster is driven by box H/ACA snoRNP assembly and pseudouridylation of snoRNA/snRNA, plus telomerase RNA processing/localization and holoenzyme assembly, pointing to a core role in H/ACA snoRNP function and telomerase biogenesis (with ribosome biogenesis linked via snoRNP-associated rRNA modification). ","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0016579","count":1},{"id":"GO:0042981","count":1},{"id":"GO:0043392","count":1},{"id":"GO:0000454","count":1}]},{"hash":"1468521467067075504","title":"Organogenesis and Signaling","description":"The top GO terms cluster around development of multiple tissues and organs (skeletal, nervous, heart, multicellular organism development) and several signaling pathways (Rho signaling, calcium-dependent exocytosis, Fc receptor signaling). This suggests proteins involved in organogenesis and intercellular communication, with a few terms reflecting broader growth programs. Confidence: Medium","confidence":"","size":9,"edges":18,"triangles":17,"max_degree":7,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0001501","count":6},{"id":"GO:0007399","count":6},{"id":"GO:0019233","count":6},{"id":"GO:0007124","count":6},{"id":"GO:0045956","count":6}]},{"hash":"211213212326059732","title":"Neural signaling and axon guidance","description":"Most top GO terms center on nervous system development, excitatory synaptic activity, and axon guidance-related signaling (ephrin, Wnt, and JNK pathways), suggesting a neural signaling/axon guidance cluster. Some mitotic cell cycle and T cell signaling terms may reflect multi-functional proteins or broader signaling cross-talk, but the dominant theme is neural signaling and axon extension. ","confidence":"Medium","size":9,"edges":8,"triangles":4,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0060079","count":5},{"id":"GO:0050852","count":4},{"id":"GO:0000086","count":4},{"id":"GO:0048013","count":4}]},{"hash":"1844442320704701142","title":"Embryonic Development and Morphogenesis","description":"This cluster highlights developmental processes: mesoderm formation, nervous system development, cartilage condensation, and neural tube patterning, as well as Hedgehog-related signaling and cell adhesion/spreading. The combination of these developmental terms with related cell-cycle activity (DNA replication, G2/M transition) suggests proteins involved in embryogenesis and tissue morphogenesis, with signaling and adhesion roles. ","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0001502","count":3},{"id":"GO:0000086","count":3},{"id":"GO:2000811","count":3},{"id":"GO:0007399","count":3}]},{"hash":"2297220568097667392","title":"Neural development and synaptic transmission","description":"The cluster\u2019s top GO terms cluster around neural development (substantia nigra development, neural crest formation) and neuronal communication (synaptic vesicle exocytosis/endocytosis, excitatory postsynaptic potential), with additional, less central terms like GPCR signaling and xenobiotic response. While some terms (mitotic cell cycle, ossification) are broader or outliers, the dominant themes point to neural development and synaptic signaling as the core function of this group.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0021762","count":4},{"id":"GO:0098907","count":4},{"id":"GO:2000300","count":4},{"id":"GO:0007205","count":4}]},{"hash":"1565587331173461130","title":"RNA processing and ribosome maturation with ciliogenesis","description":"These proteins show enrichment for RNA metabolism and ribosome assembly terms (mRNA transport, RNA guanine-N7 methylation, rRNA maturation), plus a notable intraciliary transport term tied to cilium assembly. TORC1 signaling and related regulatory processes further support a broader connection to translation and gene expression control, with a ciliogenesis-facing component. Overall, a cohesive theme centers on RNA processing and ribosome maturation, with a link to ciliogenesis pathways.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051028","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2}]},{"hash":"60047802163899092","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":8,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":2},{"id":"GO:0000467","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0006457","count":1}]},{"hash":"942857711642298014","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0042787","count":2}]},{"hash":"2135630958692961229","title":"GTPase-regulated Golgi-ER vesicle trafficking","description":"Most terms point to membrane trafficking in the secretory pathway: COPI-coated Golgi vesicles, ER-to-Golgi transport, Golgi vesicle trafficking, vesicle budding, and endosome-to-plasma membrane transport, often linked to GTPase activity. A few terms (e.g., endosomal/sodium transport) support this endomembrane theme. Together they suggest a regulatory module that promotes vesicle formation and trafficking through the Golgi/ER and related compartments. The mammary gland proliferation term is peripheral to the core trafficking theme.","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0033601","count":3},{"id":"GO:1903527","count":3},{"id":"GO:1905751","count":3},{"id":"GO:1902307","count":3}]},{"hash":"519467047136229167","title":"Innate immune response to dsRNA and LPS","description":"The top GO terms cluster around innate immunity and antiviral signaling (innate immune response, interferon-beta production, response to exogenous dsRNA, xenophagy) plus components related to bacterial LPS signaling and defense against Gram-positive bacteria. This suggests a general innate immune module responsive to viral dsRNA and bacterial LPS, with associated autophagic responses. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0016126","count":2},{"id":"GO:1904417","count":2},{"id":"GO:0043330","count":2},{"id":"GO:0050830","count":2}]},{"hash":"759346066538784177","title":"Neuronal Ca2+-Dependent Exocytosis and Glutamatergic Signaling","description":"The top GO terms point to calcium-triggered neurotransmitter release, membrane potential stabilization, and ionotropic glutamate receptor signaling, all central to neuronal communication. The inclusion of terms related to Golgi-associated calcium release and sensory nerve formation further supports a neural signaling theme, though a few regulatory terms appear peripheral. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030322","count":1},{"id":"GO:0061454","count":1},{"id":"GO:1903249","count":1},{"id":"GO:1901205","count":1},{"id":"GO:0010751","count":1}]},{"hash":"1050734307438955420","title":"Multitissue Development and Differentiation","description":"This cluster aggregates GO terms centered on development and tissue-specific differentiation across multiple organs (thyroid, thymus, inner ear, lung mesenchyme, bone growth, Bergmann glia, etc.) and includes DNA-templated transcription, suggesting a broad program of developmental regulation rather than a single pathway. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0014902","count":2},{"id":"GO:0030878","count":2},{"id":"GO:0003430","count":2},{"id":"GO:0006006","count":2}]},{"hash":"2104823356952484703","title":"Diverse Metabolite Biosynthesis","description":"The top GO terms cluster around biosynthetic processes for a range of metabolites\u2014antibiotics, alkaloids, steroids, retinoids, sphingolipids, and long-chain fatty acids\u2014suggesting proteins involved in various biosynthetic pathways. A few terms (vacuole fusion, regulation of transcription) are less aligned with metabolism, but the core theme is metabolite biosynthesis.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0006706","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0009710","count":1}]},{"hash":"945674511533235410","title":"Diverse developmental processes","description":"As the top GO terms include bone ossification, spermatid elongation, brain ventricle development, and photoperiodic flowering regulation, alongside more general cellular processes, there isn\u2019t a single cohesive function tying all proteins together. The cluster appears to span multiple development-related and basic cellular activities across different tissues, so a broad label reflecting developmental diversity is most appropriate.","confidence":"Medium","size":9,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006893","count":2},{"id":"GO:0043931","count":2},{"id":"GO:0071041","count":1},{"id":"GO:0007290","count":1},{"id":"GO:0048577","count":1}]},{"hash":"1500747280266077714","title":"RNA processing and transcription regulation","description":"The cluster prominently features miRNA processing and negative regulation of transcription elongation, pointing to a theme of gene expression control. Additional terms like protein stabilization and regulation of signaling add supporting regulatory context. The cerebellar structural organization terms likely reflect annotation biases or incidental associations rather than a single cohesive cerebellar-specific function, so the core signal centers on RNA processing and transcriptional regulation.","confidence":"Medium","size":9,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0021693","count":2},{"id":"GO:0021685","count":2},{"id":"GO:1903468","count":2},{"id":"GO:0044810","count":2},{"id":"GO:0070535","count":2}]},{"hash":"328305262659957729","title":"Ubiquitin-Dependent Protein Turnover and Autophagy","description":"The GO terms show strong enrichment for ubiquitination processes (protein monoubiquitination, autoubiquitination, K63-linked ubiquitination, and ubiquitin-dependent protein catabolic process) and autophagy-related protein targeting to the vacuole, indicating a cohesive theme of ubiquitin-mediated protein turnover and autophagic degradation, with some other terms likely representing ancillary or context-specific roles.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006513","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0060487","count":5},{"id":"GO:0032465","count":5}]},{"hash":"2084023994818169674","title":"Unknown","description":"The top terms span meiosis/chromosome condensation, translation, viral processes, tRNA gene clustering, and various heart/cardiac development and signaling terms, with no clear single biological theme linking most proteins. This broad, disparate set makes it difficult to assign a cohesive function to the cluster.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010032","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0016032","count":2},{"id":"GO:0007076","count":2},{"id":"GO:0070058","count":2}]},{"hash":"252106104168731546","title":"Developmental Chromatin Remodeling and Transcription","description":"Developmental chromatin remodeling and transcription is suggested by the top GO terms, which emphasize chromatin remodeling and DNA-templated transcription, including RNA Pol II regulatory region binding. The presence of development- and differentiation-related terms (root meristem growth, placental and trophoblast differentiation, EMT) indicates these proteins participate in gene regulatory programs governing development across tissues, likely through chromatin-mediated transcription control. Confidence: Medium","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0010082","count":2},{"id":"GO:0060806","count":2},{"id":"GO:0003323","count":2}]},{"hash":"1935672961652274448","title":"Unknown","description":"The top terms span disparate themes including barrier establishment (blood-brain barrier, placenta), membrane trafficking (Golgi to plasma membrane transport), lipid biosynthesis regulation, organ development, lysosome organization, and general responses to pH and nutrients, with little overlap pointing to a single cohesive function. Therefore a specific, intuitive label is not supported.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090212","count":1},{"id":"GO:0007040","count":1},{"id":"GO:0009268","count":1},{"id":"GO:0001892","count":1},{"id":"GO:0042360","count":1}]},{"hash":"743438668936822687","title":"Epithelial Polarity and Tight Junction Dynamics","description":"The set centers on establishment/maintenance of epithelial cell polarity and tight junction assembly, with supporting cytoskeletal remodeling (actin branching) and membrane trafficking (endocytosis). Additional signaling pathways (ephrin, Wnt, T cell receptor) likely reflect cell\u2013cell communication and junction-associated signaling, reinforcing a unified theme of polarity and junction dynamics.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902570","count":2},{"id":"GO:0070830","count":2},{"id":"GO:0090135","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0006897","count":2}]},{"hash":"2185115541439411360","title":"Endosome-Golgi Trafficking","description":"The GO terms point to a cohesive theme of intracellular vesicle transport, especially endocytic recycling, retrograde transport from endosome to Golgi, vesicle docking/fusion, and endosome organization, which together suggest movement and organization of material between endosomes and the Golgi. A couple of terms touch on mitophagy/autophagy and respiration regulation, which may reflect broader autophagic or energy-related processes but do not override the central endosome\u2013Golgi trafficking signal. Overall, the cluster seems to represent endosome-to-Golgi transport and Golgi organization.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043457","count":1},{"id":"GO:0010259","count":1},{"id":"GO:0000422","count":1},{"id":"GO:0006906","count":1},{"id":"GO:0032456","count":1}]},{"hash":"1526156016615935391","title":"RNA processing and transcription regulation","description":"The top terms are dominated by RNA processing and gene expression control\u2014mRNA splicing, transcription, and RNA guanine-N7 methylation\u2014with supporting signals from chromatin modification and related regulatory pathways, and a few terms hinting at growth and signaling roles. This suggests a cluster centered on RNA processing and transcriptional regulation, with some ancillary functions.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0034314","count":2}]},{"hash":"1331208604762903082","title":"Unknown","description":"The top GO terms include metabolism, redox and ER stress responses, transcription, brain development, ER-Golgi transport, and miscellaneous catabolic processes, indicating a heterogeneous mix rather than a single cohesive function. As no clear shared function stands out, I assign Unknown.","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0034976","count":2}]},{"hash":"1514910507187851233","title":"Keratinocyte Sphingolipid Metabolism","description":"These proteins cluster around sphingolipid biology: ceramide catabolic, sphingosine and phytosphingosine biosynthesis terms suggest sphingolipid metabolism, and keratinocyte differentiation points to skin biology. The presence of adhesion-related terms hints at sphingolipid signaling influencing epidermal cell-matrix interactions. Overall, the cluster appears to reflect sphingolipid biosynthesis/metabolism in keratinocytes/skin.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071277","count":1},{"id":"GO:0033629","count":1},{"id":"GO:0046514","count":1},{"id":"GO:0030216","count":1},{"id":"GO:0090285","count":1}]},{"hash":"2193241644494751545","title":"Actin dynamics and cell adhesion","description":"This cluster is dominated by GO terms linked to the actin cytoskeleton and its associated structures, including actin filament-based transport, pinocytosis regulation, focal adhesion assembly, and formin-nucleated actin cable formation, along with references to cytoskeleton reorganization and spindle-related processes. A weaker link to Wnt signaling is present, but the strongest signal centers on actin remodeling and adhesion, suggesting a cohesive theme of actin-driven dynamics during cell movement and division.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0031532","count":1},{"id":"GO:0048041","count":1},{"id":"GO:0045769","count":1}]},{"hash":"1199976080250257013","title":"Ubiquitin-Mediated Protein Modification","description":"This cluster is dominated by GO terms related to ubiquitination processes: monoubiquitination, polyubiquitination, autoubiquitination, and ubiquitin-dependent protein catabolic processes, including K63-linked ubiquitination. These indicate regulation of protein turnover via ubiquitin tagging. A few terms touch circadian rhythm and immune signaling, but the strongest common thread is modulation of ubiquitin pathways and protein degradation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902564","count":4},{"id":"GO:0042787","count":3},{"id":"GO:1903378","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0051865","count":2}]},{"hash":"948430908347407439","title":"Unknown","description":"The top GO terms are highly diverse, spanning RNA processing, metabolism, plant signaling, DNA repair, cell cycle, apoptosis, and stress responses, with no single unifying function or pathway tying all nine proteins together. The absence of edges and a coherent theme suggests there is no clear functional core to label, so Unknown is the appropriate label.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":2},{"id":"GO:0006196","count":1},{"id":"GO:0009742","count":1},{"id":"GO:1903799","count":1},{"id":"GO:0051321","count":1}]},{"hash":"1209829124390704265","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071031","count":1},{"id":"GO:0019076","count":1},{"id":"GO:0030260","count":1},{"id":"GO:0010587","count":1},{"id":"GO:0075713","count":1}]},{"hash":"1308105295409237537","title":"Sterol and Fatty Acid Biosynthesis","description":"Dominant GO terms include cholesterol biosynthesis via lathosterol, fatty acid biosynthesis, ergosterol biosynthesis, and ether lipid metabolism, indicating a core function in lipid biosynthesis and sterol metabolism. Minor terms like CNS myelin maintenance and sebaceous gland differentiation suggest tissue contexts where lipids are key, reinforcing the lipid metabolism theme. Therefore, the label Sterol and Fatty Acid Biosynthesis fits well.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0033490","count":1},{"id":"GO:0006633","count":1},{"id":"GO:0032286","count":1},{"id":"GO:0006696","count":1}]},{"hash":"816681176728819634","title":"Ribosome biogenesis and translation","description":"Several top GO terms repeatedly point to ribosome assembly and function (ribosome biogenesis, ribosomal subunit export from nucleus, cytoplasmic translation) and tRNA modification, indicating that this cluster represents components of the protein synthesis machinery. A few terms (cell cycle, cell septum assembly, conjugation) are less aligned and may reflect broader cellular contexts or annotation noise, but do not outweigh the ribosome/translation signal. Overall, the cluster appears to group ribosome biogenesis and translation-related proteins.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0090529","count":1},{"id":"GO:1903833","count":1},{"id":"GO:0007049","count":1}]},{"hash":"1518798980113751147","title":"Unknown","description":"The GO terms span plant development, immune signaling, hormone biosynthesis, morphogenesis, and autophagy/chromatin regulation, with no single cohesive function linking the proteins; therefore a specific label cannot be inferred.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010228","count":1},{"id":"GO:2000664","count":1},{"id":"GO:2000182","count":1},{"id":"GO:0031532","count":1},{"id":"GO:1901097","count":1}]},{"hash":"453029702320147330","title":"Unknown","description":"The top GO terms are highly diverse, including actin nucleation (cytoskeleton), mitotic spindle assembly (cell division), various growth and proliferation terms, ubiquitin-dependent proteolysis, histone acetylation, and signaling. There isn\u2019t a single cohesive biological theme tying these functions together, so a concise label cannot be confidently assigned.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034314","count":1},{"id":"GO:0060770","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0060733","count":1},{"id":"GO:0051260","count":1}]},{"hash":"1980469657779208658","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:1905768","count":1},{"id":"GO:0071947","count":1},{"id":"GO:1905765","count":1},{"id":"GO:0000122","count":1}]},{"hash":"1854054174083926433","title":"Redox balance and energy metabolism","description":"The cluster shows strong signals for oxidative-reduction processes, cellular oxidant detoxification, and redox homeostasis, paired with mitochondrial electron transport and the TCA cycle, pointing to a common theme of maintaining redox state while generating energy. The presence of photosynthesis hints at chloroplast-associated redox activity in plants, with other terms like methylamine metabolism and DNA repair being less central but present. Overall, the dominant pattern ties redox regulation to energy production.","confidence":"Medium","size":8,"edges":25,"triangles":41,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0098869","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0030416","count":2},{"id":"GO:0015979","count":2}]},{"hash":"2011552694445266027","title":"Nucleotide metabolism and salvage","description":"The top GO terms spotlight nucleotide biosynthesis and phosphate-transfer steps (AMP salvage, ADP biosynthesis, nucleoside monophosphate phosphorylation, purine ribonucleotide interconversion, ITP metabolism), suggesting a cohesive role in nucleotide production and remodeling. Development-related terms are only lone entries and likely noise, so the main theme centers on nucleotide metabolism.","confidence":"High","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0001889","count":1},{"id":"GO:0046041","count":1},{"id":"GO:0007420","count":1},{"id":"GO:0046705","count":1},{"id":"GO:0046940","count":1}]},{"hash":"183439139274531064","title":"RNA processing and translation initiation","description":"This cluster is enriched for GO terms related to mRNA splicing regulation and translation-related steps, including spliceosome-mediated regulation, splice site recognition, formation of the translation preinitiation complex, and preribosome assembly. The combination points to a functional module coordinating RNA processing with ribosome biogenesis and translation initiation.","confidence":"High","size":8,"edges":26,"triangles":45,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006378","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0090070","count":1},{"id":"GO:1902626","count":1}]},{"hash":"1632611757080387124","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":16,"triangles":17,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":5},{"id":"GO:0048026","count":5},{"id":"GO:0071031","count":3},{"id":"GO:0000716","count":3},{"id":"GO:0042766","count":3}]},{"hash":"325259046650291031","title":"Sterol and fatty acid biosynthesis","description":"The top GO terms point predominantly to lipid metabolism, notably ergosterol biosynthesis regulation, unsaturated fatty acid biosynthesis, and sphingolipid-related metabolism (MIPC). While a few terms seem peripheral or noisy (e.g., nitrate assimilation, CNS myelin maintenance), the strongest common thread among the terms is lipid biosynthesis and membrane lipid pathways, suggesting the cluster centers on sterol and fatty acid production in a membrane-related context.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0042128","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0006809","count":2}]},{"hash":"1598913849320803225","title":"Cellular stress response and detoxification","description":"The cluster shows a convergence on stress-related and xenobiotic-responsive processes: detoxification and antioxidant pathways (cellular oxidant detoxification, glutathione metabolic process, toxin catabolic process), responses to starvation and ethanol, and DNA damage response (nucleotide-excision repair), suggesting a common theme of adapting to cellular stress and maintaining genome integrity. Although mitotic cell cycle appears among terms, the dominant signal is stress adaptation and detoxification, with inflammatory signaling modulation (negative regulation of NF-kappaB) reinforcing this interpretation.","confidence":"Medium","size":8,"edges":4,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0042594","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0009072","count":2},{"id":"GO:0098869","count":2}]},{"hash":"645853408714147044","title":"Ribosome Biogenesis and Translation","description":"The dominant GO terms center on ribosome assembly, ribosomal subunit export, and cytoplasmic translation, with tRNA modification and ribosome biogenesis reinforcing a core theme of protein synthesis. A cell cycle connection is plausible given growth needs, while septum assembly and conjugation terms appear as minor outliers.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0090529","count":3},{"id":"GO:1901001","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0042254","count":3}]},{"hash":"976245193214630929","title":"Golgi vesicle trafficking and SNARE cycling","description":"Proteins in this cluster are enriched for GO terms tied to Golgi transport and SNARE machinery, including SNARE complex disassembly, Golgi-to-plasma membrane transport, and Golgi vesicle docking. While there are a few terms pointing to other cellular processes, the dominant pattern is vesicle trafficking related to the Golgi, justifying this label as representative of the cluster\u2019s shared function.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035494","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0006893","count":1},{"id":"GO:0097327","count":1}]},{"hash":"1656725966314063664","title":"Mitochondrial metabolite and ion transport","description":"The cluster is dominated by GO terms describing transport of various metabolites and metal ions across the mitochondrial membranes (CoA, citrate, deoxynucleotides, NAD, iron, manganese, magnesium) and regulation of membrane permeability, pointing to a cohesive set of mitochondrial transport proteins. An outlier term (liver regeneration) is unrelated to this core theme, and an obsolete mitochondrial maintenance term is still mitochondria-associated. ","confidence":"Medium","size":8,"edges":11,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":5},{"id":"GO:0035349","count":5},{"id":"GO:0006843","count":5},{"id":"GO:0046902","count":5},{"id":"GO:0030302","count":5}]},{"hash":"240939608721400361","title":"Synapse assembly and cell polarity","description":"The proteins here touch both synaptic processes (GABA secretion, synaptic vesicle maturation, immunological synapse formation) and polarity/junction components (epithelial polarity, tight junction assembly, centrosome localization), suggesting a shared role in organizing membrane domains during synapse formation while maintaining cell polarity and adhesion.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045197","count":1},{"id":"GO:0014051","count":1},{"id":"GO:2000821","count":1},{"id":"GO:0046037","count":1},{"id":"GO:1903286","count":1}]},{"hash":"225549377349162057","title":"Rho-GTPase signaling and cytoskeleton remodeling in development","description":"These proteins appear to co-occur around regulation of Rho GTPase signaling and GTPase activity, with supporting associations to various developmental processes (brain and multicellular development, spermatid development) and cytoskeleton-driven events (mating projection growth, vesicle exocytosis). The common thread is Rho/GTPase\u2013mediated control of cytoskeleton dynamics involved in development and morphogenesis.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0035264","count":2}]},{"hash":"408426683378300379","title":"Unknown","description":"The top GO terms span diverse areas\u2014multiple catabolic metabolic processes, a cellular stress response, differentiation and hormone-related regulation, halogen and amino acid metabolism, and even alternative mRNA splicing\u2014without a single coherent functional theme tying the proteins together. This makes a concise, specific label unreliable. ","confidence":"","size":8,"edges":22,"triangles":28,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0016575","count":6},{"id":"GO:0006212","count":6},{"id":"GO:0042208","count":6},{"id":"GO:0051068","count":6},{"id":"GO:0071455","count":6}]},{"hash":"932994600756107452","title":"Golgi-ER Vesicle Trafficking and Rab Signaling","description":"The cluster is dominated by GO terms for ER-to-Golgi vesicle transport, establishment of Golgi localization, and Rab protein signaling, all pointing to a core role in the secretory pathway and intracellular trafficking. While some terms refer to brain development and keratinocyte processes, these likely reflect tissue-specific contexts rather than the primary function of the proteins in this cluster.","confidence":"Medium","size":8,"edges":9,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0051291","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0051683","count":3},{"id":"GO:0031424","count":3}]},{"hash":"766209022963632121","title":"ER stress response and protein folding quality control","description":"Most of the top GO terms point to endoplasmic reticulum proteostasis: response to heat, ER-associated protein folding, chaperone-assisted refolding, and ubiquitin-proteasome\u2013mediated quality control (ERAD) and translational regulation under ER stress. While a couple of terms touch development (mesoderm formation, dorsal/ventral neural tube patterning), the dominant theme is maintaining protein folding and quality control in the ER. ","confidence":"Medium","size":8,"edges":9,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0071630","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1111542735649308124","title":"Mitochondrial metabolism and amino acid biosynthesis","description":"The top GO terms point to mitochondrial functions, including mitochondrial translation and the TCA cycle, along with biosynthesis of amino acids like leucine and isoleucine, suggesting a cluster centered on mitochondrial energy metabolism and amino acid production. Iron-related responses also appear, hinting at metal-ion homeostasis affecting these metabolic pathways, even though several terms are obsolete. Overall, a coherent theme around mitochondrial metabolic processes best fits this cluster.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0032543","count":1},{"id":"GO:0010040","count":1}]},{"hash":"1109272570530812080","title":"Epigenetic transcriptional regulation in embryogenesis","description":"This cluster centers on inhibition and control of RNA Polymerase II\u2013driven transcription and embryonic development, with supporting signals from chromatin-related processes (nucleosome density/positioning) and histone modifications. Even though several terms are obsolete, the overall pattern points to epigenetic regulation of transcription during development, via chromatin remodeling and modification pathways.","confidence":"Medium","size":8,"edges":12,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0016573","count":2}]},{"hash":"933211310554525209","title":"Ribosome Biogenesis and Translation Regulation","description":"The cluster is driven by terms related to translation, ribosome assembly/biogenesis, and regulation of translational fidelity, pointing to a core role in the protein synthesis machinery and its control. While a few transcription-related GO terms appear, they seem incidental to the main theme of ribosome function and translation regulation; the data collectively support a cohesive module focused on making and refining the protein synthesis apparatus.","confidence":"High","size":8,"edges":12,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":2},{"id":"GO:0017148","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0006353","count":1}]},{"hash":"1562736980601066045","title":"G-Protein Signaling in Development","description":"These proteins cluster around G-protein\u2013mediated signaling and its role in development and neuronal activity. Key terms include Rho signaling, heterotrimeric G-protein cycle, heart and skeletal development, forebrain neuron development, and neuronal signaling (glutamate receptor signaling, action potential). While some terms are broad or species-specific, the recurring theme is G-protein\u2013driven signaling affecting developmental and neural processes, which justifies the label.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:0001501","count":4},{"id":"GO:0007266","count":4},{"id":"GO:0007124","count":4},{"id":"GO:0007215","count":3}]},{"hash":"1584006427597561127","title":"Microtubule spindle dynamics and neuronal organization","description":"The top terms are dominated by microtubule- and spindle-related processes (mitotic spindle assembly/elongation, plus-end microtubule sliding, microtubule cytoskeleton polarity, nuclear migration along microtubules) with an additional hint toward brain-layer structural organization (Purkinje/granular layers). This points to a coherent theme of microtubule-based organization in both cell division and neuronal structure, so a label focusing on microtubule dynamics is appropriate.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000022","count":8},{"id":"GO:0000742","count":8},{"id":"GO:0035617","count":8},{"id":"GO:0030473","count":8},{"id":"GO:0001560","count":8}]},{"hash":"1683297853946172197","title":"Central carbon metabolism","description":"GO terms emphasize core carbohydrate and energy pathways (TCA cycle, glycolysis, and pentose phosphate pathway), plus acetyl-CoA biosynthesis from pyruvate and amino acid catabolism feeding into central metabolism. This combination points to a cohesive cluster of proteins involved in central carbon metabolism rather than a single specialized process.","confidence":"High","size":8,"edges":9,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":4},{"id":"GO:0009228","count":3},{"id":"GO:0006098","count":2},{"id":"GO:0061732","count":2},{"id":"GO:0042853","count":2}]},{"hash":"1866246121729366679","title":"Cellular stress signaling and trafficking","description":"The cluster shows enrichment for stress-related responses (response to antibiotic, hypoxia, interferon), translation and autophagy, and membrane trafficking processes (endocytic recycling, receptor internalization) and calcium-channel regulation. This suggests a cohesive theme around how cells sense and respond to stress via signaling and trafficking, with translation and autophagy supporting adaptive responses. Some terms (cell septum assembly, obsolete mitochondrial genome maintenance) are less clearly connected and may reflect broader annotations.","confidence":"Medium","size":8,"edges":17,"triangles":17,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":3},{"id":"GO:1990910","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0016236","count":2}]},{"hash":"4641155047100693","title":"ER stress response and protein quality control","description":"The top terms cluster around endoplasmic reticulum\u2013associated proteostasis: protein folding in the ER, ERAD and ubiquitin-proteasome\u2013mediated quality control, chaperone-assisted refolding, and translation upregulation in response to ER stress. Together these indicate a cohesive theme of maintaining protein homeostasis under stress within the ER, with only a few developmental terms likely incidental. ","confidence":"High","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":5},{"id":"GO:0009408","count":3},{"id":"GO:0071630","count":3},{"id":"GO:0036494","count":3},{"id":"GO:0070389","count":3}]},{"hash":"1912247943248234854","title":"Zinc ion transport and homeostasis","description":"The cluster is dominated by zinc-related functions: zinc ion import across the plasma membrane, intracellular zinc ion homeostasis, detoxification of zinc ion, and cellular response to zinc ion starvation, suggesting a coherent group centered on zinc uptake and maintenance of zinc levels. Cadmium transport and unfolded protein response terms may reflect broader metal stress handling but do not override the zinc-centric theme.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0010312","count":1},{"id":"GO:0044749","count":1},{"id":"GO:0034224","count":1},{"id":"GO:0060173","count":1},{"id":"GO:0006830","count":1}]},{"hash":"1091401331885775711","title":"Developmental growth, mitosis, and vesicle trafficking","description":"The terms point to developmental growth (multicellular growth, brain development, cell proliferation) coupled with mitotic processes (mitotic spindle assembly, cell cycle, cell division) and key secretory/trafficking pathways (ER-Golgi transport, retrograde Golgi-ER transport, COPII budding), suggesting a theme of development-driven proliferation integrated with vesicle trafficking and signaling (Smoothened). This combination is best captured by a concise label emphasizing growth, division, and trafficking.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0007224","count":2}]},{"hash":"1541240908465990686","title":"Muscle and neural development with cell cycle regulation","description":"This cluster shows several development-related terms for muscle and neural tissues (myoblast fusion, Schwann cell development, cerebellar cortex formation) plus synaptic activity and general cell cycle processes (DNA replication, mitosis). The common thread is coordinated muscle/neural development with proliferation, hence the label.","confidence":"Medium","size":8,"edges":19,"triangles":26,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0014850","count":5},{"id":"GO:0014044","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0060079","count":5},{"id":"GO:0021697","count":4}]},{"hash":"1319167036417459173","title":"Neural development and axon guidance signaling","description":"The terms cluster around nervous system development and axon guidance (hippocampus development, axon extension, Wnt/JNK signaling, ephrin receptor signaling). Some immune signaling (T cell receptor) and cytoskeleton remodeling appear, but the dominant theme is neural development and axon growth signaling, so this label captures the core function of the cluster.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":4},{"id":"GO:0048013","count":4},{"id":"GO:0046330","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0000278","count":4}]},{"hash":"1818880984887798098","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning plant defense, transport, development, neural signaling, and RNA regulatory processes with no shared function across the cluster. This lack of a unifying theme makes it inappropriate to assign a specific functional label, so the cluster is best described as Unknown.","confidence":"","size":8,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009626","count":1},{"id":"GO:0015721","count":1},{"id":"GO:0022416","count":1},{"id":"GO:0045671","count":1},{"id":"GO:1900271","count":1}]},{"hash":"795974240463867656","title":"Tissue remodeling and morphogenesis","description":"GO terms cluster around tissue remodeling, cell growth, morphogenesis, and extracellular matrix dynamics (fibrinolysis regulation, apical constriction), with a noisy signal from outliers like auxin biosynthesis.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009851","count":2},{"id":"GO:0007253","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0009409","count":2}]},{"hash":"695718527258164204","title":"Unknown","description":"The top GO terms span metal detoxification, lipid transport regulation, VEGF signaling, developmental morphogenesis, ion homeostasis, and viral processes, with no clear common function binding the cluster. The lack of a cohesive theme and the absence of edges among members suggest there isn\u2019t a single representative function for this cluster.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050787","count":2},{"id":"GO:0032369","count":1},{"id":"GO:0030949","count":1},{"id":"GO:0007377","count":1},{"id":"GO:1903281","count":1}]},{"hash":"1745289679395057001","title":"Ubiquitin-Dependent ERAD and Autoubiquitination","description":"The top GO terms are ubiquitin-dependent ERAD pathway and protein autoubiquitination, indicating a focus on ubiquitin-mediated protein quality control and degradation via ER-associated degradation. Other terms related to various biosynthetic processes and transcription regulation are present but much less frequent, suggesting they are secondary signals. Overall, the cluster appears centered on ubiquitin-proteasome\u2013mediated proteostasis, with some sporadic metabolic biosynthesis signals.","confidence":"Medium","size":8,"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:0017000","count":2},{"id":"GO:1903265","count":2},{"id":"GO:0006706","count":1}]},{"hash":"2255152987887282309","title":"Carbohydrate and cell-surface biosynthesis","description":"The top terms cluster around synthesis and metabolism of carbohydrates (starch, glycogen, sucrose, glucose) and cell-surface components (LPS, GPI anchors), suggesting a shared theme of carbohydrate metabolism and cell-envelope biosynthesis. Some terms like feeding behavior and stress responses appear peripheral, but the core signal points to biosynthetic processes for carbohydrates and cell-surface structures.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019252","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0006506","count":2},{"id":"GO:0007631","count":2}]},{"hash":"957131151127975600","title":"Ubiquitin-regulated stress and immune responses","description":"The cluster strongly features protein deubiquitination and ERAD-related GO terms, along with notes on systemic acquired resistance and responses to toxic substances. This points to a module where ubiquitin-mediated protein quality control intersects with cellular stress and immune signaling (e.g., detox, autophagy regulation, and defense responses).","confidence":"Medium","size":8,"edges":12,"triangles":9,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":3},{"id":"GO:0009627","count":2},{"id":"GO:0034140","count":2},{"id":"GO:0017085","count":2},{"id":"GO:0045648","count":2}]},{"hash":"1625854122025926465","title":"Translation Initiation and Ribosome Regulation","description":"The cluster is dominated by GO terms related to translation initiation, reinitiation, IRES-dependent initiation, translation regulation, and ribosome disassembly, suggesting proteins here work together to control the start of translation and ribosome dynamics. A few non\u2013translation terms appear as possible misannotations, but the prevailing theme remains initiation and ribosome function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0009048","count":1},{"id":"GO:0002192","count":1},{"id":"GO:1990145","count":1}]},{"hash":"1334459682832765627","title":"ER proteostasis and ER stress response","description":"These proteins are tied to endoplasmic reticulum quality control and the proteostatic response to stress: folding in the ER, ER-associated degradation (ERAD), and translation initiation changes during ER stress. The overlap of terms for protein folding in the ER, ubiquitin-proteasome\u2013mediated quality control, and upregulation of translation in response to ER stress supports a cohesive ER proteostasis/UPR theme. A few terms related to development (mesoderm formation, neural patterning) appear peripheral and do not define the main function of the cluster.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0071630","count":3},{"id":"GO:0036494","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0030433","count":3}]},{"hash":"1904362254083664670","title":"ABA-regulated vacuolar amino acid transporters","description":"The top GO terms point to an ABA response and regulation of stomatal movement, complemented by multiple transmembrane transport terms for amino acids into and out of the vacuole (lysine, arginine, tyrosine, histidine, proline) and even lithium, suggesting a coherent theme of vacuolar amino acid transport modulated by ABA in stomatal function. The cortical microtubule organization term hints at cytoskeletal involvement in stomatal dynamics, reinforcing the ABA-stomatal transport connection.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009737","count":1},{"id":"GO:0010119","count":1},{"id":"GO:0043622","count":1},{"id":"GO:0090517","count":1},{"id":"GO:1990818","count":1}]},{"hash":"719505051393625620","title":"Transcription Regulation and Growth Signaling","description":"The cluster\u2019s top GO terms are dominated by transcriptional regulation (negative regulation of transcription by RNA polymerase II, DNA-templated transcription, transcription regulation by galactose) and growth-associated signaling (positive regulation of CDK activity, ULK1 kinase complex assembly, mammary gland epithelial cell proliferation). While some terms touch on diverse contexts (early viral transcription, stomatal opening, lactation), the shared theme is regulation of gene expression coupled with cell growth/proliferation signals. This supports labeling the group as transcription control with growth-related signaling.","confidence":"Medium","size":8,"edges":9,"triangles":1,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0010165","count":3},{"id":"GO:0033601","count":3},{"id":"GO:0045737","count":3}]},{"hash":"2299621579778569609","title":"Diverse metabolite biosynthesis","description":"This cluster's top GO terms are all biosynthetic processes covering plastoquinone, chorismate/aromatic amino acids, glycerophospholipids, phospholipids, and antibiotic biosynthesis. With no edges or interactions, the proteins appear linked to general biosynthetic roles rather than a single pathway, so the label captures a shared theme of diverse biosynthetic activity.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":1},{"id":"GO:0010236","count":1},{"id":"GO:0009423","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0008654","count":1}]},{"hash":"1710411434172174355","title":"Amino acid and lipid metabolism under stress","description":"This cluster shows a combination of metabolic processes (regulation of gluconeogenesis; L-valine catabolic process; L-threonine biosynthetic process; fatty-acyl-CoA biosynthetic process) along with stress-related responses (cellular response to hydroperoxide, response to cold, response to starvation). The proteins seem tied to adjusting metabolism during stress conditions, rather than a single well-defined pathway, which justifies a metabolism-under-stress label.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903204","count":1},{"id":"GO:0071447","count":1},{"id":"GO:1902083","count":1},{"id":"GO:0042594","count":1},{"id":"GO:0009791","count":1}]},{"hash":"983092811878097689","title":"Oxidative Stress and Mitochondrial Apoptosis","description":"The terms cluster around cellular stress responses (response to ozone, ROS metabolic process) and mitochondrial involvement (protein insertion into mitochondrial inner membrane), plus apoptotic signaling pathways (extrinsic/intrinsic pathways). This suggests a cohesive theme of stress sensing linked to mitochondrial-mediated apoptosis.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":1},{"id":"GO:0010236","count":1},{"id":"GO:0072593","count":1},{"id":"GO:0045732","count":1},{"id":"GO:0045039","count":1}]},{"hash":"692628879633878318","title":"Unknown","description":"The Top Terms cover apoptotic process, various biosynthetic and metabolic pathways, erythrocyte differentiation regulation, defense response, hormone biosynthesis, carotenoid biosynthesis, and splicing, which are broadly disparate. There is no clear, cohesive functional theme tying these terms together, so a specific function label isn\u2019t justifiable; thus Unknown with no confidence.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0016575","count":1},{"id":"GO:0019805","count":1},{"id":"GO:0051068","count":1},{"id":"GO:0046203","count":1}]},{"hash":"1593013331225574640","title":"Unknown","description":"The proteins map to a mix of neural/glial development, immune signaling, and disparate metabolic/development terms, with no clear single theme connecting them; thus a coherent, specific label is not supported.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021943","count":2},{"id":"GO:0021861","count":2},{"id":"GO:0015979","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0006461","count":1}]},{"hash":"2125455438429683301","title":"Unknown","description":"Top terms are scattered across DNA replication, nucleotide biosynthesis, development, and signaling with no shared pathway or interactions; the cluster lacks a cohesive function, so it cannot be meaningfully named.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902979","count":1},{"id":"GO:0040022","count":1},{"id":"GO:0009640","count":1},{"id":"GO:0071171","count":1},{"id":"GO:0050999","count":1}]},{"hash":"623693353040757849","title":"Cytoskeletal and Ciliary Transport in Development","description":"The top GO terms cluster around cytoskeletal dynamics (microtubule anchoring, centrosome cycle, Arp2/3 actin nucleation), intraflagellar transport and cilium assembly, plus development-related processes (brain development, multicellular growth) and Rac signaling. This suggests the proteins collectively participate in shaping cell architecture and movement during development, including ciliary function and spindle organization.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0007098","count":1},{"id":"GO:0035020","count":1},{"id":"GO:0035735","count":1},{"id":"GO:1990810","count":1}]},{"hash":"1598743257406872079","title":"Pain and thermoception signaling","description":"The top GO terms are dominated by sensory pain and temperature detection (mechanical stimulus detection, thermoception, capsazepine response), pointing to nociception in neural contexts. While some terms touch on neural development and signaling, the prominent pattern centers on pain/temperature sensing and related neural signaling, justifying this label.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090501","count":2},{"id":"GO:0050966","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0050955","count":2},{"id":"GO:0070212","count":2}]},{"hash":"1653283596088092003","title":"Galactose-Linked Metabolism","description":"This set spans several metabolic and biosynthetic processes, with a notable emphasis on carbohydrate metabolism linked to galactose (glycolytic conversion from galactose, galactitol metabolism, and galactose-regulated transcription). Other terms point to broader biosynthetic pathways (isoprenoid mevalonate/IPP and cholesterol biosynthesis, GDP-L-fucose salvage, L-threonine and L-homoserine amino acid biosynthesis). The connection is that these proteins participate in sugar- and carbohydrate-related metabolism and related biosynthetic steps, rather than a single cohesive pathway, thus a label capturing a Galactose-associated Metabolic cluster is most representative.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009092","count":1},{"id":"GO:0046835","count":1},{"id":"GO:0006695","count":1},{"id":"GO:0019402","count":1},{"id":"GO:0009086","count":1}]},{"hash":"676236174771257373","title":"Fatty acid and branched-chain amino acid catabolism","description":"This cluster centers on fatty acid beta-oxidation, fatty-acyl-CoA biosynthesis, and valine (branched-chain amino acid) catabolism, with supporting links to energy metabolism (response to starvation, regulation of gluconeogenesis) and some tissue-development signals (liver and heart development). The common theme is metabolic catabolism driving energy production from lipids and BCAAs, with possible tissue maturation context.","confidence":"Medium","size":7,"edges":10,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042594","count":1},{"id":"GO:0009791","count":1},{"id":"GO:0006111","count":1},{"id":"GO:0006574","count":1},{"id":"GO:0042758","count":1}]},{"hash":"2302049513451991332","title":"Chloroplast Pigment and Quinone Biosynthesis","description":"The top GO terms are dominated by biosynthetic processes for chlorophyll and for quinone/vitamin cofactors (phylloquinone, plastoquinone, menaquinone, ubiquinone). This points to a coherent cluster of enzymes involved in pigment production and electron-carrier cofactor biosynthesis in chloroplasts/organelles, with translation appearing as a related organellar process.","confidence":"Medium","size":7,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042371","count":2},{"id":"GO:0048034","count":2},{"id":"GO:0015995","count":2},{"id":"GO:0010236","count":2},{"id":"GO:0009234","count":2}]},{"hash":"162440616421247611","title":"Chromatin Regulation and Transcription Control","description":"The top GO terms cluster around DNA-templated transcription and chromatin organization, including subtelomeric heterochromatin formation and nucleosome density\u2013related gene silencing, pointing to regulation of transcription through chromatin state. Additional terms touch on stress signaling and protein quality control, but the dominant theme remains chromatin-mediated transcription control.","confidence":"Medium","size":7,"edges":10,"triangles":5,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0070842","count":4},{"id":"GO:0006348","count":4},{"id":"GO:0060766","count":3},{"id":"GO:0014894","count":3}]},{"hash":"621504600225300617","title":"Glycerophospholipid Biosynthesis Cluster","description":"This cluster is best described as a glycerophospholipid biosynthesis module, given multiple GO terms for phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylserine biosynthesis, plus platelet activating factor biosynthesis. A few terms point to lipid signaling or regulation of PI biosynthesis, but the dominant theme is lipid membrane lipid production.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1905711","count":1},{"id":"GO:0006646","count":1},{"id":"GO:0070317","count":1},{"id":"GO:0006655","count":1},{"id":"GO:0006659","count":1}]},{"hash":"1093942258182875789","title":"Central carbon metabolism and amino acid pathways","description":"The cluster peaks include TCA cycle and one-carbon metabolism terms, plus alanine catabolism and branched-chain amino acid biosynthesis (valine, isoleucine), pointing to core metabolic and amino acid turnover functions. Some transcription-related and obsolete GO terms appear, but the dominant signal is central metabolism and amino acid processing, possibly reflecting metabolic remodeling under stress like hypoxia.","confidence":"Medium","size":7,"edges":11,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0042853","count":2},{"id":"GO:0019629","count":2},{"id":"GO:0006351","count":2}]},{"hash":"551618405872168509","title":"Unknown","description":"Top terms are scattered across amino acid metabolism (arginine/citrulline/urea cycle, serine biosynthesis) and unrelated processes (copper ion transport, stilbene catabolic, laminar flow response, dephosphorylation), with no edges or cohesive pathway linking them. This lack of a unifying function makes it hard to assign a meaningful label beyond Unknown.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071499","count":1},{"id":"GO:0000052","count":1},{"id":"GO:0000053","count":1},{"id":"GO:0006526","count":1},{"id":"GO:0000050","count":1}]},{"hash":"1984170572649315290","title":"Unknown","description":"The proteins in this cluster are associated with a highly diverse set of GO terms (metabolic pathways like menaquinone biosynthesis and triglyceride catabolism, signaling regulation, autophagy, development, xenobiotic response) and there are no edges connecting them, suggesting no cohesive shared function. Therefore a specific, representative label cannot be assigned.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":2},{"id":"GO:2000124","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0045820","count":1},{"id":"GO:0016311","count":1}]},{"hash":"327466255401361366","title":"Photosynthesis light harvesting and photoprotection","description":"This cluster centers on photosynthesis and how cells respond to different light conditions, with terms for light harvesting in photosystems I and II, nonphotochemical quenching (photoprotection), and responses to various light qualities/intensities (UV-A, red light, high/low light). The presence of phytol biosynthesis regulation further supports chlorophyll-related light capture processes. Overall, a cohesive group of light-dependent photosynthetic functions.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":4},{"id":"GO:0010196","count":3},{"id":"GO:0018298","count":2},{"id":"GO:0009768","count":2},{"id":"GO:0071492","count":2}]},{"hash":"884742897267173764","title":"Ubiquitin-Dependent ERAD and Autophagy Regulation","description":"The proteins cluster around ubiquitin-related quality control: deubiquitination, ubiquitin-dependent ERAD, and autophagosome maturation regulation, plus autoubiquitination. Several terms also reflect proteostatic stress responses and modulation of immune signaling (e.g., negative regulation of TLR3). This points to a cohesive theme of ubiquitin-mediated proteostasis and ERAD/autophagy control.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":4},{"id":"GO:0034140","count":3},{"id":"GO:0017085","count":3},{"id":"GO:0045648","count":3},{"id":"GO:1901097","count":3}]},{"hash":"2293492504341199240","title":"Heat and Oxidative Stress with mRNA Stability","description":"These proteins are enriched for heat and oxidative stress responses (heat, hydrogen peroxide, ROS regulation), plus deubiquitination and regulation of mRNA stability, suggesting a cohesive cellular stress response involving protein turnover and post-transcriptional control.","confidence":"Medium","size":7,"edges":11,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:2000378","count":2},{"id":"GO:0042542","count":2},{"id":"GO:0016579","count":2},{"id":"GO:0043488","count":2}]},{"hash":"938499944856255306","title":"Unknown","description":"The top GO terms are very disparate, ranging from plant brassinosteroid signaling and hydrogen peroxide response to meiotic cell cycle, mitochondrial repair, and metabolism, with only a single edge connecting proteins. There\u2019s no clear, cohesive biological function uniting these proteins, so a single intuitive label isn\u2019t apparent.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":3},{"id":"GO:0070301","count":3},{"id":"GO:0051348","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0006196","count":2}]},{"hash":"130359350190661891","title":"Unknown","description":"The top GO terms span very disparate areas (metabolism, signaling, RNA processing, meiosis, DNA repair, apoptosis, and stress responses) with no single dominant shared function. While brassinosteroid signaling hints at a plant-specific context, the diversity of other terms prevents a cohesive, specific label. Therefore, there isn\u2019t a clear common theme to assign a precise cluster name.","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006196","count":7},{"id":"GO:0009742","count":7},{"id":"GO:1903799","count":7},{"id":"GO:0051321","count":7},{"id":"GO:0097552","count":7}]},{"hash":"2302960836381232906","title":"Multi-Organ Development and Metabolism","description":"The top GO terms point to organogenesis across multiple tissues (brain, liver, kidney) while also highlighting various metabolic and regulatory processes (cholesterol metabolism, amino acid catabolism, hormone response, and starvation response) plus protein homooligomerization. This suggests a cluster of proteins involved in developmental programs that are linked to metabolic regulation, rather than a single specific pathway. Confidence: Medium","confidence":"","size":7,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0072229","count":1},{"id":"GO:0009725","count":1},{"id":"GO:0042594","count":1},{"id":"GO:0008203","count":1}]},{"hash":"267043591134911159","title":"Neuronal vesicle trafficking regulation","description":"Primarily driven by GO terms for endocytosis and negative regulation of exocytosis, with a nervous system development term pointing to neuronal vesicle trafficking. Oxidative stress response (hydrogen peroxide) also appears, suggesting regulation of trafficking under stress. Some nucleotide biosynthesis terms are more general metabolism and don\u2019t define the cluster\u2019s core theme. ","confidence":"Medium","size":7,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":2},{"id":"GO:0045920","count":1},{"id":"GO:0050765","count":1},{"id":"GO:0018106","count":1},{"id":"GO:0030819","count":1}]},{"hash":"2009629988745623106","title":"Nuclear RNA Processing and DNA Replication in Development","description":"Top terms point to nuclear-centric processes such as DNA replication, spliceosome-mediated mRNA splicing, regulatory ncRNA-mediated gene silencing, and protein localization to the nuclear periphery, along with development-related cues like embryonic cranial skeleton morphogenesis and a JNK signaling link. This suggests a cluster of proteins coordinating genome maintenance and RNA processing during development, with some signaling integration. ","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2}]},{"hash":"2155704257287120770","title":"Nuclear RNA Processing","description":"The proteins cluster around nuclear RNA metabolism: tRNA processing (GO:0008033), intronic box C/D snoRNA processing (GO:0034965), RNase MRP-dependent mRNA catabolic process (GO:0000294), and related RNA processing/hydrolysis activities (GO:0090502; GO:0006457 is general protein folding, but overall the signal centers on RNA processing). Some terms (e.g., pollen sperm cell differentiation, symbiont entry into host) are unrelated or noisy, while others hint at chromatin dynamics (chromosome condensation) and transcription-related regulation, which can accompany RNA processing in the nucleus. Taken together, the dominant theme is nuclear RNA processing and RNA metabolism.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":2},{"id":"GO:0048235","count":1},{"id":"GO:0034965","count":1},{"id":"GO:0008033","count":1},{"id":"GO:0030261","count":1}]},{"hash":"155053706422748600","title":"Spliceosome-Mediated mRNA Processing under Stress","description":"Top GO terms center on mRNA splicing via the spliceosome, splice-site recognition, and alternative splicing, with accompanying regulation of mRNA stability in response to stress and localization to cytoplasmic stress granules; translation preinitiation complex formation also appears, linking splicing and translation control under stress. This pattern suggests a cluster of proteins involved in post-transcriptional mRNA processing, especially splicing, and stress-associated regulation of mRNA fate.","confidence":"High","size":7,"edges":18,"triangles":23,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":5},{"id":"GO:0031047","count":4},{"id":"GO:0010610","count":4},{"id":"GO:1903608","count":3},{"id":"GO:0000398","count":3}]},{"hash":"1107915589529355699","title":"Cell migration and ECM remodeling","description":"The top GO terms cluster around cell movement and matrix interactions\u2014chemotaxis, endothelial chemotaxis, hyaluronan metabolic process, and regulation of metallopeptidase activity\u2014pointing to coordinated cell migration and extracellular matrix remodeling. Some terms like sperm capacitation and retina vasculature development are more tissue-specific, but the shared signals are dominated by migration and ECM dynamics.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045793","count":3},{"id":"GO:0046827","count":2},{"id":"GO:0006935","count":2},{"id":"GO:0048240","count":2},{"id":"GO:1905050","count":2}]},{"hash":"1454802956306733462","title":"Ribosome Biogenesis and Translational Control","description":"The dominant GO terms center on rRNA processing (maturation of LSU-rRNA and 5.8S rRNA), RNA methylation (guanine-N7), and translation (translation; regulation of translational fidelity; GCN2 signaling). Together these indicate proteins involved in ribosome assembly and regulation of protein synthesis; a few unrelated terms (Arp2/3 actin nucleation, development) likely reflect pleiotropy or annotation noise, but the core signal is ribosome/translation related.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0006450","count":1}]},{"hash":"68816594981983102","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":6,"triangles":1,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":5},{"id":"GO:0071031","count":4},{"id":"GO:1900050","count":4},{"id":"GO:0034476","count":4}]},{"hash":"1058401607477714528","title":"Cellular stress responses and cytoskeletal dynamics","description":"The top GO terms cluster around stress-response pathways (ER stress\u2013triggered apoptotic signaling, ERAD, GCN2 signaling) and cytoskeletal/cell-division processes (Arp2/3 actin nucleation, mitotic spindle assembly), with a couple of broader growth-related terms. This combination suggests a unifying theme of managing stress while supporting structural and division-related cellular functions, justifying a label focused on stress responses and cytoskeletal dynamics.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0070059","count":3},{"id":"GO:0034314","count":2},{"id":"GO:0060770","count":2}]},{"hash":"382789704153592982","title":"snoRNP biogenesis and telomerase RNA processing","description":"Most terms cluster around snoRNA-guided pseudouridylation and box H/ACA snoRNP assembly, together with ribosome biogenesis and telomerase RNA assembly/stabilization. This points to a nuclear RNA-processing module coordinating snoRNA/snoRNP maturation with ribosome and telomerase RNP maintenance. The leaf senescence term is plant-specific and not indicative of the core function, so the label reflects the RNA-protein assembly theme.","confidence":"High","size":7,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1900056","count":2},{"id":"GO:0000454","count":1},{"id":"GO:0042254","count":1},{"id":"GO:1904874","count":1},{"id":"GO:1905323","count":1}]},{"hash":"1181739043024527418","title":"Chloroplast Photosynthesis and Calvin Cycle","description":"The top GO terms include photosynthesis, carbon fixation, photorespiration, and the reductive pentose-phosphate cycle, which collectively point to chloroplast/metabolic processes (Calvin cycle). While there are a few nuclear gene-expression terms in the list, the strongest signal is plastid photosynthesis-related functions.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903026","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0032298","count":1},{"id":"GO:0019253","count":1}]},{"hash":"715555569290655749","title":"Unknown","description":"The top GO terms are scattered across actin nucleation regulation, spindle assembly, cell growth, signaling, and chromatin modification, with no single cohesive function linking the proteins, and there are no edges connecting cluster members. This lack of a unified theme makes a reliable, specific label unlikely.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034314","count":1},{"id":"GO:0060770","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0060733","count":1},{"id":"GO:0051260","count":1}]},{"hash":"2041559634190231465","title":"Oxidative Stress Detoxification","description":"The cluster centers on detoxification and redox regulation (cellular oxidant detoxification, detoxification of nitrogen compounds, regulation of superoxide generation) with accompanying inflammatory modulation terms, suggesting a focus on oxidative stress responses; some developmental terms appear ancillary to this core theme.","confidence":"Medium","size":7,"edges":17,"triangles":21,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:0045669","count":2},{"id":"GO:0070458","count":2},{"id":"GO:0002674","count":2},{"id":"GO:0032930","count":2}]},{"hash":"185379857850244802","title":"Golgi-ER and endosome vesicle trafficking","description":"This cluster is dominated by GO terms describing vesicle formation and trafficking among the Golgi, endosomes, and endoplasmic reticulum (e.g., COPII vesicles, retrograde Golgi-ER transport, endosome-to-Golgi/lysosome transport, CVT pathway). While there are some cell division terms present, the strongest and most consistent signal is vesicle trafficking between these organelles.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0090114","count":2},{"id":"GO:0034498","count":2}]},{"hash":"104225385739794555","title":"Unknown","description":"The GO terms are highly diverse, spanning transcriptional regulation, redox/RNA metabolism, sensory perception, multiple signaling pathways, and differentiation processes. There isn\u2019t a single dominant function linking the proteins, suggesting either heterogeneity or limited, unclear common biology. Therefore, Unknown with no clear confidence.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0090501","count":2},{"id":"GO:0050966","count":2},{"id":"GO:0070431","count":2}]},{"hash":"2281827806435954207","title":"Cardiac Potassium Transport and Action Potential","description":"The top GO terms cluster around potassium ion export/import across membranes, intracellular potassium homeostasis, and membrane depolarization/repolarization in cardiac tissues (atrial and His bundle). This points to a cohesive theme of potassium channels/transporters governing cardiac electrophysiology, with secondary terms on mechanosensation and hypoxia likely incidental annotations. Overall, the cluster appears to reflect potassium handling linked to cardiac action potentials.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097623","count":4},{"id":"GO:1990573","count":4},{"id":"GO:0098914","count":4},{"id":"GO:0050976","count":4},{"id":"GO:0030007","count":3}]},{"hash":"658612068648358790","title":"Ion transport and cyclic nucleotide signaling in excitable tissues","description":"This cluster is characterized by strong representations of potassium and sodium ion transport, calcium release from the sarcoplasmic reticulum, and responses to cAMP/cGMP, all of which drive excitability and muscle contraction in nerve/muscle cells. The presence of smooth muscle contraction and receptor guanylyl cyclase signaling further supports a cohesive theme of ion-channel\u2013cyclic nucleotide\u2013calcium signaling in excitable tissues, despite a few outliers like aerotaxis and pain terms.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0006939","count":3},{"id":"GO:0048680","count":3},{"id":"GO:0014808","count":3},{"id":"GO:0071321","count":2}]},{"hash":"1823144957970653032","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006914","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0042787","count":2}]},{"hash":"2193999446666561999","title":"Neural development and growth signaling","description":"The top GO terms cluster around neural development (brain and spinal cord development) and organismal growth, with supportive signals for growth pathways (TORC1 signaling, regulation of GTPase activity, phosphorylation/dephosphorylation) and mRNA transport, plus a note of actin nucleation relevant to neural development. Although there are no reported edges, these terms together point to a developmental/neural growth regulatory theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0050731","count":2}]},{"hash":"2015805288297377554","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0032066","count":1},{"id":"GO:0034476","count":1}]},{"hash":"613214562696148224","title":"Rho/Rac GTPase\u2013driven cytoskeletal remodeling","description":"These proteins are collectively enriched for actin cytoskeleton remodeling and cell motility, driven by Rho family GTPases. Terms like lamellipodium and filopodium assembly, Rac/Rho/Ras signaling, and small GTPase\u2013mediated transduction indicate dynamic cytoskeletal reorganization and adhesion-dependent spreading, which underlie cell migration and immune synapse formation. The heart development and B cell maturation terms may reflect broader developmental roles but do not override the dominant cytoskeletal signaling theme.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:0032633","count":4},{"id":"GO:0002344","count":4},{"id":"GO:0030032","count":4},{"id":"GO:0035020","count":4}]},{"hash":"1221181360446256007","title":"Plant cell wall remodeling and oxidative stress response","description":"The GO terms cluster around plant-type cell wall organization, lignin/lignin catabolic processes, hydrogen peroxide catabolic activity, and detoxification of reactive oxygen species, all pointing to cell wall remodeling and oxidative stress responses in plants. A few unrelated terms (e.g., autophagy targeting, differentiation) are present but appear less representative of the core theme. ","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009664","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0042744","count":2},{"id":"GO:0046274","count":2}]},{"hash":"165456155355750477","title":"Unknown","description":"The GO terms span diverse processes including membrane proton/sodium transport, Arp2/3-mediated actin nucleation, various aspects of cell proliferation and growth, mitotic spindle assembly, signaling (GCN2), and histone acetylation, with no single cohesive function tying them together. This makes it unclear to assign a specific, representative name.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015992","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0034314","count":1},{"id":"GO:0060770","count":1},{"id":"GO:0035264","count":1}]},{"hash":"2002403938939964470","title":"Aromatic amino acid and tetrapyrrole biosynthesis","description":"The top GO terms are dominated by biosynthetic processes: aromatic amino acid biosynthesis via chorismate, and tetrapyrrole biosynthesis including protoporphyrinogen IX, heme, and chlorophyll formation. While there are a few transmembrane transport terms, the central theme appears to be production of these metabolites, suggesting a metabolism-focused cluster rather than a single transport role.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":2},{"id":"GO:0009073","count":1},{"id":"GO:0009423","count":1},{"id":"GO:0006730","count":1},{"id":"GO:0019353","count":1}]},{"hash":"1735133629377513435","title":"Proteostasis and metal-stress signaling","description":"The set centers on ubiquitin-related regulation and protein turnover (polyubiquitination, ubiquitin ligase activity), plus stress-response processes including heavy-metal exposure (arsenic/cadmium) and circadian regulation. The mix suggests a theme of proteostasis under chemical stress, with ubiquitin-mediated pathways as a common mechanism, so a label focusing on proteostasis and stress signaling is representative.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051436","count":1},{"id":"GO:1903378","count":1},{"id":"GO:0042752","count":1},{"id":"GO:1902916","count":1},{"id":"GO:0046685","count":1}]},{"hash":"366260719876198117","title":"Vesicle trafficking and endocytosis","description":"Dominant terms describe intracellular protein transport, vesicle trafficking, clathrin-mediated endocytosis, and vesicle sorting to vacuole/MVB pathways, indicating a cohesive cluster of proteins involved in vesicle formation and endocytosis. A few outliers (NAD transport, tissue homeostasis) exist but do not define the main function.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0016183","count":1},{"id":"GO:0072583","count":1},{"id":"GO:1901998","count":1},{"id":"GO:0043328","count":1}]},{"hash":"1262566704137719668","title":"Mitochondrial tRNA aminoacylation and translation","description":"The co-occurring GO terms are dominated by translation and mitochondrial tRNA charging (valyl-, tryptophanyl-, tyrosyl-tRNA aminoacylation), suggesting a shared role in mitochondrial protein synthesis. While other terms relate to angiogenesis or steroid metabolism, the strongest signal is mitochondrial translation machinery.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0006438","count":1},{"id":"GO:0070183","count":1},{"id":"GO:0001570","count":1},{"id":"GO:0001525","count":1}]},{"hash":"863351046610790911","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019805","count":1},{"id":"GO:0050665","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0034354","count":1},{"id":"GO:0042420","count":1}]},{"hash":"2281891963566518006","title":"Unknown","description":"The top GO terms are scattered across fatty acid metabolism, osmolyte and secondary metabolite biosynthesis, vitamin-related processes, and even obsolete terms, with no clear shared function linking the proteins. There are no edges to suggest a cohesive interaction network, so a single interpretable theme cannot be established. ","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097089","count":1},{"id":"GO:0019491","count":1},{"id":"GO:0001561","count":1},{"id":"GO:1902181","count":1},{"id":"GO:0042400","count":1}]},{"hash":"2260958458629344311","title":"Cellular stress response and protein quality control","description":"The top GO terms point to mechanisms that maintain protein homeostasis under stress: stress granule disassembly, inclusion body assembly, and regulation of deubiquitinase activity, along with proteins involved in protein oligomerization. Energy-related terms (ATP metabolism and biosynthesis) support these quality-control and remodeling processes, with additional signals from chromatin assembly and microtubule dynamics suggesting broader cell-cycle integration. Together, these factors indicate a cluster of proteins coordinating stress responses and protein quality control rather than a single, narrow function.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0046034","count":1},{"id":"GO:0051013","count":1},{"id":"GO:0061641","count":1},{"id":"GO:2000158","count":1}]},{"hash":"1869447959387909651","title":"Ribosome biogenesis and translation regulation","description":"The proteins are enriched for translation and ribosome biogenesis processes (translation, ribosome biogenesis, preribosome assembly) and include regulators of translation fidelity, with some transcription-related terms present as co-regulated expression. A subset also links to antibiotic response, fitting stress-related modulation of the translation machinery. Taken together, the core theme is assembly and regulation of the protein synthesis apparatus.","confidence":"High","size":6,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0046677","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006353","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1609062868661425705","title":"Amino acid biosynthesis and catabolism","description":"This cluster shows multiple GO terms tied to amino acid metabolism, including L-serine catabolic, D-serine biosynthetic, L-homocysteine catabolic, L-tryptophan biosynthetic, transsulfuration, and cyanide metabolism. The convergence on both biosynthetic and degradative pathways for amino acids suggests a group of enzymes focused on amino acid metabolism. Some terms like response to morphine and obsolete pathway terms appear as outliers, likely annotation noise rather than core function. Therefore, the label reflects the dominant theme.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006565","count":2},{"id":"GO:0043418","count":2},{"id":"GO:0070179","count":2},{"id":"GO:0000162","count":2},{"id":"GO:0019295","count":2}]},{"hash":"1236736254308324584","title":"Cytosolic and mitochondrial translation machinery","description":"The top GO terms repeatedly reference translation and mitochondrial translation (cytosolic translation, mitochondrial translation/elongation, and translational fidelity), indicating a cohesive cluster centered on protein synthesis across cellular compartments. A few outliers (rhamnose catabolic process, hematopoietic differentiation, muscle contraction) appear noisy but do not override the core translation theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006415","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0019301","count":1},{"id":"GO:1902802","count":1},{"id":"GO:0002244","count":1}]},{"hash":"1543830144495522163","title":"Transcription and Translation Initiation Regulators","description":"The GO profile centers on DNA-templated transcription and the formation/regulation of translation initiation complexes, including cap-dependent and IRES-dependent initiation, suggesting proteins that coordinate gene expression at both transcriptional and translational levels. The presence of a viral response term hints at antiviral signaling connected to translation control. Together, these terms point to a cohesive theme of regulators that link transcription with initiation of translation and mRNA binding, with possible antiviral involvement.","confidence":"Medium","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0045787","count":1},{"id":"GO:0006417","count":1}]},{"hash":"1014935272113724740","title":"Neuronal signaling and membrane remodeling","description":"This cluster centers on neuronal communication and membrane dynamics: terms for neurotransmitter secretion, neuropeptide signaling, and dendrite extension point to neuronal signaling and morphology, while ER membrane organization and plasma membrane repair reflect ongoing membrane remodeling. Lipid signaling (phosphatidylinositol dephosphorylation) and fatty acid biosynthesis regulation further link to membrane composition and signaling pathways. A few terms (apoptotic regulation, mismatched repair, vascular remodeling) appear peripheral, but the core theme is neuronal signaling coupled with membrane dynamics and growth.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0043065","count":3},{"id":"GO:0007269","count":3},{"id":"GO:0090158","count":3},{"id":"GO:1903861","count":3},{"id":"GO:0060313","count":3}]},{"hash":"1937722279674517478","title":"Unknown","description":"The top GO terms span cell division, multiple metabolic pathways (retinol/retinal and androgen/testosterone), transcription regulation, stress responses, neuronal signaling, and even lipopolysaccharide biosynthesis, showing no single coherent function that binds the cluster together. Therefore a specific, descriptive label is not supported.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0009414","count":2},{"id":"GO:0042574","count":2},{"id":"GO:0008209","count":2},{"id":"GO:0042572","count":2}]},{"hash":"1899575424124919924","title":"Vacuolar transport and ion homeostasis","description":"Top GO terms point to vacuolar targeting, organization, and acidification, with accompanying proton and sodium transport and copper ion homeostasis, suggesting a common theme of vacuolar function and ion regulation. Although ribosome biogenesis and translation appear, they seem incidental to the dominant vacuolar/ion homeostasis signals. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":1},{"id":"GO:0006878","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0007033","count":1},{"id":"GO:0007035","count":1}]},{"hash":"120059585096424918","title":"Mitotic regulation and ubiquitination","description":"The cluster shows enrichment for mitotic processes (positive regulation of exit from mitosis; mitotic spindle assembly) and ubiquitin signaling (positive regulation of K48- and K63-linked ubiquitination), suggesting a module that controls cell cycle progression and protein turnover via ubiquitination. Other terms like translation appear less central and may reflect background associations. Overall, the dominant theme is cell-cycle control through ubiquitin pathways, so this label captures the core function of the cluster.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:1902530","count":1},{"id":"GO:0061178","count":1},{"id":"GO:0031536","count":1},{"id":"GO:1902524","count":1}]},{"hash":"1598760137553842070","title":"Protein Translation Components","description":"The top GO term is translation (GO:0006412), appearing twice, which suggests the core function of this cluster centers on the protein synthesis machinery. The remaining terms span diverse areas (development in liver/brain, nucleotide metabolism, sperm axoneme assembly, sensory detection), which likely reflects annotation breadth or multifunctional proteins, but translation remains the strongest shared theme. Confidence: Medium","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0001889","count":1},{"id":"GO:0046041","count":1},{"id":"GO:0007420","count":1},{"id":"GO:0046705","count":1}]},{"hash":"2289469714953364132","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":2},{"id":"GO:0034965","count":1},{"id":"GO:0006364","count":1},{"id":"GO:0001682","count":1},{"id":"GO:1905267","count":1}]},{"hash":"2263040357906677047","title":"Protein and polyamine acetylation","description":"Most terms are acetylation-related: N-terminal acetylations of various residues, lysine/H4 acetylation, and spermine acetylation, plus acetylation-associated metabolism (N-acetylglucosamine, mycothiol). A melatonin biosynthesis term (via acetyltransferases) and angiogenesis may be indirect connections. Overall, the cluster appears defined by acetylation-modifying activities across substrates, supporting a label centered on acetylation. ","confidence":"High","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030187","count":2},{"id":"GO:0017196","count":2},{"id":"GO:0043967","count":2},{"id":"GO:0010125","count":2},{"id":"GO:0018002","count":2}]},{"hash":"1530231832932613981","title":"Developmental Differentiation and Apoptosis Regulation","description":"The proteins show representation across multiple developmental contexts (brain patterning, neural and germline development, organ induction) and are linked to actin cytoskeleton remodeling and apoptotic signaling, suggesting a role in coordinating differentiation, morphogenesis, and cell fate decisions via cytoskeletal dynamics and apoptosis.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0022006","count":3},{"id":"GO:0030720","count":3},{"id":"GO:0090138","count":3},{"id":"GO:0043065","count":3},{"id":"GO:1903538","count":3}]},{"hash":"730614537892070490","title":"SRP-Dependent Translation and Membrane Targeting","description":"The cluster shows a clear emphasis on translation and SRP-mediated cotranslational targeting to membranes (GO:0006614, GO:0006617, GO:0006616, GO:0006412), i.e., ribosome-associated protein targeting to the membrane. Although a few terms are obscure or unrelated (DNA metabolism, septum assembly), the dominant theme is protein synthesis machinery and SRP-dependent membrane targeting, suggesting a function in ribosome-associated translocation and processing near membranes.","confidence":"Medium","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006614","count":1},{"id":"GO:0006617","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006259","count":1}]},{"hash":"843964663372806690","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071031","count":2},{"id":"GO:0034476","count":2},{"id":"GO:0000716","count":2},{"id":"GO:0071042","count":2},{"id":"GO:0070417","count":2}]},{"hash":"282756480424224387","title":"Microtubule Dynamics and Spindle Organization","description":"The top GO terms are dominated by microtubule-related processes: mitotic spindle elongation and assembly, plus-end directed microtubule sliding, and establishment/maintenance of microtubule cytoskeleton polarity, as well as nuclear migration along microtubules. The cerebellar layer structural organization terms point to neuronal cytoskeleton architecture, reinforcing the microtubule-centric theme; the stress granule disassembly term may reflect cytoskeletal interactions with RNA granules, but the core signal is microtubule dynamics and spindle/cytoskeleton organization.","confidence":"High","size":6,"edges":10,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000022","count":5},{"id":"GO:0000742","count":5},{"id":"GO:0035617","count":5},{"id":"GO:0030473","count":5},{"id":"GO:0001560","count":5}]},{"hash":"1710822591037537236","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015786","count":1},{"id":"GO:0036085","count":1},{"id":"GO:0034221","count":1},{"id":"GO:1990569","count":1},{"id":"GO:0046963","count":1}]},{"hash":"1626322229196661150","title":"Nuclear DNA replication and recombination","description":"The strongest terms are DNA replication and DNA recombination, both nuclear processes tied to genome maintenance. A related item, protein localization to the nuclear periphery, supports a nuclear/chromatin-associated theme. The other terms (peptide hormone signaling, apoptosis, development) are present but less represented, likely representing secondary annotations rather than the cluster\u2019s core function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0071375","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0048701","count":2}]},{"hash":"1574966105051071317","title":"Regulation of Signaling Pathways","description":"The GO terms cluster around regulation of signaling cascades (positive/negative regulation of TGF-beta receptor signaling, non-canonical NF-kappaB signaling, MAPK-related processes), along with related cellular responses (glucose stimulus, defense response) and developmental contexts (angiogenesis, meristem identity). This pattern suggests a shared theme of modulating signaling rather than a single specific process, hence the label.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0071333","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0014068","count":3},{"id":"GO:0045766","count":3}]},{"hash":"1272929734446128493","title":"Viral entry and replication in host","description":"This cluster is dominated by GO terms describing viral entry into host, uncoating, fusion of the viral membrane, and progression to replication and release, plus host-driven activation or latency of viral genomes. The presence of protein folding/isomerization terms suggests chaperone involvement in viral protein maturation. Overall, the terms align with a viral life cycle inside the host.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006457","count":2},{"id":"GO:0030260","count":2},{"id":"GO:0071492","count":2},{"id":"GO:0019061","count":2},{"id":"GO:0075713","count":2}]},{"hash":"2224076908634144316","title":"Cell-cycle and organelle assembly regulation","description":"Top GO terms point to growth control and signaling (response to pheromone, Hippo signaling, budding growth) alongside cell division and chromosome dynamics (kinetochore localization, chromosome passenger complex) and vesicle/organelle processes (endosome size, protein secretion, cilium assembly, tRNA wobble modification). This mix suggests a coherent theme of coordinating growth, division, and organelle biogenesis, justifying the label.","confidence":"Medium","size":6,"edges":8,"triangles":3,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019236","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0006547","count":5},{"id":"GO:0050709","count":5},{"id":"GO:0007117","count":5}]},{"hash":"634016877512781324","title":"Vesicle trafficking and cell polarity","description":"The top GO terms point to intracellular transport pathways (endosome-to-lysosome, endosome-to-melanosome, and Golgi-to-plasma membrane), with an accompanying term on establishing epithelial cell polarity, suggesting a cohesive theme around vesicle trafficking and spatial organization. The other terms are more diverse, but the strongest signal is vesicular transport and polarity. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008333","count":6},{"id":"GO:0035646","count":6},{"id":"GO:0045197","count":5},{"id":"GO:0006893","count":5},{"id":"GO:0035264","count":5}]},{"hash":"1692457152437484951","title":"RNA Splicing and Translation Initiation","description":"The top GO terms cluster around spliceosome-mediated mRNA splicing and splice-site recognition, with additional terms for small-subunit processome assembly and formation of the translation preinitiation complex, suggesting these proteins participate in RNA processing and early steps of ribosome assembly/translation\u2014reflecting a functional link between mRNA maturation and translation control.","confidence":"Medium","size":6,"edges":11,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0006376","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0000380","count":1},{"id":"GO:1905663","count":1}]},{"hash":"1652223460166382523","title":"RNA Splicing and ncRNA-Mediated Silencing","description":"The top GO terms point to core RNA processing activities\u2014spliceosome-mediated splicing, splice site recognition, and splicing complex assembly\u2014alongside ncRNA/miRNA-driven post-transcriptional gene silencing, indicating a cohesive theme around RNA processing and RNA-guided regulation of gene expression.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0006376","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0000380","count":2},{"id":"GO:1905663","count":2}]},{"hash":"1433869338882799673","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0006414","count":1},{"id":"GO:0061158","count":1},{"id":"GO:0001782","count":1}]},{"hash":"915234798300018833","title":"Unknown","description":"The top GO terms span xenobiotic response, neuronal development and differentiation, epithelial polarity, Golgi-to-plasma membrane trafficking, growth, RNA turnover, mitotic spindle assembly, cell migration, and sporulation. This broad mix shows no single coherent function linking all six proteins, so a specific label with confidence cannot be assigned.","confidence":"","size":6,"edges":8,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":4},{"id":"GO:0043524","count":4},{"id":"GO:0045197","count":2},{"id":"GO:0006893","count":2},{"id":"GO:0035264","count":2}]},{"hash":"721942529683637942","title":"ER Targeting and Signal Peptide Processing","description":"The top GO terms point to directing proteins to the endoplasmic reticulum and processing of signal peptides, both key to the secretory pathway. With six proteins and several connections among them, the cluster most likely represents ER targeting machinery and associated processing steps. One term is marked obsolete, but the remaining term still aligns with ER targeting.","confidence":"Medium","size":6,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006465","count":1},{"id":"GO:0045047","count":1}]},{"hash":"1103988132048416351","title":"Growth Factor Signaling and Cardiac/Immune Regulation","description":"The top GO terms point to broad signaling and stimulus-response pathways: PI-mediated signaling, EGF stimulus response, GPCR-PKC signaling, and GTPase activity regulation. Cardiac-related terms (heart development, cardiac muscle contraction) together with immune-related terms (B cell homeostasis, GM-CSF response) suggest a theme of signaling networks that govern cardiovascular and immune functions. There is one outlier term about fungal sporulation membrane formation, but the dominant signal is coordinated cell signaling and growth factor\u2013responsive regulation. This cluster seems best described as growth factor signaling and its cardiovascular/immune regulatory contexts.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0071364","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0048015","count":2},{"id":"GO:0032120","count":2}]},{"hash":"1568242814592291216","title":"Unknown","description":"The terms are a disparate mix (nuclear membrane reassembly; sister chromatid biorientation; cell death; ubiquitin regulation; NF-kappaB sequestration; innate immune signaling) with several obsolete GO entries, indicating no clear shared function across the proteins. Without a coherent theme, a single representative label cannot be confidently assigned.","confidence":"","size":6,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048213","count":1},{"id":"GO:1903094","count":1},{"id":"GO:0031468","count":1},{"id":"GO:0008219","count":1},{"id":"GO:0007253","count":1}]},{"hash":"1251701295030565673","title":"Viral infection cycle in host","description":"The cluster's top GO terms point to steps of viral life cycle inside a host: entry, uncoating, genome replication activation by host factors, replication, and release, plus proviral latency. These shared functions suggest a cohesive label about the host-virus infection process. A couple of terms like leukocyte migration and protein folding are more general cellular processes that can accompany infection but do not define the cluster core.","confidence":"High","size":6,"edges":8,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0050900","count":2},{"id":"GO:0006457","count":1},{"id":"GO:0030260","count":1},{"id":"GO:0071492","count":1},{"id":"GO:0019061","count":1}]},{"hash":"1081258939145605747","title":"Macrophage differentiation and immune response","description":"Based on the top GO terms, the cluster is dominated by immune-related processes: macrophage differentiation, defense response to protozoan, and cellular responses to IL-4, indicating involvement in macrophage activation and cytokine signaling. A few other terms point to RNA processing and transcription regulation, which may reflect incidental annotations or broad housekeeping functions in a mixed dataset. The strongest signal, however, is immune differentiation and response, supporting the chosen label.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030225","count":2},{"id":"GO:0042832","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0016310","count":1}]},{"hash":"1765703285756057831","title":"Redox detoxification and immune regulation","description":"The cluster\u2019s GO terms are dominated by oxidative stress and detoxification (oxidation-reduction processes, cellular oxidant detoxification, regulation of reactive oxygen species) along with immune/inflammatory modulation (response to lipopolysaccharide, negative regulation of acute inflammatory response, negative regulation of leukocyte proliferation). This suggests the proteins collectively participate in maintaining redox balance while modulating inflammatory signaling, rather than representing a single developmental pathway; a couple growth-related terms appear secondary to this core theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0045669","count":2},{"id":"GO:0070458","count":2},{"id":"GO:0035264","count":2},{"id":"GO:2000774","count":2}]},{"hash":"149098157188492062","title":"Nucleotide Metabolism and Ribose Supply","description":"These proteins show enrichment for the pentose-phosphate shunt (providing ribose-5-phosphate) and for nucleoside/nucleotide salvage and interconversion (guanosine, inosine, cytidine, purine nucleosides). The common theme is nucleotide biosynthesis and ribose availability, tying together PPP flux with nucleotide pool maintenance. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006098","count":2},{"id":"GO:0046109","count":1},{"id":"GO:0009052","count":1},{"id":"GO:0006014","count":1},{"id":"GO:0006216","count":1}]},{"hash":"1504536723932723511","title":"Mitotic division and ER-Golgi trafficking","description":"This cluster is driven by GO terms tied to cell division and mitosis (mitotic spindle assembly; mitotic cell cycle; cell division; cell population proliferation) and by vesicle trafficking between the endoplasmic reticulum and Golgi apparatus (ER-Golgi transport; retrograde Golgi-to-ER transport; COPII-coated vesicle budding). The co-occurrence of these processes suggests proteins involved in both mitotic progression and secretory pathway dynamics, with brain development and multicellular growth reflecting the broader developmental context of proliferative and biosynthetic activity. Overall, the shared theme appears to be coordination of cell division with secretory vesicle trafficking. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0006888","count":2}]},{"hash":"1993650760220481575","title":"Germline development and germ plasm organization","description":"The terms cluster around germline specification and germ plasm dynamics in Drosophila, including oocyte/pole plasm localization (oskar), P granule organization, maternal determinants for axis formation, piRNA processing, and spermatogenesis, indicating a cohesive theme of germline development and germ plasm regulation.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007286","count":1},{"id":"GO:0030720","count":1},{"id":"GO:0030719","count":1},{"id":"GO:0009566","count":1},{"id":"GO:0007277","count":1}]},{"hash":"255453869148552294","title":"RNA methylation and RNA processing","description":"The terms cluster around methylation of RNA species (rRNA, tRNA, mRNA capping) and RNA processing steps such as splicing and translation initiation, suggesting a shared focus on RNA modification and maturation. While there is a stray term about DNA methylation, the dominant signals are RNA-centric\u2014methylation and processing events critical for RNA maturation and translation readiness.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080180","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0030488","count":1},{"id":"GO:0009452","count":1},{"id":"GO:0006479","count":1}]},{"hash":"556897281849022514","title":"Unknown","description":"The top GO terms are highly diverse and non-overlapping (response to X-ray, mammary gland proliferation, transcription regulation, CDK activity, autophagy, chaeta development, plant stomatal opening, lactation, viral transcription, etc.), and there are no edges or coherent shared functions among the proteins. This suggests the cluster does not reflect a single, interpretable biological theme, so a specific functional label isn\u2019t reliably identifiable.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010165","count":1},{"id":"GO:0033601","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0045737","count":1},{"id":"GO:1905866","count":1}]},{"hash":"666350553176705242","title":"RNA Pol II Transcription Regulation","description":"This cluster is dominated by GO terms related to transcription initiated by RNA polymerase II (RNA-templated transcription; transcription initiation at RNA Pol II promoter). There are also terms about regulation of translation initiation under stress, suggesting broader gene expression control. A few entries (e.g., DMAPP biosynthesis, obsolete terms) seem unrelated or noisy. Overall, the proteins cluster around RNA Pol II\u2013mediated transcription regulation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001172","count":2},{"id":"GO:0050992","count":1},{"id":"GO:0097394","count":1},{"id":"GO:1905098","count":1},{"id":"GO:0010590","count":1}]},{"hash":"1311885456210053097","title":"Angiogenesis Regulation and Metabolism","description":"The term set includes several items that suppress vascular development (negative regulation of vasculogenesis, negative regulation of endothelial cell differentiation, and negative regulation of VEGF signaling), suggesting an anti-angiogenic core. Other terms indicate metabolic activity (ATP synthesis coupled electron transport, ferredoxin metabolism, xanthine and phenylacetate catabolism) and ion transport, which align with cellular metabolism but are less cohesive with the angiogenesis theme. Some terms (lactation, nitrogen fixation) are outliers, so the overall cluster centers on vascular regulation with accompanying metabolism. Medium","confidence":"Medium","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009115","count":2},{"id":"GO:2001213","count":2},{"id":"GO:0042773","count":2},{"id":"GO:0006814","count":2},{"id":"GO:1900747","count":2}]},{"hash":"23739354412985433","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080167","count":1},{"id":"GO:0009813","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0000413","count":1},{"id":"GO:0015031","count":1}]},{"hash":"2176273065857659083","title":"Ubiquitin-mediated protein degradation","description":"The dominant GO terms point to ubiquitination processes (protein ubiquitination, polyubiquitination, autoubiquitination, K63/K48-linked ubiquitination) and ubiquitin-dependent protein catabolic processes, including ERAD. Together these indicate a cluster of proteins involved in tagging substrates for proteasomal degradation, with vitamin D response and TNF signaling appearing as related contextual functions.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0000209","count":2}]},{"hash":"1660243666642686619","title":"Unknown","description":"The proteins in this cluster touch a highly mixed set of GO terms, including uracil catabolic process, antibiotic biosynthetic process, ferrichrome biosynthetic process, thiamine biosynthetic process, regulation of DNA-templated transcription, and even multicellular development and dopamine metabolism. Several terms are marked obsolete, and there are no reported interactions (Edges: 0). This combination does not reveal a single coherent function or pathway linking the proteins, so a specific functional label cannot be confidently assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006212","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0031169","count":1}]},{"hash":"386840850137610157","title":"Chromatin remodeling and histone modification","description":"Most of the top GO terms point to chromatin-related processes: nucleosome density, histone exchange/modification (including H2B ubiquitination), and heterochromatin maintenance/assembly, plus regulation of transcription by RNA polymerase II. While a few terms are obsolete or unrelated (calcium signaling, morphogenesis), the dominant theme across the cluster is chromatin regulation. Confidence: Medium","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900050","count":1},{"id":"GO:0060303","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0071894","count":1},{"id":"GO:0042766","count":1}]},{"hash":"1475442514017064937","title":"Membrane transporters for metabolites and xenobiotics","description":"The top GO terms are dominated by membrane transport activities, including xenobiotic, sialic acid, fucose, urate, and potassium ion transport, suggesting these proteins function as diverse substrate transporters across membranes. A secondary term on metabolism and stress response aligns with transporter regulation under nutrient limitation. This supports labeling the cluster as membrane transporters for metabolites and xenobiotics.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042891","count":1},{"id":"GO:0006004","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0015739","count":1},{"id":"GO:0042908","count":1}]},{"hash":"1433535891556697893","title":"Unknown","description":"The top GO terms cover diverse processes including one-carbon metabolism, formate catabolism, and phosphatidylcholine biosynthesis, but also stress/nutrient response terms. Many items are obsolete, and there is no single dominant function linking the proteins. Because of this heterogeneity, there is no clear, specific label that captures the cluster's biology.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006730","count":1},{"id":"GO:0019551","count":1},{"id":"GO:1903758","count":1},{"id":"GO:0001666","count":1},{"id":"GO:0009097","count":1}]},{"hash":"1773415654044181489","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":2},{"id":"GO:0030488","count":2},{"id":"GO:0018026","count":1},{"id":"GO:0000453","count":1},{"id":"GO:0002098","count":1}]},{"hash":"1042990995672588610","title":"Unknown","description":"The GO terms in this cluster span several unrelated biological areas, including energy metabolism (ATP synthesis, catabolic processes), ion transport, various redox/ferredoxin-related processes, nitrogen fixation, and vascular/endothelial development regulation. There isn\u2019t a cohesive, single function tying these proteins together, so a clear, intuitive cluster label isn\u2019t identifiable.","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009115","count":2},{"id":"GO:2001213","count":2},{"id":"GO:0042773","count":2},{"id":"GO:0006814","count":2},{"id":"GO:1900747","count":2}]},{"hash":"424737326885787141","title":"Glycolysis and TCA Cycle","description":"The top GO terms are dominated by central carbon metabolism: glycolytic process, pyruvate metabolism, gluconeogenesis, isocitrate and 2-oxoglutarate metabolism, and the TCA cycle, with an accompanying phosphorylation term. This pattern strongly indicates a cluster of proteins involved in sugar catabolism and energy production via glycolysis and the citric acid cycle. An outlier term for female gonad development is likely annotation noise rather than a meaningful cluster-driven function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":1},{"id":"GO:0009401","count":1},{"id":"GO:0006096","count":1},{"id":"GO:0006090","count":1},{"id":"GO:0006094","count":1}]},{"hash":"160636392603492898","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097171","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0009244","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0016311","count":2}]},{"hash":"900632667157333438","title":"Glycolysis-Linked Carbohydrate Metabolism","description":"The prominent GO term is canonical glycolysis (GO:0061621) with related carbohydrate metabolism terms such as fructose biosynthesis, supporting a central theme of sugar metabolism. Other terms are more peripheral (responses to drugs, copper ion, plant lignin biosynthesis), but the strongest signal ties to glycolytic flux and carbohydrate processing, justifying a glycolysis-related metabolic cluster.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0061621","count":2},{"id":"GO:0019518","count":1},{"id":"GO:0006069","count":1},{"id":"GO:0097327","count":1}]},{"hash":"706264096669759930","title":"Xenobiotic/antibiotic stress response","description":"The GO terms cluster around responses to xenobiotics, lipopolysaccharide, and antibiotics, plus related transcription and metabolic terms, suggesting a shared theme of defense or stress response to external chemical stimuli.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019518","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0042572","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0032496","count":2}]},{"hash":"381378799267152103","title":"Plant stress response and metabolism","description":"The terms point to plant defense signaling (salicylic acid, camalexin) and stress-adaptation (aerenchyma), plus several catabolic and lipid remodeling processes, suggesting a cluster of plant stress response with metabolic remodeling components.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0042136","count":2},{"id":"GO:1901183","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0030245","count":2}]},{"hash":"751835018765155942","title":"Unknown","description":"The GO terms span diverse processes (protein transport, metabolism, signaling, RNA processing, DNA repair, apoptosis, and stress responses) with no clear, unifying function for the protein set, 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:0015031","count":2},{"id":"GO:0006196","count":2},{"id":"GO:0009742","count":2},{"id":"GO:1903799","count":2},{"id":"GO:0051321","count":2}]},{"hash":"1396056190422154304","title":"Developmental Growth and Cellular Organization","description":"This cluster includes terms related to organ and neural development (brain, liver), epithelial polarity and tight junction assembly, and fundamental protein synthesis and complex localization processes (ribosome biogenesis, translation, protein-containing complex localization). Together, they point to development-driven growth and the organization/assembly of cellular structures.","confidence":"Medium","size":5,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0045197","count":2},{"id":"GO:0000001","count":2}]},{"hash":"829213214392354496","title":"Microtubule Organization and Cell Division","description":"This cluster centers on cytoskeletal dynamics and division, with multiple terms for microtubule organization, nucleation, spindle functions, and the cell cycle (plus septum assembly). These repeatedly point to microtubule-based processes governing cell division, making Microtubule Organization and Cell Division the best descriptive label. Some terms like neuron differentiation and cytokine response are less central.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006470","count":2},{"id":"GO:0051258","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0031122","count":2},{"id":"GO:0030182","count":2}]},{"hash":"2156016778382715667","title":"Viral entry, uncoating, and replication","description":"The GO terms converge on stages of viral infection: entry into the host, membrane fusion, uncoating, genome activation and replication, and eventual release, including proviral latency establishment and host-driven activation of viral replication. A couple of terms about protein folding and isomerization likely reflect chaperone involvement during these processes. Overall, the cluster centers on the viral infection cycle and its progression inside the host.","confidence":"High","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006457","count":2},{"id":"GO:0030260","count":2},{"id":"GO:0071492","count":2},{"id":"GO:0019061","count":2},{"id":"GO:0075713","count":2}]},{"hash":"1298374914363840246","title":"Cofactor Biosynthesis and RNA Modification","description":"The top GO terms are various biosynthetic processes for cofactors (e.g., protoporphyrinogen IX, biotin, lipoate, molybdopterin, PQQ, queuosine) and RNA modification steps (rRNA base methylation, tRNA methylation). This suggests a cluster centered on biosynthetic pathways producing cofactors and modifying RNA, rather than a single unified function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006782","count":2},{"id":"GO:0018189","count":2},{"id":"GO:0042426","count":2},{"id":"GO:0070475","count":2},{"id":"GO:0008616","count":2}]},{"hash":"126462341498206865","title":"ER Stress Response and Protein Quality Control","description":"The cluster prominently features GO terms tied to endoplasmic reticulum processes\u2014protein folding in the ER, ER-associated degradation via the ubiquitin-proteasome system, and regulation of translation initiation under ER stress\u2014indicating a cohesive proteostasis/ER stress theme. Some terms relate to development or other processes, but the ER stress/protein QC theme is strongest.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048024","count":2},{"id":"GO:0009408","count":1},{"id":"GO:0071630","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0070389","count":1}]},{"hash":"366061039786874565","title":"Unknown","description":"The top terms cover stress response, hormone signaling, calcium signaling, various metabolic processes, and development, with no single dominant function linking them. This suggests the proteins have diverse roles rather than a coherent, shared pathway, so the cluster cannot be meaningfully labeled beyond Unknown.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009414","count":2},{"id":"GO:0046427","count":1},{"id":"GO:0071277","count":1},{"id":"GO:0097066","count":1},{"id":"GO:0006707","count":1}]},{"hash":"1956746630308225702","title":"Translation machinery and mRNA decay","description":"The terms center on translation across multiple stages (initiation, elongation, termination) and mRNA decay, with selenocysteine incorporation, indicating a cohesive translation/mRNA turnover module; a couple ancillary terms (glial proliferation, antibiotic response) are likely incidental.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0001514","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006413","count":2}]},{"hash":"353149637652494381","title":"Transmembrane Ion Transport","description":"The cluster is enriched for GO terms describing monoatomic and potassium ion transmembrane transport, indicating a shared role in moving ions across membranes. While a few ER-related terms suggest potential ER-associated roles for some proteins, the strongest and most consistent signal is ion transport across membranes.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0099133","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0009408","count":1},{"id":"GO:0046685","count":1}]},{"hash":"1915587891002067943","title":"Membrane trafficking and remodeling","description":"The top GO terms cluster around endosome-to-endosome transport, plasma membrane tubulation, vacuole-ER tethering, and prospore/membrane formation, plus phosphatidylinositol-mediated signaling and podosome assembly. Although translation appears, the dominant signals point to membrane dynamics and intracellular transport, indicating a cluster of proteins involved in membrane remodeling and vesicle trafficking rather than a single metabolic pathway.","confidence":"Medium","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0010252","count":1},{"id":"GO:0097320","count":1},{"id":"GO:0048310","count":1},{"id":"GO:0045022","count":1}]},{"hash":"1209337393626022574","title":"Ribosome Biogenesis and Translation","description":"The top terms cluster around ribosome assembly and processing (ribosome biogenesis, ribosomal subunit biogenesis, ribosomal large subunit export from nucleus, cytoplasmic translation, rRNA processing), indicating a shared function in ribosome production and use; the other terms seem ancillary or less central to the core function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0090529","count":1},{"id":"GO:1903833","count":1},{"id":"GO:0007049","count":1}]},{"hash":"1585029521554796157","title":"Inflammation and heat-shock protein response","description":"The top GO terms indicate immune activation (positive regulation of IL-6 production; positive regulation of T cell\u2013mediated immune response to tumor cells) together with cellular stress and protein quality control (response to heat; detection of misfolded protein; chaperone-related activities). This points to a cluster where inflammatory signaling co-occurs with proteostasis/heat-shock responses, suggesting cells under inflammatory and heat-stress conditions engage protein-folding quality control. Some terms are obsolete, but the core theme remains immune/stress and proteostasis.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:2000778","count":5},{"id":"GO:1904851","count":5},{"id":"GO:0009408","count":5},{"id":"GO:0014823","count":5},{"id":"GO:0052212","count":5}]},{"hash":"580279270767656031","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":4},{"id":"GO:0000464","count":3},{"id":"GO:0000245","count":3},{"id":"GO:0071031","count":2},{"id":"GO:0000716","count":2}]},{"hash":"34995100818034451","title":"DNA replication and chromatin regulation","description":"The cluster is dominated by terms related to DNA replication initiation and the assembly of replication machinery (pre-replicative complex, MCM complex, mitotic initiation) along with chromatin effects at telomeres and subtelomeric regions, suggesting a shared role in replication and chromatin maintenance during the cell cycle. Some terms (bacteriochlorophyll biosynthesis, gamete generation, xenobiotic response) appear unrelated and may reflect annotation noise rather than core clustering signals.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030494","count":2},{"id":"GO:0031939","count":2},{"id":"GO:0007292","count":2},{"id":"GO:0006267","count":2},{"id":"GO:0006348","count":2}]},{"hash":"1260515538428832045","title":"Unknown","description":"The GO terms span very diverse processes, including nuclear export regulation, protein dephosphorylation, various signaling pathways (TGF-beta/BMP, NF-kappaB), developmental processes (meristem identity, germ-line masculinization), and even photosystem adjustments, indicating no single cohesive function ties these proteins together.","confidence":"","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0035970","count":4},{"id":"GO:0030512","count":3},{"id":"GO:0042006","count":3},{"id":"GO:0042347","count":3}]},{"hash":"1975735663276482266","title":"Inflammation and tissue remodeling","description":"The cluster includes terms tied to immune/inflammatory responses (acute-phase response, complement activation, neutrophil-mediated killing) and tissue remodeling processes (angiogenesis, collagen catabolic process, fibrinolysis), suggesting a coherent theme of host defense coupled with tissue remodeling, despite some transcription-related terms.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":2},{"id":"GO:0007586","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0044130","count":1},{"id":"GO:0070946","count":1}]},{"hash":"1923346144515384172","title":"Chromatin dynamics and DNA repair","description":"The cluster includes terms related to chromatin structure and organization (nucleosome mobilization, pericentric heterochromatin formation), genome maintenance (DNA damage tolerance, meiotic gene conversion), and transcription regulation in the nucleolus (rRNA transcription by RNA Pol I). Ubiquitination of proteins also aligns with signaling and regulation in DNA damage response. Although several terms are obsolete, the dominant theme ties chromatin dynamics to genome integrity and regulation. This makes the label concise and representative of the cluster\u2019s functional signals.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":3},{"id":"GO:1902661","count":2},{"id":"GO:0042766","count":2},{"id":"GO:0031508","count":2},{"id":"GO:0042790","count":2}]},{"hash":"1959596396921891412","title":"Splicing and ubiquitin regulation","description":"This cluster is dominated by GO terms for mRNA splicing via the spliceosome and for ubiquitin-related processes (deubiquitination with several linkage types and ubiquitination), suggesting proteins that connect RNA processing with ubiquitin signaling. While a couple of other terms touch RNA maintenance and repair, the core signal is coordinated RNA processing coupled to ubiquitin modification, pointing to regulators of spliceosome function and ubiquitin-mediated control.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0071947","count":2},{"id":"GO:0070536","count":2},{"id":"GO:1990168","count":2},{"id":"GO:0035523","count":2}]},{"hash":"2210456153839928379","title":"RNA Splicing and Processing Machinery","description":"The top GO terms are dominated by mRNA splicing and spliceosome-related processes (cis splicing via spliceosome, splice site recognition, alternative mRNA splicing) and also include small-subunit processome assembly and translation preinitiation complex formation, indicating a cluster of RNA processing and ribosome biogenesis factors. Some terms are obsolete or peripheral, but the core theme is RNA maturation and processing ahead of translation.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0006376","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0000380","count":1}]},{"hash":"534728926496811431","title":"SCF-Dependent Proteasomal Degradation","description":"The top GO terms emphasize ubiquitin-dependent protein catabolic processes, especially SCF-dependent proteasomal degradation, suggesting these proteins are linked to targeted protein turnover via the ubiquitin-proteasome system. Other terms (neuron differentiation, T cell homeostasis, cell division) may reflect broader roles of proteostasis in diverse processes, but the recurring theme is proteolysis through ubiquitination and proteasome activity.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0030182","count":2},{"id":"GO:0043029","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1405170260339342680","title":"Carbohydrate metabolism and glycosylation","description":"The Top Terms include several sugar-related metabolic processes (glucose, sucrose, starch biosynthesis), responses to sugars and mannitol, and GPI anchor biosynthesis, plus mycothiol biosynthesis, which ties to carbohydrate chemistry in some bacteria. Together these suggest a theme centered on carbohydrate handling and glycosylation pathways, rather than a single narrowly defined function. Confidence: Medium","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":1},{"id":"GO:0007631","count":1},{"id":"GO:0010125","count":1},{"id":"GO:0005985","count":1},{"id":"GO:0009414","count":1}]},{"hash":"1400856534296049244","title":"Redox Homeostasis and Xenobiotic Stress Response","description":"The strongest signal is cellular redox homeostasis, complemented by a xenobiotic stimulus response, suggesting a stress-related module focused on redox balance and detoxification. Additional weaker terms for mRNA stability regulation, cellular response to cAMP, and cell cycle regulation imply broader regulatory activity rather than a single pathway.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:2000327","count":1},{"id":"GO:0080111","count":1},{"id":"GO:1900087","count":1},{"id":"GO:0043488","count":1}]},{"hash":"1250221918607598034","title":"Developmental signaling and cell cycle regulation","description":"The top GO terms reveal involvement in development (neuron development, keratinocyte differentiation) and major signaling pathways (Wnt, Hippo), plus regulation of the cell cycle (CDK activity, kinetochore localization). This suggests a group of proteins that modulate developmental signaling and proliferation, not a single pathway.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032435","count":2},{"id":"GO:0048666","count":2},{"id":"GO:0035335","count":2},{"id":"GO:0060044","count":2},{"id":"GO:0090263","count":2}]},{"hash":"2146051181455824700","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090394","count":2},{"id":"GO:0007021","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0034976","count":2},{"id":"GO:0007399","count":2}]},{"hash":"151073634133331195","title":"Neural Development and Stress Signaling","description":"The top GO terms strongly point to neural development (forebrain development, neural tube closure), suggesting a neural context. Other terms indicate cellular signaling and stress responses (phosphorylation, ER stress\u2013related apoptotic signaling) and some immune/defense or broad developmental terms, which may reflect broader roles of the proteins or annotation noise. Overall, there is a plausible though not tight connection to neural development with accompanying stress signaling, so the label is tentative. ","confidence":"Low","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0006349","count":2}]},{"hash":"1327511469488427443","title":"Developmental gene expression and RNA processing","description":"The top terms center on developmental processes (forebrain and neural tube development, skeletal system development) alongside RNA-level regulation (mRNA splicing via spliceosome, DNA-templated transcription). Some stress-related terms are present, but the dominant theme ties developmental regulation to RNA processing. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071276","count":2}]},{"hash":"1773661644561720530","title":"Neuronal signaling and dendrite dynamics","description":"The GO terms cluster around neuronal communication (neurotransmitter secretion, neuropeptide signaling) and dendritic remodeling (positive regulation of dendrite extension), with supporting membrane-related processes (ER membrane organization, plasma membrane repair) that fit neuronal membrane dynamics and synaptic maintenance. While other terms are broader, the core theme centers on neural signaling and dendrite/membrane remodeling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":1},{"id":"GO:0007269","count":1},{"id":"GO:0090158","count":1},{"id":"GO:1903861","count":1},{"id":"GO:0060313","count":1}]},{"hash":"2071817979540860666","title":"DNA Damage Response and Chromatin Maintenance","description":"The cluster\u2019s GO terms converge on nuclear genome maintenance and chromatin regulation: protein sumoylation (modulating transcription and repair), telomere maintenance, histone mRNA catabolic process, and classical nonhomologous end joining for DSB repair. Muscle differentiation terms are present but less representative of the core function. Overall, the proteins appear linked to genome integrity and chromatin dynamics rather than cytoskeletal or extracellular signaling.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":2},{"id":"GO:0051152","count":1},{"id":"GO:0010667","count":1},{"id":"GO:0071475","count":1},{"id":"GO:2000727","count":1}]},{"hash":"2178436379606789358","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045723","count":2},{"id":"GO:0001822","count":1},{"id":"GO:0061158","count":1},{"id":"GO:0043496","count":1},{"id":"GO:0051344","count":1}]},{"hash":"450242147792271184","title":"Chromatin modification and transcription initiation","description":"The dominant GO terms point to chromatin regulation (histone deubiquitination, histone H3 acetylation) and the transcription initiation machinery (DNA-templated transcription initiation, RNA polymerase II preinitiation complex assembly). Developmental and cell-cycle terms are present but secondary to the chromatin\u2013transcription theme, suggesting these proteins function in modifying chromatin to enable transcription initiation.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016578","count":1},{"id":"GO:0006352","count":1},{"id":"GO:0043966","count":1},{"id":"GO:0070365","count":1},{"id":"GO:0035264","count":1}]},{"hash":"678097293736044093","title":"Neural tube development and ciliogenesis with PCP signaling","description":"The term set centers on neural tube closure and brain development, plus dorsal-ventral patterning and ciliary processes (ciliary assembly, stereocilium organization) and Wnt/PCP signaling, indicating a cohesive program of early neural development coordinated by ciliary and planar cell polarity pathways.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001843","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0001944","count":1},{"id":"GO:1990403","count":1},{"id":"GO:1901620","count":1}]},{"hash":"2288380853772847833","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032066","count":1},{"id":"GO:0034476","count":1},{"id":"GO:0071042","count":1},{"id":"GO:0071044","count":1},{"id":"GO:0061820","count":1}]},{"hash":"1206099796944907426","title":"Chromatin-Linked Transcription Regulation","description":"This cluster centers on transcription control by RNA polymerase II and chromatin dynamics, highlighted by terms for negative regulation of Pol II transcription, preinitiation complex regulation, histone H3 acetylation, and CENP-A\u2013dependent chromatin assembly, suggesting a cohesive role in regulating transcription via chromatin state.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:2000306","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0045898","count":2},{"id":"GO:0043457","count":2}]},{"hash":"1757668791519718712","title":"Vacuolar maintenance and autophagy cluster","description":"The Top Terms point to vacuolar processes: vacuolar transport, vacuole fusion, and microautophagy, plus polyphosphate biosynthesis. Together these suggest roles in vacuole dynamics and autophagy-related pathways. A minor cell polarity term appears but is less representative. With no edges among the proteins, this cluster may reflect shared annotation rather than direct interactions, supporting a cohesive vacuolar/autophagy theme.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000769","count":1},{"id":"GO:0048016","count":1},{"id":"GO:0007034","count":1},{"id":"GO:0006799","count":1},{"id":"GO:0016237","count":1}]},{"hash":"654757909288811909","title":"Unknown","description":"The listed GO terms are highly diverse (purine catabolism, vascular and endothelial regulation, mitochondrial ATP synthesis, ion transport, lactation, various catabolic and metabolic processes, nitrogen fixation), with no single shared function; the proteins have no edges, suggesting weak or no functional linkage. This makes it inappropriate to assign a cohesive biological theme, so Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009115","count":1},{"id":"GO:2001213","count":1},{"id":"GO:0042773","count":1},{"id":"GO:0006814","count":1},{"id":"GO:1900747","count":1}]},{"hash":"1498573007141601448","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061158","count":2},{"id":"GO:1903883","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0010586","count":2},{"id":"GO:1903265","count":2}]},{"hash":"872905754341899787","title":"Unknown","description":"There are no GO terms or functional signals provided for this cluster, and there are no edges or interactions (Max Degree 0). With no shared functional annotations or connectivity, a meaningful, specific label cannot be inferred.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1195382652474465092","title":"Protein homeostasis and stress response","description":"The top GO terms point to stress-related protein handling (stress granule disassembly, inclusion body assembly), proteostasis regulation (positive regulation of ubiquitin-specific protease activity), and energy management (ATP metabolic and biosynthetic processes). Although terms span different cellular processes and organelles, they collectively suggest a theme around maintaining proteome integrity and energy supply under cellular stress, justifying a label like \u201cProtein homeostasis and stress response.\u201d Given the small, heterogeneous set, the confidence is Medium.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046034","count":1},{"id":"GO:0051013","count":1},{"id":"GO:0061641","count":1},{"id":"GO:2000158","count":1},{"id":"GO:2001171","count":1}]},{"hash":"1053005518982055486","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006296","count":2},{"id":"GO:0006294","count":2},{"id":"GO:0006295","count":2},{"id":"GO:0036297","count":2},{"id":"GO:0006293","count":1}]},{"hash":"2068274407980312417","title":"Cellular Stress Response and Apoptosis","description":"Top GO terms cluster around stress-related processes, including cellular response to reactive oxygen species, hypoxia detection, and p53-mediated apoptotic signaling, with supportive terms for protein folding and transcriptional regulation. Although a few terms relate to metabolism or development, the predominant pattern points to stress adaptation and cell survival pathways, suggesting a shared function in stress response or apoptotic decision-making.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010906","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0017006","count":1},{"id":"GO:0072332","count":1},{"id":"GO:0034614","count":1}]},{"hash":"1455271319424170568","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046726","count":2},{"id":"GO:0006293","count":1},{"id":"GO:0006296","count":1},{"id":"GO:0016055","count":1},{"id":"GO:0042769","count":1}]},{"hash":"176327158982519788","title":"Mitochondrial electron transport and ATP synthesis","description":"This cluster is dominated by terms tied to mitochondrial energy production: electron transport (GO:0006123), proton motive force-driven ATP synthesis (GO:0015986), mitochondrial respirasome assembly (GO:0097250), and aerobic respiration (GO:0009060). Additional terms on protein complex oligomerization (GO:0035786) support assembly of mitochondrial protein complexes. A single outlier term on substantia nigra development is likely incidental. Together, they suggest a mitochondrial respiration/ATP synthesis function.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015986","count":1},{"id":"GO:0035786","count":1},{"id":"GO:0021762","count":1},{"id":"GO:0097250","count":1},{"id":"GO:1902600","count":1}]},{"hash":"123057460202481040","title":"Nucleotide Metabolism and Salvage","description":"The top GO terms are dominated by nucleotide biosynthesis and phosphorylation (ADP, CDP, AMP salvage, purine ribonucleotide interconversion, GTP/ITP metabolism), indicating a shared function in nucleotide metabolism and energy charge maintenance. Developmental terms appear peripheral rather than central to the cluster\u2019s core function.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001889","count":2},{"id":"GO:0046041","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0046705","count":2},{"id":"GO:0046940","count":2}]},{"hash":"1701786467006851444","title":"Unknown","description":"The top GO terms span a wide range of very different biosynthetic processes (putrescine, protoporphyrinogen IX, beta-alanine, biotin, ectoine, antibiotic, lysine biosynthesis) and also include unrelated entries like responses to flooding and behavioral responses to cocaine. With only a single edge and no clear shared function or pathway tying these proteins together, there isn't a coherent theme to name a specific cluster; thus Unknown. ","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009447","count":1},{"id":"GO:0006782","count":1},{"id":"GO:0010121","count":1},{"id":"GO:0019483","count":1},{"id":"GO:0009102","count":1}]},{"hash":"1700869442436132423","title":"Folate-dependent one-carbon metabolism","description":"These proteins strongly group around folate and one-carbon metabolic processes: multiple terms for tetrahydrofolate interconversion and biosynthesis, one-carbon metabolism, dihydrofolate metabolism, glycine biosynthesis, and methylation. Although a couple terms touch on tissue contexts (intestinal epithelial cell maturation, liver regeneration) these are peripheral to the core metabolic theme. Overall, the cluster appears to be centered on folate-associated one-carbon metabolism and related methylation/glycine pathways.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006730","count":1},{"id":"GO:0035999","count":1},{"id":"GO:0006545","count":1},{"id":"GO:0060574","count":1}]},{"hash":"1286761995318954588","title":"Unknown","description":"The GO terms include redox homeostasis, quinolinate and dihydrolipoamide metabolism, sterol/cholesterol pathways, alternative splicing, histone deacetylation, and differentiation/hormone regulation. This broad mix lacks a single, cohesive function that ties all four proteins together, so a specific label would be speculative.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0016575","count":1},{"id":"GO:0019805","count":1},{"id":"GO:0051068","count":1}]},{"hash":"186148549001072356","title":"Diverse metabolite biosynthesis","description":"The top GO terms point to a broad set of biosynthetic processes (alkaloids, steroids, retinoids, fatty acids, sphingolipids, vitamins, pigments, antibiotics) across different biological contexts. There isn't a single cohesive pathway; rather, the common theme is involvement in various metabolite biosynthesis, suggesting a cluster of proteins linked to diverse biosynthetic activities rather than a single function.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":1},{"id":"GO:0009710","count":1},{"id":"GO:0006704","count":1},{"id":"GO:0002138","count":1},{"id":"GO:0006710","count":1}]},{"hash":"1454938685229229468","title":"Nuclear transcription and chromatin regulation","description":"The cluster shows strong signals for transcriptional control (negative regulation of RNA Pol II) and chromatin organization, along with related nuclear processes like mRNA surveillance, translation preinitiation complex formation, and proteasome assembly, pointing to a core theme of gene expression regulation and protein processing in the nucleus. Some terms (e.g., collagen catabolic process) are less connected, representing noise rather than the main theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0030574","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0035551","count":1}]},{"hash":"360638856783476983","title":"GPCR Signaling and Developmental Regulation","description":"The top GO terms point to GPCR-related processes (G protein-coupled receptor internalization; tachykinin receptor signaling) and negative regulation of signaling pathways, alongside developmental processes such as heart rudiment formation and intramembranous ossification. The mix suggests a cluster where signaling modulation, especially via GPCRs, intersects with developmental and neural functions, with additional links to Wnt signaling and synaptic plasticity. This makes a cohesive label centered on GPCR signaling in developmental contexts.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003315","count":1},{"id":"GO:0032423","count":1},{"id":"GO:0035414","count":1},{"id":"GO:0021881","count":1},{"id":"GO:0031914","count":1}]},{"hash":"791084790476719918","title":"Transcription Regulation and Redox Modulation","description":"The proteins are tied to RNA polymerase II\u2013mediated transcription (DNA-templated transcription and negative regulation of Pol II activity). Redox-related terms (deglutathionylation, cellular oxidant detoxification, oxidation-reduction) imply modulation of transcription by the redox state, supporting a cohesive theme of transcriptional control influenced by redox biology. The viral process term is peripheral to the core theme.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0080058","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0033158","count":1},{"id":"GO:0000122","count":1}]},{"hash":"76976738601702026","title":"Protein Synthesis and Amino Acid Biosynthesis","description":"The top GO terms cluster around translation and tRNA charging/modification (translation, tRNA modification, glutaminyl-tRNA and glutamyl-tRNA aminoacylation) alongside biosynthesis of branched-chain amino acids (leucine, isoleucine, valine) and related folic acid metabolism, suggesting a cohesive role in both protein production and amino acid metabolism. Confidence in this label is Moderate because some terms are peripheral, but the core signals point to these two linked functions.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0006400","count":1},{"id":"GO:0006425","count":1},{"id":"GO:0006424","count":1},{"id":"GO:0046656","count":1}]},{"hash":"2095575993249324868","title":"CAAX-box protein processing","description":"This cluster is defined by the single top GO term CAAX-box protein processing, suggesting the proteins participate in maturation of CAAX-box\u2013bearing, prenylated proteins (including prenylation, proteolysis, and methylation). With no edges or triangles, the grouping likely reflects shared function rather than direct interactions, supporting a theme of CAAX-processing activity.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071586","count":1}]},{"hash":"1312032197491394118","title":"Biosynthesis and cell wall assembly","description":"The top GO terms point to multiple biosynthetic processes (L-aspartate, kynurenic acid, antibiotic, and O antigen biosynthesis) and a term for cell wall organization, suggesting the proteins participate in producing and modifying cell envelope components. While some terms are obsolete or less directly connected (DNA-templated transcription, insulin response), the strongest signal is biosynthetic pathways and cell wall\u2013related metabolism. Confidence in this label is Medium.","confidence":"","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":3},{"id":"GO:0019551","count":2},{"id":"GO:0006532","count":2},{"id":"GO:0019518","count":2},{"id":"GO:0071555","count":2}]},{"hash":"187564896833364829","title":"Neural and sensory development","description":"The GO terms strongly point to neural and sensory organ development and function (GABA catabolic process, righting reflex, embryonic eye development, retina-related retinoic acid biosynthesis), with cardiovascular terms likely reflecting broader developmental contexts or annotation noise. This makes a neural/sensory development label the most representative and specific for the cluster.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048738","count":3},{"id":"GO:0001568","count":3},{"id":"GO:0042904","count":3},{"id":"GO:0060013","count":3},{"id":"GO:0031076","count":3}]},{"hash":"1960020381012846311","title":"Mitochondrial lipid biosynthesis and energy production","description":"The cluster\u2019s terms cluster around mitochondrial energy generation (mitochondrial ATP synthesis coupled electron transport) and lipid biosynthesis/remodeling (cardiolipin remodeling, ether lipids, CDP-diacylglycerol, triglyceride synthesis), suggesting a theme of mitochondria-associated lipid metabolism supporting respiration. Some immune and developmental terms appear as potential secondary associations, but the core signal is mitochondrial lipid metabolism with energy production.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042775","count":2},{"id":"GO:0019432","count":2},{"id":"GO:0070970","count":2},{"id":"GO:0002071","count":2},{"id":"GO:0008611","count":2}]},{"hash":"1048312953978540976","title":"Translation machinery and ribosome biogenesis","description":"The terms cluster around translation and ribosome biology\u2014translation, initiation/termination, cytoplasmic translation, and ribosomal small subunit biogenesis\u2014with selenocysteine incorporation and mRNA deadenylation-dependent decay reflecting linked mRNA surveillance during translation. An antibiotic response term also ties to translation inhibitors, reinforcing a core role in protein synthesis machinery.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0000288","count":2},{"id":"GO:0001514","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006413","count":2}]},{"hash":"1414620529142578816","title":"Translation and ribosome assembly","description":"The top GO terms are dominated by translation-related processes (translation, translational termination) and ribosomal large subunit assembly, indicating a core cluster around protein synthesis and ribosome biogenesis. The additional terms (e.g., endosomal/mitochondrial acidification, angiogenesis, transcription regulation) appear to be incidental or background, so the primary theme remains translation/ribosome assembly.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006415","count":1},{"id":"GO:0015968","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0048388","count":1}]},{"hash":"479571285086629211","title":"Endoreduplication and cell cycle control","description":"This cluster centers on genome duplication without cell division (DNA endoreduplication), regulation of the G1/S transition, and p53-related apoptotic signaling, suggesting a module tied to cell-cycle control and endoreduplication. Some development terms appear ancillary to the core theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061668","count":1},{"id":"GO:0032877","count":1},{"id":"GO:0072332","count":1},{"id":"GO:0042023","count":1},{"id":"GO:0033301","count":1}]},{"hash":"688301328609938204","title":"Wnt signaling and apoptotic transcription regulation","description":"The cluster\u2019s prominent GO terms center on regulating apoptosis (positive regulation) and inhibiting canonical Wnt signaling, alongside DNA-templated transcription, implying coordination between signaling control of cell fate and transcriptional programs. Additional terms like cell migration and chemotaxis hint at developmental contexts where these processes interact, with some stress-related terms (cadmium response) augmenting the environmental regulation aspect.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":2},{"id":"GO:0090090","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006935","count":2}]},{"hash":"1548974984791421106","title":"Plant Hormone Response and Leaf Development","description":"The cluster shows enrichment for plant hormone responses (jasmonic acid, ethylene, abscisic acid), leaf formation, and chlorophyll biosynthesis regulation, suggesting a module integrating developmental processes with hormone signaling. While there are some chromatin-related terms present, the dominant theme centers on plant development and hormone-driven regulation.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":3},{"id":"GO:0010338","count":2},{"id":"GO:0035522","count":2},{"id":"GO:1904911","count":2},{"id":"GO:1905778","count":2}]},{"hash":"2066369171126030315","title":"Plant stress-responsive RNA processing and translation control","description":"This cluster combines RNA metabolism and translation regulation: splicing via spliceosome, deadenylation-dependent decapping, and assembly/regulation of translation initiation and preinitiation complexes, including IRES-dependent and reinitiation/termination processes. The inclusion of ABA and water-deprivation responses points to plant stress biology, suggesting these proteins coordinate RNA processing and translational control under abiotic stress. Confidence: Medium","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0075522","count":2}]},{"hash":"1390887738687736445","title":"Transcriptional Regulation of Metabolic Pathways","description":"Based on the top GO terms, the cluster centers on DNA-templated transcription and transcriptional regulation (including RNA polymerase II\u2013driven transcription influenced by oleic acid) and intersects with metabolic processes (cellular respiration, nucleotide biosynthesis). Although some terms are obsolete, the common theme ties transcriptional control to metabolism, suggesting these proteins jointly regulate metabolic gene expression.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0070932","count":2},{"id":"GO:0061429","count":2},{"id":"GO:0043457","count":2},{"id":"GO:0035959","count":2}]},{"hash":"965179064976682822","title":"Ion transport and ribosome biogenesis","description":"The top GO terms center on potassium and sodium ion export/homeostasis, indicating ion transport as the main shared function. Additional signals for ribosome biogenesis and cell division suggest a possible secondary link to growth-related processes, but the ion transport theme is the strongest across the cluster. Confidence: Medium","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0036376","count":2},{"id":"GO:0042274","count":1},{"id":"GO:0042254","count":1}]},{"hash":"2022960697489116241","title":"RNA polymerase transcription initiation complexes","description":"The terms point to transcription initiation and preinitiation complex assembly across RNA polymerases I, II, and III, with regulation of transcription initiation; a single outlier term about transposon integration is likely an annotation quirk rather than a core cluster feature.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045893","count":2},{"id":"GO:0006352","count":1},{"id":"GO:0070893","count":1},{"id":"GO:0006383","count":1},{"id":"GO:1903357","count":1}]},{"hash":"77948211230596707","title":"Developmental Epigenetic Regulation","description":"The top GO terms include histone modification and chromatin regulation (e.g., H3-K4 methylation, H3/H4 acetylation, DNA methylation-dependent heterochromatin formation) alongside several developmental processes (cerebellar cortex development, gliogenesis, atrial septum morphogenesis, uterine gland development, extrathymic T cell differentiation). This points to a theme of epigenetic control coordinating development across tissues, despite some terms being obsolete. ","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0003289","count":1},{"id":"GO:0080182","count":1},{"id":"GO:0033082","count":1},{"id":"GO:0014013","count":1},{"id":"GO:0021695","count":1}]},{"hash":"1106507262505874648","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006268","count":3},{"id":"GO:0009432","count":3},{"id":"GO:0000184","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0048701","count":3}]},{"hash":"517693429206847044","title":"Neuro-Muscular Development and Axonogenesis","description":"This cluster combines GO terms tied to muscle formation (myoblast fusion, mitotic cell cycle/G2M transition) with neural development and connectivity (axogenesis, Schwann cell development, long-term synaptic potentiation, response to muscle activity) and vascular growth (angiogenesis), suggesting a shared theme of neuromuscular development and maintenance, including glial support and activity-dependent synaptic maturation. Some cell cycle terms may reflect proliferative states during development, but the dominant pattern points to coordinated muscle-nerve development and connectivity.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000086","count":4},{"id":"GO:0007520","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0007409","count":4},{"id":"GO:0010800","count":4}]},{"hash":"1753596116307822568","title":"Unknown","description":"The GO terms span a wide range of processes (cell cycle, development including myoblast fusion and axonogenesis, angiogenesis, synaptic potentiation, nuclear export, bud site selection, phosphorylation regulation, and even plant ABA signaling), with no clear single theme linking them. This prevents a specific, meaningful label beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0007520","count":2},{"id":"GO:0007121","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1227316388478799006","title":"Neuronal development and synaptic vesicle regulation","description":"This cluster shows solid enrichment for brain-related processes, including brain development, midbrain dopaminergic neuron differentiation, and regulation of synaptic vesicle exocytosis, indicating a neuronal development and synaptic function theme. Some terms touch on trafficking and polarity, which can accompany neuronal maturation, but the core signal points to neural differentiation and synaptic activity.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0031384","count":3},{"id":"GO:2000300","count":3},{"id":"GO:0010796","count":3},{"id":"GO:0045197","count":2}]},{"hash":"1451054928334871930","title":"Post-transcriptional RNA regulation","description":"The GO terms cluster around RNA processing, stability, and decay, notably positive regulation of miRNA-mediated gene silencing, mitochondrial mRNA polyadenylation, and mRNA catabolic processes, suggesting a common theme of post-transcriptional RNA control, despite some noisy or obsolete terms.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000637","count":3},{"id":"GO:0097222","count":3},{"id":"GO:0090503","count":3},{"id":"GO:0045716","count":3},{"id":"GO:0010738","count":3}]},{"hash":"1619081373630577126","title":"Translation Initiation and RNA Processing","description":"These proteins are primarily tied to translation initiation and its regulation (preinitiation complex formation, IRES-dependent viral initiation, and translation reinitiation), with a few weaker signals for mRNA splicing/RNA processing. The dominant theme is translational control, though some RNA processing terms are present. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0075525","count":2}]},{"hash":"1097237322871143939","title":"ER\u2013peroxisome Biogenesis and Protein Transport","description":"These GO terms cluster around endoplasmic reticulum functions (calcium homeostasis, protein folding, exit/trafficking) and peroxisome biogenesis and maintenance (membrane biogenesis, inheritance, organization, and import). The overlap suggests a module of proteins involved in trafficking from the ER to peroxisomes and in ER-dependent peroxisome biogenesis. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032469","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0032527","count":1},{"id":"GO:0016557","count":1},{"id":"GO:0045033","count":1}]},{"hash":"1227717703119835194","title":"Lipid Mediator Biosynthesis and Inflammation","description":"The top GO terms cluster around lipid-derived signaling molecules, especially prostaglandin and oxylipin biosynthesis, and inflammatory regulation, indicating a set of proteins involved in lipid mediator production and immune modulation. Additional terms touching retinoic acid, vitamin D response, and cholesterol catabolism support a broader lipid metabolism and signaling theme that can influence inflammation and tissue development (e.g., retina vasculature). Overall, these signals point to a cohesive function in lipid signaling pathways and inflammatory control, with some metabolic cross-talk. ","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":4},{"id":"GO:0002677","count":3},{"id":"GO:0033280","count":3},{"id":"GO:0006707","count":3},{"id":"GO:0042904","count":3}]},{"hash":"811406032144799959","title":"RNA Processing and Transcription Regulation","description":"The cluster centers on RNA modification (tRNA pseudouridine synthesis, RNA Pol II CTD dephosphorylation) and transcription-related functions (mRNA stability regulation), with a few terms touching DNA recombination and cell cycle, suggesting a nuclear gene expression/regulation theme. This supports labeling as RNA processing and transcription control.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":2},{"id":"GO:0000455","count":1},{"id":"GO:0031119","count":1},{"id":"GO:2000327","count":1},{"id":"GO:0080111","count":1}]},{"hash":"1525899344436170578","title":"Telomere maintenance and nuclear mRNA processing","description":"These proteins show enrichment in telomere-related regulation (telomerase-mediated maintenance and telomere capping) and nuclear-associated processes (mRNA processing and localization to the nuclear periphery), suggesting a module focused on genome maintenance and RNA processing within the nucleus. Some terms about adipogenesis or muscle stretch are likely peripheral. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045736","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0045444","count":2},{"id":"GO:1904355","count":2}]},{"hash":"2081518778762115181","title":"Unknown","description":"The listed GO terms are quite diverse (spinal cord development, transcription, redox homeostasis, actin nucleation, signaling, and growth-related processes) with no clear, single functional theme. The absence of interactions (Edges: 0, Triangles: 0) further suggests a heterogeneous mix rather than a cohesive pathway, so a specific label is not warranted.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0034314","count":1}]},{"hash":"556996284995522291","title":"Cross-tissue developmental differentiation","description":"Based on the GO terms, the cluster centers on development and differentiation across various tissues, with several heart/muscle\u2013related processes (muscle cell fate determination, ventricular cardiac myofibril assembly, primary heart field specification) alongside other tissue differentiation terms (neural crest, nephron tubule, stamen). The mix suggests a broad theme of developmental differentiation rather than a single, cohesive pathway, and with only four proteins and no observed edges, a high-specificity label isn\u2019t justified. Therefore, a broad, cross-tissue development label is most appropriate.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007521","count":1},{"id":"GO:0048455","count":1},{"id":"GO:0060862","count":1},{"id":"GO:0071277","count":1},{"id":"GO:0014033","count":1}]},{"hash":"836089690892070401","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080022","count":1},{"id":"GO:0055121","count":1},{"id":"GO:1904667","count":1},{"id":"GO:0010099","count":1},{"id":"GO:0000350","count":1}]},{"hash":"301727218844764805","title":"Diverse solute membrane transporters","description":"These proteins appear to function primarily as membrane transporters for a variety of substrates, as reflected by GO terms for transmembrane transport of phosphate ions, sialic acid, urate, 4-hydroxyphenylacetate, potassium ions, and xenobiotics. The dominant pattern is transporter activity across diverse solutes, with only a few outliers (e.g., a metabolic process term and an obsolete transport term) that do not override the overall theme. ","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":2},{"id":"GO:0042891","count":1},{"id":"GO:0006004","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0015739","count":1}]},{"hash":"2022763380993675429","title":"Unknown","description":"With 4 proteins and no interactions, the top GO terms are defense response to oomycetes and glutathione transport, each represented by a single protein. These terms point to distinct themes (defense vs. transport) and lack a shared function or pathway linking the cluster, so no cohesive label can be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002229","count":1},{"id":"GO:0034635","count":1}]},{"hash":"510864096410252833","title":"Unknown","description":"The top terms point to a mix of amino acid biosynthesis (threonine, homoserine, isoleucine, methionine), NAD/NADP metabolism, and even stress responses (gamma radiation, UV-C), with no apparent single coherent function. The lack of edges and the presence of obsolete GO terms make it hard to derive a unified theme, so a precise, representative label isn\u2019t supported.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0009086","count":1},{"id":"GO:0019310","count":1},{"id":"GO:0009097","count":1},{"id":"GO:0009088","count":1}]},{"hash":"482843575282308815","title":"Oxidative stress response and redox homeostasis","description":"The cluster's terms cluster around redox biology: cellular response to oxidative stress, redox homeostasis, oxidant detoxification, oxidation-reduction processes, and deglutathionylation. These indicate a cohesive redox/antioxidant functional theme. Some unrelated terms (nucleotide biosynthesis and neural crest-related migration) appear but do not redefine the core function.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080058","count":1},{"id":"GO:0009263","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0098869","count":1}]},{"hash":"197085505904564899","title":"Ubiquitin-mediated protein modification and degradation","description":"This cluster is dominated by ubiquitination-related GO terms (monoubiquitination, autoubiquitination, K63-linked ubiquitination) and ubiquitin-dependent protein catabolic processes, with additional signals for JNK pathway regulation and transcription. The shared theme is tagging proteins with ubiquitin to regulate turnover and signaling.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006513","count":2},{"id":"GO:0046328","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0042787","count":2}]},{"hash":"308242354111554540","title":"Iron and manganese ion transport and homeostasis","description":"The top GO terms point to manganese ion transmembrane transport and intracellular manganese ion homeostasis, plus iron ion response and sequestration. This strongly suggests a cluster whose proteins are involved in maintaining intracellular metal ion balance and responding to iron/manganese levels. The ethylene stimulus term is less related and may reflect broader plant stress responses. Overall, the cluster is best described as related to metal ion transport and homeostasis.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071421","count":1},{"id":"GO:0030026","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0071281","count":1},{"id":"GO:0071369","count":1}]},{"hash":"1098457691252222712","title":"SNARE-Mediated Vesicle Trafficking","description":"The top GO terms cluster around Golgi-to-plasma membrane transport, exocytic insertion of receptors, intra-Golgi vesicle trafficking, SNARE complex assembly, and receptor recycling, indicating a coherent theme of SNARE-driven vesicle trafficking and exocytosis (including neurotransmitter receptor trafficking).","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":2},{"id":"GO:0043001","count":1},{"id":"GO:0098967","count":1},{"id":"GO:0042147","count":1},{"id":"GO:0006891","count":1}]},{"hash":"1831190156440375152","title":"Unknown","description":"Top terms are mixed and many are obsolete; only one term hints at cell cycle regulation and others cover mRNA stability, xenobiotic response, DNA recombination, cAMP signaling, and aging, with no cohesive theme across all four proteins. Therefore no reliable single functional label.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000327","count":1},{"id":"GO:0080111","count":1},{"id":"GO:1900087","count":1},{"id":"GO:0043488","count":1},{"id":"GO:0071320","count":1}]},{"hash":"700090594575561812","title":"Nuclear RNA Processing and Chromatin Regulation","description":"This cluster centers on nuclear processes, with chromatin remodeling and histone deacetylation regulation pointing to chromatin regulation, and box C/D snoRNP assembly plus snoRNA localization indicating RNA processing in the nucleus. The remaining terms (myelin, wing formation, platelet activation, Wnt signaling) appear as outliers, but the core signals tie to nuclear RNA handling and chromatin modification.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006338","count":1},{"id":"GO:0031063","count":1},{"id":"GO:0000492","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0010925","count":1}]},{"hash":"429425933467154031","title":"N- and lysine acetylation cluster","description":"The top GO terms are dominated by various acetylation processes\u2014N-terminal acetylation, peptidyl-lysine acetylation, histone acetylation, and related acetyl transfer activities\u2014suggesting an acetyltransferase/acetylation-focused protein group. Some terms (melatonin biosynthesis, angiogenesis, mycothiol biosynthesis) are less directly connected and likely noise, but the core signal is acetylation-related function.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030187","count":4},{"id":"GO:0017196","count":4},{"id":"GO:0043967","count":4},{"id":"GO:0010125","count":4},{"id":"GO:0018002","count":4}]},{"hash":"141235787019628136","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:1900745","count":1},{"id":"GO:0046330","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0048025","count":1}]},{"hash":"1370914076707111261","title":"Unknown","description":"This cluster includes four proteins with no reported GO terms and no observed edges or triangles, offering no clear functional signal or shared pathway to identify a common theme. Without GO enrichment or interaction evidence, a specific function label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1649291070786234961","title":"Unknown","description":"This cluster shows a mix of GO terms including cellular response to cadmium ion, K11-linked ubiquitination, cellular response to type I interferon, and protein heterooligomerization, with several obsolete terms. The terms do not converge on a single clear biological function or pathway, suggesting no cohesive theme for a specific label beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0071357","count":1},{"id":"GO:0051291","count":1},{"id":"GO:0051348","count":1}]},{"hash":"1217003313581809471","title":"Endocytic vesicle trafficking and Rab signaling","description":"The four proteins show a shared involvement in endocytosis and vesicle transport, with top GO terms covering synaptic vesicle endocytosis, endocytic recycling, endocytosis, and Golgi to endosome transport, plus regulation of Rab signaling. These points together suggest a common role in vesicular trafficking processes, despite a few unrelated terms present. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048488","count":1},{"id":"GO:0032456","count":1},{"id":"GO:0009997","count":1},{"id":"GO:0032483","count":1},{"id":"GO:0006897","count":1}]},{"hash":"2063583966220630503","title":"Protein Translation Machinery","description":"This cluster is dominated by translation-related GO terms (cytoplasmic and mitochondrial translation, translation in general, and ribosomal large subunit assembly), suggesting proteins involved in protein synthesis and ribosome assembly. A few other terms (copper ion transport and redox homeostasis) are present but appear secondary to the core translation-related functions.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990090","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0071353","count":1}]},{"hash":"206488914350677450","title":"Ribosome Biogenesis and Translation","description":"The terms cluster around ribosome assembly and biogenesis, rRNA maturation, and translation, indicating proteins involved in producing and assembling ribosomal subunits for protein synthesis.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000462","count":1},{"id":"GO:0006407","count":1},{"id":"GO:0000028","count":1},{"id":"GO:0042254","count":1}]},{"hash":"1930229841209846877","title":"Unknown","description":"The terms span diverse bacterial processes\u2014from photosynthesis-related steps and bacteriochlorophyll biosynthesis to stress responses (heat, arsenic, metal ions), nitrogen fixation, flagellum organization, and even tRNA modification\u2014with no single, cohesive function linking all members of this cluster. This makes it difficult to assign a specific, representative label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009408","count":1},{"id":"GO:0044781","count":1},{"id":"GO:0010038","count":1},{"id":"GO:0036070","count":1}]},{"hash":"1009069442342391050","title":"Ribosome biogenesis and translation","description":"The two top GO terms point to ribosomal large subunit assembly and translation, indicating the cluster centers on ribosome assembly and the protein synthesis process. This suggests the proteins are related to ribosome biogenesis and function, justifying a combined label that captures both assembly and translation.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":1},{"id":"GO:0006412","count":1}]},{"hash":"219098366103288245","title":"Unknown","description":"The Top Terms are a disparate mix (DNA repair, cell wall biosynthesis, ribosome-associated degradation, apoptosis-related signaling, and other unrelated processes) with no clear, cohesive functional theme tying the proteins together, and the network shows no interactions. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":1},{"id":"GO:0070178","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0009252","count":1},{"id":"GO:0071555","count":1}]},{"hash":"42382402422360996","title":"Unknown","description":"The top GO terms span divergent areas: various catabolic/metabolic processes (propylene, uracil, L-isoleucine, dihydrolipoamide, halogen), plus regulatory processes (positive regulation of erythrocyte differentiation and hormone biosynthesis) and gene expression/modification (alternative mRNA splicing, histone deacetylation/demethylation). With no interactions among proteins (Edges 0, Triangles 0) and little overlap among terms, there isn\u2019t a coherent, single functional theme tying the cluster together.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042208","count":2},{"id":"GO:0016575","count":1},{"id":"GO:0006212","count":1},{"id":"GO:0051068","count":1},{"id":"GO:0045648","count":1}]},{"hash":"1671047194413971499","title":"Phosphate-containing compound metabolism","description":"The cluster\u2019s top GO term is GO:0006796, phosphate-containing compound metabolic process, suggesting a broad link to phosphate metabolism. However, only one protein in the set directly links to this term and the cluster is small with minimal connectivity, so this label is tentative and represents a general metabolic theme rather than a specific pathway.","confidence":"Low","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006796","count":1}]},{"hash":"1416361226455905123","title":"Small-molecule Metabolism","description":"Top GO terms indicate diverse small-molecule processing, including catabolic and biosynthetic steps for ethanol, formaldehyde, xylitol, fructose, and amino acids, with some broader metabolic terms. This points to a general metabolism-focused cluster rather than a single specific pathway.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019518","count":1},{"id":"GO:0006069","count":1},{"id":"GO:0003016","count":1},{"id":"GO:0009809","count":1},{"id":"GO:0046688","count":1}]},{"hash":"1547053175021644483","title":"Tubulin/microtubule assembly and proteostasis","description":"The top GO terms cluster around tubulin complex assembly and cortical microtubule organization, with supporting terms for protein folding, chaperone-mediated assembly, and ubiquitin-proteasome\u2013mediated quality control. This points to a theme of cytoskeletal assembly maintained by proteostasis machinery. Additional terms for Golgi to plasma membrane transport and epithelial polarity suggest links to trafficking and cell organization, possibly in developmental contexts like neuron differentiation. Overall, the cluster appears to combine cytoskeletal assembly with protein homeostasis.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":2},{"id":"GO:0032968","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0051131","count":1},{"id":"GO:0071629","count":1}]},{"hash":"1935641521105568916","title":"Ribosome Biogenesis and Cell Growth","description":"The most represented GO terms point to ribosome biogenesis (both small and large subunits) and nuclear export of ribosomal subunits, aligning with a role in ribosome assembly and protein synthesis. Related terms about the cell cycle and septum formation suggest a broader link to cellular growth and division, which fits a cluster tied to growth-related translation machinery. Some terms (arsenic response, symbiont-related host modification) are less cohesive with this theme, so the overall signal centers on ribosome-associated processes.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0052046","count":1},{"id":"GO:0035335","count":1},{"id":"GO:0046685","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0042254","count":1}]},{"hash":"1040173731950217377","title":"Unknown","description":"The top GO terms span plant-specific processes (seed coat development), broad lipid metabolism (fatty acid biosynthesis, transport, and long-chain/very long-chain fatty acids), and microbial processes (phenylacetate catabolic, siderophore biosynthesis, bioluminescence), with no clear, cohesive function linking the three proteins. There is no single common theme to confidently name this cluster.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010214","count":1},{"id":"GO:0001579","count":1},{"id":"GO:0010124","count":1},{"id":"GO:0044539","count":1},{"id":"GO:0009698","count":1}]},{"hash":"8559919081265185","title":"Cerebellar cortex layer organization","description":"This cluster is driven by GO terms describing structural organization of cerebellar cortex layers, specifically the Purkinje cell layer and the granular layer, suggesting a shared theme of cerebellar cortex architecture. The other terms are less tightly connected, so the cerebellar layering theme is the best overall label, though with partial support.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009190","count":2},{"id":"GO:0021693","count":1},{"id":"GO:0021685","count":1},{"id":"GO:1903468","count":1},{"id":"GO:0044810","count":1}]},{"hash":"1272763307122779829","title":"Unknown","description":"The listed GO terms are highly diverse, spanning neurotransmitter biosynthesis, receptor internalization, plant hormone signaling, sugar biosynthesis, lipid metabolism, cellulose breakdown, xenobiotic response, learning, alkaloid response, and fatty acid metabolism. There is no shared biological process, cellular component, or molecular function that ties these proteins into a coherent single theme, and the lack of edges/triangles supports a random assemblage rather than a connected functional cluster. Therefore, no meaningful functional label can be assigned beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042136","count":1},{"id":"GO:0031623","count":1},{"id":"GO:0009939","count":1},{"id":"GO:0010325","count":1},{"id":"GO:0090122","count":1}]},{"hash":"1722208186887778508","title":"Nucleotide metabolism and cofactor biosynthesis","description":"This cluster's GO terms cluster around nucleotide metabolism\u2014phosphorylation of nucleosides, salvage pathways, and interconversion of purine ribonucleotides\u2014as well as biosynthesis of key cofactors such as NAD+ and CoA. The brain and liver development terms appear less central to the core activity and may reflect broader or incidental annotations; the dominant theme is nucleotide metabolism and cofactor production.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001889","count":2},{"id":"GO:0046041","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0046705","count":2},{"id":"GO:0015937","count":2}]},{"hash":"1436083657890341509","title":"Folate-Linked Nucleotide and Amino Acid Biosynthesis","description":"The cluster is dominated by biosynthetic processes for nucleotides and amino acids, especially folate-dependent steps (10-formyltetrahydrofolate biosynthesis, folate interconversion) and purine/nucleobase synthesis, with the TCA cycle suggesting broader central metabolism involvement. Some terms appear obsolete or less relevant (neutrophil homeostasis, chloramphenicol response), but the core theme points to folate-mediated biosynthesis pathways. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0035999","count":1},{"id":"GO:0006164","count":1},{"id":"GO:0009086","count":1},{"id":"GO:0009257","count":1}]},{"hash":"2234264551290232730","title":"Autophagy and Proteostasis Regulation","description":"This cluster centers on autophagy and proteasome-linked protein quality control (negative regulation of proteasomal degradation, autophagy, deglycation-related processes) with accompanying signaling and transcription-regulatory activity, suggesting a broader role in cellular stress response and protein homeostasis.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032435","count":1},{"id":"GO:0036528","count":1},{"id":"GO:0036529","count":1},{"id":"GO:2000679","count":1},{"id":"GO:0006914","count":1}]},{"hash":"890437730186274792","title":"Ribosome Biogenesis and Translation","description":"The proteins in this cluster are linked by GO terms centered on ribosome assembly and function: ribosome biogenesis, rRNA pseudouridine synthesis, translation, translation initiation regulation, and tRNA aminoacylation, all pointing to components of ribosome-based protein synthesis. Some terms like cellular stress or vasculogenesis appear tangential, but the dominant signal is ribosome-related processes.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000455","count":1},{"id":"GO:0031564","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0045947","count":1},{"id":"GO:0006412","count":1}]},{"hash":"1495662206010292082","title":"Ubiquitin-proteasome regulation and NF-\u03baB signaling","description":"The GO terms cluster around ubiquitin-related processes (deubiquitination, ubiquitin ligase activity regulation, proteasomal degradation) and proteasome assembly, with additional links to cell cycle control (G2/M regulation) and mRNA stability. They also point to immune signaling pathways, including TNF-mediated signaling and non-canonical NF-\u03baB signaling, plus Fc-epsilon receptor signaling. This combination suggests a functional module where protein turnover via the ubiquitin-proteasome system interfaces with NF-\u03baB\u2013driven immune signaling and cell-cycle regulation, rather than a single narrow process. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":1},{"id":"GO:0051436","count":1},{"id":"GO:0080129","count":1},{"id":"GO:0033209","count":1},{"id":"GO:0038061","count":1}]},{"hash":"119743922044075644","title":"Ubiquitin-Mediated Protein Quality Control","description":"The cluster centers on protein quality control and degradation pathways, with multiple GO terms for deubiquitination, ER-associated degradation (ERAD), and regulation of autophagy-related processes. This points to a cohesive theme around ubiquitin-dependent regulation of protein folding, turnover, and cellular stress responses, rather than unrelated signaling or metabolic functions.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902260","count":2},{"id":"GO:0016579","count":2},{"id":"GO:0034140","count":2},{"id":"GO:0017085","count":2},{"id":"GO:0045648","count":2}]},{"hash":"796575070378894248","title":"Mitochondrial apoptosis signaling and nuclear export","description":"The cluster\u2019s GO terms center on mitochondria-related apoptosis (release of cytochrome c, regulation of apoptotic proteolysis) and processes linking to cell growth, protein targeting, and nuclear trafficking (protein export from nucleus, protein targeting, CDK activity regulation). This suggests proteins that participate in intrinsic apoptosis signaling with concurrent roles in cellular transport and cell-cycle regulation, rather than a single, narrow function.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":3},{"id":"GO:0043154","count":2},{"id":"GO:0030307","count":2},{"id":"GO:0001836","count":2},{"id":"GO:0006605","count":2}]},{"hash":"77322134092141515","title":"Unknown","description":"No single, cohesive function ties the GO terms together: they span immune signaling (T cell polarity, IL-2 production), kidney podocyte development and excretion, mitochondrial processes, and neuronal signaling, with no consistent pathway link across the three proteins. Therefore, no meaningful cluster label can be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903905","count":1},{"id":"GO:0072249","count":1},{"id":"GO:0007588","count":1},{"id":"GO:0032623","count":1},{"id":"GO:0030433","count":1}]},{"hash":"2118390293219697145","title":"Pentose Phosphate Pathway","description":"The top GO terms all point to the pentose-phosphate shunt, including the non-oxidative branch and pentose catabolic/metabolic processes, indicating these proteins are related to PPP enzymes or regulation. The inclusion of an obsolete term does not override the PPP-focused theme.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009052","count":1},{"id":"GO:0006098","count":1},{"id":"GO:0044262","count":1},{"id":"GO:0019323","count":1}]},{"hash":"1254903145976306682","title":"Unknown","description":"Top GO terms are scattered across microtubule-based movement, CNS development, ureteric bud morphogenesis, immune and transcriptional regulation, and vascular/inflammatory processes, with no clear shared pathway or function linking the three proteins. The lack of a cohesive theme and absence of interactions suggests no reliable, specific label can be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007018","count":1},{"id":"GO:0007417","count":1},{"id":"GO:0001658","count":1},{"id":"GO:0045657","count":1},{"id":"GO:0045669","count":1}]},{"hash":"382707299056856126","title":"RNA Processing and Transcription Regulation","description":"The cluster\u2019s top GO terms cluster around RNA metabolism and transcription control\u2014pre-miRNA processing, miRNA catabolic process, CRD-mediated mRNA stabilization, DNA-templated transcription, transcription termination regulation, and transcription antitermination\u2014suggesting the proteins participate in RNA maturation and regulation of gene expression. A few metabolic terms appear but do not define a cohesive alternative function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":2},{"id":"GO:0031564","count":1},{"id":"GO:0046272","count":1},{"id":"GO:0070934","count":1},{"id":"GO:0019700","count":1}]},{"hash":"1447716835782775341","title":"Acetylation-Linked Metabolic and Chromatin Regulation","description":"The top GO terms are dominated by acetylation-related processes (various N-terminal and histone acetylations, spermine acetylation), along with acetyl-CoA\u2013dependent pathways (melatonin biosynthesis, N-acetylglucosamine metabolism) and chromatin regulation (subtelomeric heterochromatin formation). This suggests a unifying theme around acetylation-driven regulation and metabolism, with a chromatin connection. Confidence: Medium","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030187","count":2},{"id":"GO:0017196","count":2},{"id":"GO:0043967","count":2},{"id":"GO:0010125","count":2},{"id":"GO:0018002","count":2}]},{"hash":"2179624513485530056","title":"DNA replication initiation and replication complex assembly","description":"This cluster is dominated by GO terms related to DNA replication initiation and replication machinery (pre-replicative complex assembly, MCM complex assembly, mitotic DNA replication initiation, and related repair processes). Although a few outlier terms exist (chromatin, xenobiotic response), the strongest signal centers on replication initiation and complex assembly. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030494","count":2},{"id":"GO:0031939","count":2},{"id":"GO:0007292","count":2},{"id":"GO:0006267","count":2},{"id":"GO:0006348","count":2}]},{"hash":"1106198501605784006","title":"Unknown","description":"The top terms come from a mix of nuclear transcription (DNA-templated transcription) and various protein assembly/oligomerization processes (snoRNP assembly, protein hexamerization, homooligomerization), plus some mitochondrial/peroxisomal functions, and several entries noted as obsolete. There isn\u2019t a clear, single functional theme binding all items, so a cohesive label isn\u2019t justifiable. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0060303","count":2},{"id":"GO:0070414","count":1},{"id":"GO:0016562","count":1},{"id":"GO:0000492","count":1}]},{"hash":"1540269212614121096","title":"Ammonium Transport and Nitrogen Utilization","description":"The top GO terms cluster around ammonium transport (ammonium transmembrane transport, transepithelial ammonium transport) and nitrogen utilization, with related terms for regulation of nitrogen utilization, indicating a function centered on nitrogen uptake and assimilation. Additional signals for carbon dioxide transport and nutrient-stress\u2013associated growth patterns echo broader nutrient response, but the core theme remains ammonium transport and nitrogen metabolism.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007124","count":3},{"id":"GO:0070634","count":3},{"id":"GO:0060586","count":3},{"id":"GO:0072488","count":3},{"id":"GO:0019740","count":3}]},{"hash":"1928394125094493754","title":"RNA Pol II Transcription Regulation","description":"The set of GO terms is dominated by transcription-related activities, including DNA-templated transcription, negative and positive regulation of transcription by RNA polymerase II, and regulation of DNA binding, suggesting the proteins mainly function in gene expression control. While a few terms touch on redox and ER processes, the central theme points to transcription regulation by RNA Pol II rather than a single metabolic pathway. Confidence: Medium","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0080058","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0018401","count":1}]},{"hash":"429664368248442229","title":"Ubiquitin-like modification and autophagy","description":"The cluster centers on ubiquitin-like modifiers (sumoylation, neddylation) and protein degradation pathways (ubiquitin-dependent ERAD, macroautophagy), suggesting a theme of post-translational modification coupled to cellular quality control. A few peripheral terms (tRNA wobble thiolation, molybdopterin biosynthesis) are less connected but don\u2019t outweigh the core pattern.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0016236","count":1},{"id":"GO:0006777","count":1},{"id":"GO:0045116","count":1}]},{"hash":"2082142799361279435","title":"RNA Processing and Ribosome Biogenesis","description":"The top GO terms include regulation of alternative mRNA splicing via the spliceosome and small-subunit processome assembly, both core to RNA processing and ribosome biogenesis. Although other terms touch development and signaling, the RNA-centric terms dominate, suggesting the cluster centers on RNA processing and ribosome-related functions.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0010954","count":1},{"id":"GO:0072675","count":1},{"id":"GO:0048666","count":1},{"id":"GO:0048170","count":1}]},{"hash":"1840944265659676505","title":"Unknown","description":"No common function can be inferred: there are no GO terms, no edges or triangles, and only three proteins with no connectivity. The ReCIPE re-additions do not indicate a shared function.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1018028480590275605","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006414","count":1},{"id":"GO:0061158","count":1},{"id":"GO:0001782","count":1},{"id":"GO:0038066","count":1},{"id":"GO:0061470","count":1}]},{"hash":"2282450595417539533","title":"Endosome-to-Golgi Retrograde Transport","description":"The GO terms point to intracellular protein trafficking with emphasis on endocytic recycling, retrograde transport from endosome to Golgi, and retention in the Golgi. Together, they describe a cohesive process centered on Golgi-associated trafficking and recycling pathways.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":1},{"id":"GO:1990126","count":1},{"id":"GO:0042147","count":1},{"id":"GO:0045053","count":1}]},{"hash":"2280083601989097943","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":1},{"id":"GO:0019062","count":1},{"id":"GO:0097309","count":1},{"id":"GO:0002128","count":1},{"id":"GO:0097310","count":1}]},{"hash":"1750951718729632407","title":"Tissue remodeling and morphogenesis","description":"This cluster repeatedly features processes related to remodeling of tissues and developmental morphogenesis across different contexts (collagen catabolism, ossification, epithelial branching in lung morphogenesis, decidualization). While individual terms span bone, lung, uterus, and peptide/protease activity, the common theme is extracellular matrix remodeling and morphogenetic events rather than a single specific pathway. Confidence: Medium","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030574","count":3},{"id":"GO:0001957","count":3},{"id":"GO:0010813","count":3},{"id":"GO:0097067","count":3},{"id":"GO:0010815","count":3}]},{"hash":"393338401886423869","title":"Unknown","description":"There are no edges and no enriched GO terms to connect the proteins, so there is no coherent functional theme to name.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"727800600419418620","title":"Diverse substrate catabolism","description":"The top GO terms cluster around catabolic processes for a variety of substrates (glucuronoside, lactose, uracil, propylene, isoleucine) and related metabolic steps, pointing to a general theme of substrate breakdown. A few regulatory terms are present but likely incidental rather than representing a core function of the cluster. The common thread is metabolic catabolism across diverse substrates.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019391","count":1},{"id":"GO:0005990","count":1},{"id":"GO:0016575","count":1},{"id":"GO:0006212","count":1},{"id":"GO:0042208","count":1}]},{"hash":"381680271550833655","title":"Unknown","description":"Top GO terms cover very disparate themes, from locomotor rhythm and axonemal dynein assembly to heart function, DNA repair, post-translational modification, proteolysis, and innate immune signaling. There is no clear, shared function or pathway linking the proteins, so a single coherent label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904059","count":1},{"id":"GO:0070286","count":1},{"id":"GO:0003146","count":1},{"id":"GO:2000672","count":1},{"id":"GO:1902260","count":1}]},{"hash":"2160051636574477057","title":"Unknown","description":"The top GO terms span diverse processes (meiosis chiasma assembly, ubiquitination, peroxisomal import, dipeptide transport regulation, DNA repair, JNK signaling, mitosis exit, and fungal cell wall organization) with no clear, single common function binding the cluster. This heterogeneity makes it difficult to assign a concise, representative label. ","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0051026","count":3},{"id":"GO:0070936","count":3},{"id":"GO:0016562","count":3},{"id":"GO:0090089","count":3},{"id":"GO:1902916","count":3}]},{"hash":"1187179702412473645","title":"Stress-Response Signaling Pathways","description":"The GO terms cluster around stress sensing and signaling cascades (DNA damage checkpoint signaling, JNK cascade, cortisol response, zinc/cadmium stress, PI3K/AKT signaling) that regulate proliferation and survival, with some related localization and immune signaling terms. This suggests a cohesive theme of cells activating stress-response signaling networks rather than a single, strict process. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031571","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0038093","count":1},{"id":"GO:1990139","count":1},{"id":"GO:2000686","count":1}]},{"hash":"768898651653362849","title":"Unknown","description":"The top GO terms span histone modification/ubiquitination, TNF signaling and I-kappaB regulation, spermatocyte division, and photomorphogenesis, with no clear shared function or interaction pattern among the proteins. Because there is no cohesive theme linking the terms, a concise functional label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036205","count":1},{"id":"GO:0033209","count":1},{"id":"GO:0090073","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0007112","count":1}]},{"hash":"367015812546566096","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006631","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0045964","count":1},{"id":"GO:1902114","count":1},{"id":"GO:0098869","count":1}]},{"hash":"2284638743287381967","title":"Photosynthesis and light-response proteins","description":"The GO terms are centered on photosynthesis and light harvesting in photosystems I and II, with multiple light-related responses (red light, far red light, UV-A, high/low light) and chlorophyll-related processes, indicating this cluster represents chloroplast light-capture and photosynthetic machinery.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018298","count":1},{"id":"GO:0009768","count":1},{"id":"GO:0071492","count":1},{"id":"GO:0010114","count":1},{"id":"GO:0071486","count":1}]},{"hash":"924571060516547361","title":"Hypoxia-driven angiogenesis and endothelial remodeling","description":"This cluster has GO terms strongly linked to hypoxia response (GO:0001666, GO:0071456) and to angiogenesis-related processes (GO:0016525, GO:0043542) as well as endothelial cell migration and integrin-mediated adhesion regulation, suggesting a vascular remodeling/angiogenic theme driven by hypoxic signaling. A few outlier terms (uracil catabolic process, beta-ketoadipate pathway) are peripheral and do not obscure the core pattern. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":2},{"id":"GO:0006096","count":1},{"id":"GO:0016525","count":1},{"id":"GO:0031639","count":1},{"id":"GO:0071456","count":1}]},{"hash":"587252574062358341","title":"Nuclear transcription and RNA methylation","description":"The cluster is driven by transcription-related terms (DNA-templated transcription and transcriptional regulation) and a suite of methylation processes (rRNA, tRNA, histone methylation), plus nucleologenesis, indicating a core function in gene expression regulation through epigenetic and RNA maturation/modification in the nucleus. The presence of mitochondrial tRNA methylation is a tangential note but does not override the central theme of transcription and methylation interactions.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0016049","count":2},{"id":"GO:0031167","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0034970","count":1}]},{"hash":"133562389011431888","title":"Triglyceride and phospholipid catabolism","description":"The top terms point to triglyceride catabolic processes (including mobilization and acyl-chain remodeling) and phospholipid catabolism (phosphatidylethanolamine and phosphatidylcholine catabolic processes). This suggests a cohesive role in lipid breakdown and remodeling, separate from signaling but potentially linked through metabolic regulation (e.g., negative regulation of PKA activity). Thus, the cluster is best described as lipid catabolism and remodeling, focused on triglyceride and phospholipid pathways.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036153","count":2},{"id":"GO:2000480","count":2},{"id":"GO:0010898","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0046338","count":2}]}]