[{"hash":"1511481964582992560","title":"Immune Cell Development and PI3K-Akt Signaling","description":"This cluster is driven by GO terms related to immune cell maturation and function (B cell affinity maturation, NK T cell differentiation, IL-4 production, cellular response to IL-7) and is connected to survival/ growth signaling (insulin receptor signaling, PI3K/Akt pathway). While it also touches on broader developmental processes (heart development) and cell migration, the strongest themes center on immune development and cytokine signaling intertwined with PI3K-Akt\u2013mediated survival pathways. Confidence: Medium.","confidence":"","size":29,"edges":404,"triangles":3600,"max_degree":28,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0002344","count":6},{"id":"GO:0008286","count":6},{"id":"GO:0016477","count":6},{"id":"GO:0007507","count":6},{"id":"GO:0032633","count":6}]},{"hash":"1149534944470953649","title":"Nucleobase and vitamin transmembrane transport","description":"The top terms are dominated by transmembrane transport of nucleobases and vitamins (cytosine and uracil transport, thiamine transport) and related compound transport (AICAR), pointing to a cluster of membrane transporters for nucleobases and vitamins. A few developmental terms appear but are less representative of the cluster\u2019s primary function; overall the theme is transport across membranes for nucleobases/vitamins. ","confidence":"High","size":29,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903088","count":4},{"id":"GO:0015856","count":4},{"id":"GO:0006209","count":4},{"id":"GO:0015888","count":4},{"id":"GO:1903791","count":4}]},{"hash":"1736183366761427737","title":"Transcription Regulation and Chromatin Remodeling","description":"This cluster is enriched for DNA-templated transcription, transcription initiation-coupled chromatin remodeling, and heterochromatin formation (rDNA and silent mating-type loci), pointing to a shared role in transcription control via chromatin state. While some terms touch development or stress responses, the dominant theme is transcription regulation coupled with chromatin organization.","confidence":"High","size":29,"edges":17,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0043457","count":3},{"id":"GO:0035948","count":3},{"id":"GO:0045815","count":2},{"id":"GO:0048477","count":2}]},{"hash":"1657693163729834003","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":400,"triangles":3497,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":4},{"id":"GO:0055114","count":4},{"id":"GO:1902600","count":3},{"id":"GO:0022417","count":3},{"id":"GO:0006122","count":2}]},{"hash":"2184623186919969565","title":"RNA Pol II Transcription Regulation","description":"Top terms are dominated by DNA-templated transcription and transcription from RNA polymerase II promoter, with several \u201cpositive regulation of transcription\u201d terms, indicating a transcription-regulatory cluster. Occasional cell-cycle or development terms likely reflect context-dependent regulation rather than a separate module. Overall, labeling as RNA Pol II Transcription Regulation captures the central theme.","confidence":"High","size":29,"edges":10,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0097421","count":5},{"id":"GO:0035959","count":4},{"id":"GO:0061414","count":4},{"id":"GO:2001158","count":4}]},{"hash":"727364917255616725","title":"Diverse substrate membrane transporters","description":"The top GO terms show transmembrane transport for many substrates (arabinose, phosphate ions, potassium, nitrate/nitrite, vitamin, sialic acid) and a vesicular neurotransmitter loading process, all pointing to membrane transporter proteins with broad substrate specificity. This common theme of transporting diverse molecules across membranes explains the cluster, including a neurotransmitter-related transporter activity. ","confidence":"High","size":28,"edges":18,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":14},{"id":"GO:0035435","count":14},{"id":"GO:0071805","count":14},{"id":"GO:0042128","count":14},{"id":"GO:0015706","count":14}]},{"hash":"1930748717575707721","title":"RNA processing and splicing regulation","description":"The top GO terms cluster around nuclear mRNA processing events: export, splicing (via spliceosome), modification, poly(A) tail regulation, and RNA silencing by miRNAs and regulatory ncRNAs, indicating a cohesive role in post-transcriptional mRNA maturation and regulation.","confidence":"High","size":28,"edges":179,"triangles":474,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0016556","count":5},{"id":"GO:0006406","count":5},{"id":"GO:0035278","count":5},{"id":"GO:0006376","count":5},{"id":"GO:0010610","count":5}]},{"hash":"2203110357526549451","title":"Cell division and vesicle trafficking","description":"The cluster includes GO terms tied to cell cycle events (cell division, mitotic DNA replication checkpoint signaling) and to membrane trafficking/cytoskeletal dynamics (SNARE complex disassembly, actin cortical patch localization, late endosomal microautophagy). This combination suggests a broad theme around intracellular transport and membrane remodeling in the context of cell cycle processes, rather than a single isolated function. Hence, a concise label that highlights both division and trafficking is appropriate.","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0035494","count":3},{"id":"GO:0051666","count":2},{"id":"GO:0061738","count":2}]},{"hash":"2011493665616762463","title":"Chromatin-modifying factors in neural development","description":"This cluster is enriched for DNA-templated transcription and multiple histone modification terms (deacetylation, H3K4 methylation, acetylation) alongside neural development processes (forebrain development, neural tube closure) and broader multicellular development, suggesting proteins that regulate gene expression via chromatin changes to drive neural development.","confidence":"High","size":28,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0016575","count":5},{"id":"GO:0030900","count":4},{"id":"GO:0001843","count":4},{"id":"GO:0051568","count":4}]},{"hash":"1799670803789822661","title":"RNA processing and mitochondrial transcription","description":"The proteins connect mainly to RNA processing steps (polyadenylation, pre-mRNA cleavage, rRNA maturation, tRNA methylation) and mitochondrial transcription regulation (mitochondrial promoter transcription, regulation of mitochondrial transcription), suggesting a core theme of RNA processing and mitochondrial gene transcription control. Some related terms on protein methylation and poly-ADP-ribosylation indicate broader regulatory roles, but the strongest signal is RNA processing and mitochondrial transcription. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0098789","count":2},{"id":"GO:0070212","count":2},{"id":"GO:0035556","count":2},{"id":"GO:0000083","count":2}]},{"hash":"2212141202190827948","title":"Embryonic and neural development with epigenetic control","description":"This cluster shows multiple development-related terms, notably cerebral cortex development and neuron projection extension, along with embryogenesis (in utero development) and various lineage differentiations (pituitary, megakaryocytes, erythrocytes) plus stem cell proliferation regulation. The presence of histone modification terms suggests an epigenetic layer modulating these differentiation processes. Overall, it looks like a group of proteins involved in broad developmental differentiation, with a focus on neural/embryonic development and epigenetic regulation. ","confidence":"Medium","size":27,"edges":53,"triangles":66,"max_degree":11,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0051572","count":10},{"id":"GO:0045654","count":10},{"id":"GO:0021987","count":10},{"id":"GO:1990138","count":10},{"id":"GO:0055114","count":10}]},{"hash":"640760146146740219","title":"Transmembrane Transporters","description":"This cluster is enriched for diverse transmembrane transport GO terms (xenobiotic, arabinose, potassium, sodium, nitrate, vitamin), with an additional related term for neurotransmitter loading into synaptic vesicles, pointing to a common theme of membrane transport proteins handling various substrates. Some metabolism-related terms are present but do not override the transport signal, supporting a transporter-focused interpretation. ","confidence":"Medium","size":27,"edges":14,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":8},{"id":"GO:0015751","count":8},{"id":"GO:0071805","count":8},{"id":"GO:0042128","count":8},{"id":"GO:0006004","count":8}]},{"hash":"316352947700984590","title":"Mitotic Cell Cycle Regulation","description":"The top GO terms clustering here are dominated by mitosis and cell cycle-related processes (mitotic cell cycle, G2/M transition, exit from mitosis, and cell division), indicating proteins involved in controlling progression through mitosis. Some terms like phylloquinone biosynthesis or sugar metabolism appear as noise rather than central themes, but the core is clearly mitotic regulation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031536","count":2},{"id":"GO:0042372","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0045792","count":1},{"id":"GO:0051301","count":1}]},{"hash":"735887262494875217","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms for ribosome biogenesis, ribosomal large subunit biogenesis, and export from the nucleus, plus cytoplasmic translation and tRNA modification, all pointing to ribosome assembly and protein synthesis. The presence of cell cycle and cell division terms suggests coordination between ribosome production and proliferation, while other terms like conjugation and stress response appear peripheral and do not redefine the main function. Overall, the functions cluster around ribosome biogenesis and translation machinery with growth coordination.","confidence":"High","size":27,"edges":345,"triangles":2786,"max_degree":26,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":8},{"id":"GO:0000055","count":6},{"id":"GO:0042273","count":5},{"id":"GO:0002181","count":4},{"id":"GO:0007049","count":4}]},{"hash":"893825173816643431","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms for translation and ribosome biogenesis (translation, cytoplasmic translation, ribosome biogenesis, ribosomal large subunit biogenesis/assembly). While there are additional terms related to transcription and RNA splicing, the primary signal is ribosome production and protein synthesis, with a link to cotranslational targeting to membranes via SRP. ","confidence":"High","size":27,"edges":262,"triangles":1392,"max_degree":25,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0042273","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0002181","count":3},{"id":"GO:0000027","count":3}]},{"hash":"1838981306245248674","title":"Unknown","description":"The GO terms are highly heterogeneous across metabolism, cell wall biosynthesis, development, immune regulation, and even plant gravitropism; there isn't a clear, common function linking these proteins, so the cluster cannot be assigned a meaningful label.","confidence":"","size":27,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0005975","count":2},{"id":"GO:0009252","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0072358","count":2}]},{"hash":"2136058741228305799","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":351,"triangles":2925,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0006450","count":2},{"id":"GO:1905639","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0031425","count":2}]},{"hash":"2118552385462072010","title":"Neural development and axon guidance","description":"Top GO terms cluster around nervous system development, cerebral cortex and hippocampus development, and positive regulation of axon extension, calcium signaling, and exocytosis, pointing to neuronal differentiation and neurite outgrowth. Focal adhesion regulation and ERK signaling support pathways for neurite navigation and synaptic maturation, while some mitotic cycle terms are broader cellular processes. Overall, the cluster appears to reflect brain development and axon growth programs.","confidence":"High","size":26,"edges":273,"triangles":1632,"max_degree":25,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":6},{"id":"GO:0045773","count":6},{"id":"GO:0050850","count":5},{"id":"GO:0051893","count":5},{"id":"GO:0045956","count":5}]},{"hash":"146827018111891813","title":"Mitochondrial energy metabolism and placental development","description":"The dominant terms point to mitochondrial energy metabolism (respiratory chain complex assembly, proton motive force-driven ATP synthesis, mitochondrial outer membrane permeabilization). A secondary theme centers on maternal/placental biology (placental development and parturition). The co-occurrence suggests proteins involved in mitochondrial function with potential roles in placental biology, though the mixed terms reduce certainty.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033108","count":1},{"id":"GO:0001893","count":1},{"id":"GO:1903547","count":1},{"id":"GO:0097345","count":1},{"id":"GO:0060137","count":1}]},{"hash":"2009082079122560209","title":"Keratinocyte Differentiation and Hippo-Mediated Growth Control","description":"The cluster is dominated by keratinocyte-related terms (differentiation and apoptotic regulation) and Hippo signaling, which together suggest regulation of epidermal cell growth, survival, and tissue homeostasis. Additional signals such as negative regulation of cell motility and responses to growth factors align with epithelial morphogenesis. Outliers like bone resorption and general transcription exist but do not override the epidermal growth-control theme.","confidence":"Medium","size":26,"edges":200,"triangles":733,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0045453","count":2},{"id":"GO:0030216","count":2},{"id":"GO:0035729","count":2},{"id":"GO:0042989","count":2}]},{"hash":"844184463944281366","title":"Unknown","description":"The Top Terms span Golgi retention, folic acid response, chromatin assembly, DNA methylation regulation, cellular senescence, protein oligomerization regulation, ion transport, and metabolism, with no single dominant function linking them. This lack of a coherent theme makes a concise, representative label untenable.","confidence":"","size":26,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045053","count":2},{"id":"GO:0051593","count":2},{"id":"GO:0034080","count":1},{"id":"GO:0044030","count":1},{"id":"GO:2000774","count":1}]},{"hash":"1411438084077280784","title":"Core Metabolic Biosynthesis and Phosphorylation","description":"Most top GO terms describe biosynthetic and metabolic processes (ADP-L-glycero-beta-D-manno-heptose biosynthesis, CoA biosynthesis, carbohydrate phosphorylation, lipopolysaccharide biosynthesis, L-serine biosynthesis, dephosphorylation). A few terms like brain development and aging appear as noise, but the primary signal links to metabolic biosynthesis and phosphorylation activities.","confidence":"Medium","size":26,"edges":111,"triangles":204,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":5},{"id":"GO:0097171","count":5},{"id":"GO:0015937","count":4},{"id":"GO:0046835","count":3},{"id":"GO:0007420","count":3}]},{"hash":"1794027866150941853","title":"DNA repair and cell cycle checkpoints","description":"The cluster includes proteins involved in DNA repair (NER), DNA replication checkpoints, telomere maintenance, and cell cycle regulation (APC/C-dependent processes and meiotic checkpoints), suggesting a cohesive role in genome integrity maintenance and coordinated progression through mitosis/meiosis.","confidence":"High","size":26,"edges":137,"triangles":275,"max_degree":17,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0010950","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0032508","count":2},{"id":"GO:0031145","count":2}]},{"hash":"2105417781891955993","title":"Ribosome biogenesis and translation","description":"These proteins are strongly enriched for ribosome-related processes: translation and cytoplasmic translation are central, with supporting terms for ribosome biogenesis, rRNA maturation (SSU/LSU), and small subunit assembly. This pattern points to a cohesive module dedicated to ribosome production and proper protein synthesis, including maintenance of translational fidelity. The antibiotic response term is peripheral to the core theme.","confidence":"High","size":26,"edges":315,"triangles":2379,"max_degree":25,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":18},{"id":"GO:0042254","count":9},{"id":"GO:0006407","count":5},{"id":"GO:0046677","count":4},{"id":"GO:0000462","count":4}]},{"hash":"2095843373895948377","title":"Ribosome biogenesis and translation","description":"The cluster is strongly enriched for GO terms related to translation, ribosome assembly, and ribosome biogenesis, including mitochondrial translation, indicating a core role in ribosome function and protein synthesis across different compartments; some transcription-related terms appear but the translation/biogenesis signal dominates.","confidence":"High","size":26,"edges":296,"triangles":2013,"max_degree":25,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":16},{"id":"GO:0000027","count":5},{"id":"GO:0032543","count":3},{"id":"GO:0006415","count":3},{"id":"GO:0006353","count":3}]},{"hash":"829722555010068135","title":"ER Protein Quality Control and Retrograde Trafficking","description":"This cluster centers on protein processing and quality control linked to the endoplasmic reticulum, highlighted by GO terms for protein retention in the ER lumen, retrograde ER-to-cytosol transport, and ER-associated degradation pathways (including GPI-anchor attachment). While a couple terms (e.g., DNA repair and neuronal apoptosis) are tangential, the dominant signal is ER-based quality control and trafficking.","confidence":"High","size":26,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":1},{"id":"GO:0005975","count":1},{"id":"GO:0045910","count":1},{"id":"GO:0006298","count":1},{"id":"GO:0016255","count":1}]},{"hash":"1570150898859587066","title":"Phosphoinositide signaling and inositol phosphate metabolism","description":"The top GO terms are dominated by inositol phosphate biosynthesis/metabolic processes and phosphatidylinositol phosphate biosynthesis, pointing to a phosphoinositide signaling/metabolism theme for this cluster. A number of other terms (spine maintenance, pollen-related processes, thymic T cell selection, arginine metabolism) are more heterogeneous and likely reflect broader or cross-species annotations, but the core connection among most terms is lipid signaling via phosphoinositides. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0032958","count":2},{"id":"GO:0097062","count":2},{"id":"GO:0046854","count":2},{"id":"GO:0006525","count":2}]},{"hash":"1617955027993953494","title":"Dopamine metabolism and nigral development","description":"Based on the prominent dopamine-related terms in the cluster (dopamine catabolic process; positive regulation of dopamine metabolic process) and the brain-region term substantia nigra development, the core theme appears to be dopaminergic function and development. Additional terms like response to ethanol also align with dopaminergic signaling, though some terms (e.g., abscisic acid biosynthesis, aluminum ion response) may reflect broader or non-neuronal processes. Overall, the label captures the central theme of dopamine metabolism and nigral neuron development.","confidence":"High","size":26,"edges":33,"triangles":14,"max_degree":8,"top_function":"protein folding","top_go_terms":[{"id":"GO:0009636","count":5},{"id":"GO:0021762","count":5},{"id":"GO:0045471","count":5},{"id":"GO:0009688","count":5},{"id":"GO:0006569","count":5}]},{"hash":"743437309529287293","title":"RNA Splicing and Post-Transcriptional Regulation","description":"The cluster shows strong representation of mRNA splicing and regulation (spliceosome-mediated alternative splicing, splice site recognition, mRNA export, and mRNA modification), along with components of mRNA stability control and ncRNA- or miRNA-mediated gene silencing. This points to a cohesive group of proteins involved in RNA processing and post-transcriptional control of gene expression.","confidence":"High","size":26,"edges":323,"triangles":2552,"max_degree":25,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006376","count":11},{"id":"GO:0010610","count":11},{"id":"GO:0006378","count":11},{"id":"GO:1901407","count":11},{"id":"GO:0016556","count":10}]},{"hash":"1076331192992617703","title":"Neural development and axon guidance","description":"This cluster centers on neural development processes, including cell migration, motor neuron axon guidance, and synaptic potentiation, along with transcriptional regulation and cell-matrix adhesion, suggesting proteins coordinating neural connectivity and maturation.","confidence":"High","size":25,"edges":266,"triangles":1649,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001275","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0034351","count":4},{"id":"GO:0060291","count":3},{"id":"GO:0006351","count":3}]},{"hash":"722039330358895572","title":"Polyamine acetylation and Rap signaling","description":"This cluster shows a strong representation of polyamine metabolism, with acetylation of putrescine and spermine and spermine catabolism, alongside Rap protein\u2013mediated signal transduction and activation of GTPase activity, suggesting a bacterial signaling/modification theme. Other terms like intracellular transport and subtelomeric heterochromatin formation appear but are less representative of the core function. Therefore, the label focuses on the prominent link between polyamine modification and Rap-driven signaling. ","confidence":"Medium","size":25,"edges":80,"triangles":77,"max_degree":14,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0090630","count":3},{"id":"GO:0006886","count":3},{"id":"GO:0032486","count":3},{"id":"GO:0032920","count":2},{"id":"GO:0006348","count":2}]},{"hash":"1598471053732050647","title":"Multicellular development and signaling","description":"The proteins in this cluster are linked to broad developmental processes (neural development, placenta development, multicellular organism development) and signaling regulation (NF-kB, NFAT, calcium-mediated signaling, PI3K signaling), suggesting a role in coordinating development through signaling networks. The presence of a cell cycle transition term hints at proliferation aspects tied to development as well.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051092","count":4},{"id":"GO:0021954","count":4},{"id":"GO:0000082","count":4},{"id":"GO:0035372","count":4},{"id":"GO:0014068","count":4}]},{"hash":"2042888186004828732","title":"DNA Replication and RNA Processing Factors","description":"The cluster is dominated by GO terms for DNA replication and related processes (DNA replication, primer synthesis, unwinding, SOS response, viral genome replication), suggesting core involvement in nuclear DNA metabolism. In addition, multiple RNA processing terms (spliceosome-mediated splicing, nuclear mRNA surveillance, transcription regulation by RNA polymerase II) indicate co-occurring functions in RNA processing and transcription. Together, these signals point to a cohesive set of nuclear factors coordinating DNA replication with RNA processing and transcription, with DNA replication as the central theme and RNA processing as a closely linked function. Confidence: High","confidence":"","size":25,"edges":297,"triangles":2232,"max_degree":24,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":17},{"id":"GO:0019079","count":12},{"id":"GO:0006268","count":12},{"id":"GO:0009432","count":12},{"id":"GO:0006269","count":11}]},{"hash":"1488839642976237700","title":"Ciliary and centrosomal assembly regulators","description":"The proteins show a cohesive emphasis on cilium-related processes (intraciliary transport, regulation of cilium assembly, centrosome localization) and cell cycle events (spindle assembly checkpoint, re-entry into mitosis) with symmetry determination, pointing to a shared ciliary-centrosomal regulatory role that also interfaces with cell cycle control. Some outliers (e.g., stomatal opening, tyrosine dephosphorylation) exist but do not dominate the motif.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":1},{"id":"GO:0034599","count":1},{"id":"GO:1902017","count":1},{"id":"GO:0090267","count":1},{"id":"GO:0051642","count":1}]},{"hash":"864925120553205753","title":"Unknown","description":"There are no GO terms or functional signals provided for this cluster, and the network is empty (Edges 0, Triangles 0, Max Degree 0), so there is no clear shared function to group the proteins. Without a detectable theme, the appropriate label is Unknown.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1049094255572381252","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":291,"triangles":2103,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0071276","count":5},{"id":"GO:0006349","count":5},{"id":"GO:0000480","count":4}]},{"hash":"1390703361379365649","title":"Ribosome and Cytoplasmic Translation Machinery","description":"This cluster shows strong enrichment for translation- and ribosome-related terms (translation, cytoplasmic translation, ribosome biogenesis/disassembly, initiation/termination, and selenocysteine incorporation), pointing to proteins involved in protein synthesis and ribosome dynamics. Antibiotic response and glial proliferation terms are ancillary but can reflect related cellular contexts. Overall, it represents the ribosome/translation machinery.","confidence":"High","size":25,"edges":238,"triangles":1232,"max_degree":24,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":13},{"id":"GO:0042254","count":6},{"id":"GO:0046677","count":4},{"id":"GO:0002181","count":4},{"id":"GO:0006415","count":3}]},{"hash":"431887202726235796","title":"Membrane transport of ions and metabolites","description":"The cluster shows strong enrichment for transmembrane transport terms across a range of substrates (manganese ions, NAD, pyridoxal phosphate, deoxynucleotides, phosphate ions, heme), plus related mitochondrial localization and metabolic regulation cues. This pattern suggests a cohesive theme of membrane transporters handling diverse ions and small molecules necessary for energy metabolism and redox balance.","confidence":"High","size":25,"edges":295,"triangles":2190,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":21},{"id":"GO:0035352","count":21},{"id":"GO:0090152","count":21},{"id":"GO:0031921","count":21},{"id":"GO:1990845","count":21}]},{"hash":"2062985419292329808","title":"Membrane Transporters","description":"The cluster is dominated by GO terms for various transmembrane transport activities (phosphate, xenobiotic, arabinose, potassium, sodium, nitrate, vitamin) and a related vesicular transport term for neurotransmitter loading, pointing to a cohesive group of membrane transporter proteins that shuttle diverse substrates across membranes.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":9},{"id":"GO:0006855","count":8},{"id":"GO:0015751","count":8},{"id":"GO:0071805","count":8},{"id":"GO:0042128","count":8}]},{"hash":"1367831502578054453","title":"Broad Substrate Transmembrane Transporters","description":"The top GO terms are all transmembrane transport activities for a wide variety of substrates (phosphate, sialic acid, xenobiotics, arabinose, potassium, nitrate, fucose, vitamins, sodium, etc.), indicating a cluster of membrane transporter proteins with broad substrate specificity rather than enzymes or signaling components.","confidence":"High","size":24,"edges":144,"triangles":418,"max_degree":22,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0035435","count":8},{"id":"GO:0015739","count":8},{"id":"GO:0006855","count":7},{"id":"GO:0015751","count":7},{"id":"GO:0071805","count":7}]},{"hash":"1081400243265712987","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":50,"triangles":36,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0000722","count":2},{"id":"GO:0071035","count":2},{"id":"GO:0071051","count":2},{"id":"GO:0070651","count":2}]},{"hash":"496854464380934185","title":"Cerebral Cortex Development and Neurogenesis","description":"The top terms are dominated by neural development signals: cerebral cortex development, neuron projection extension, pituitary gland development, and positive regulation of stem cell proliferation, pointing to a brain development/neurogenesis program. Metabolic terms (folate and thiamine biosynthesis) likely support proliferating neural cells rather than define the core function, so the neural development theme best represents the cluster.","confidence":"High","size":24,"edges":171,"triangles":612,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0046653","count":22},{"id":"GO:0009228","count":22},{"id":"GO:0051572","count":20},{"id":"GO:0045654","count":20},{"id":"GO:0021987","count":20}]},{"hash":"1405638690880593904","title":"Metal Ion Transport and Calcium Homeostasis","description":"The top GO terms cluster around copper and zinc transport and intracellular calcium ion homeostasis, with additional related transport and metabolic terms. This suggests the proteins collectively function in ion transport and regulation of metal ion balance, with some broader metabolic roles reflected by carbohydrate metabolism and serine biosynthesis terms. The absence of network edges indicates annotations rather than direct interactions, but the shared emphasis on metal ion transport and calcium regulation supports this label.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046839","count":3},{"id":"GO:0097755","count":3},{"id":"GO:0046272","count":3},{"id":"GO:0019373","count":3},{"id":"GO:0006874","count":2}]},{"hash":"204092457067016087","title":"Cellular stress response and membrane signaling","description":"Based on GO terms such as protein repair, cellular responses to heat and osmotic stress, and plasma membrane organization, the cluster appears to group proteins involved in sensing and responding to stress and in signaling at the plasma membrane. While terms like spermatogenesis and magnesium ion transport are present, they are less representative of the core theme, so the central function is stress response and membrane-associated signaling.","confidence":"Medium","size":24,"edges":57,"triangles":61,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0030091","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0071470","count":2},{"id":"GO:0007009","count":2},{"id":"GO:0010972","count":2}]},{"hash":"2024368610149224685","title":"Amino and fatty acid catabolism in liver and heart","description":"The top GO terms point to amino acid (valine/leucine) and fatty acid (long/medium-chain) catabolic processes, along with starvation response, and liver/heart development signals. This suggests the proteins are tied to energy metabolism in liver and heart tissues, with development terms likely reflecting tissue context. Overall, a metabolic catabolism theme is strongest.","confidence":"Medium","size":24,"edges":79,"triangles":109,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0006574","count":6},{"id":"GO:0001889","count":5},{"id":"GO:0042594","count":5},{"id":"GO:0006552","count":4}]},{"hash":"1273996103964417907","title":"Nuclear transcription and cell cycle regulation","description":"The cluster centers on DNA-templated transcription and transcription regulation, with supporting terms in protein ubiquitination, nuclear processes (ribosomal protein import into nucleus, mitotic nuclear membrane reassembly), and cell division/mieotic spindle elongation. While some apoptosis and interferon-related terms appear, the dominant theme ties to nuclear gene expression control and progression through the cell cycle, justifying this label.","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0001080","count":2},{"id":"GO:0016567","count":2},{"id":"GO:2000347","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1164668056879876978","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms related to ribosome biogenesis (large and small subunit biogenesis, ribosomal export from the nucleus) and translation (cytoplasmic translation, tRNA modification), with additional signals for cell growth/division (cell cycle, cell division). This points to a core theme of ribosome production and protein synthesis, which often co-occurs with proliferation-related processes.","confidence":"High","size":24,"edges":29,"triangles":6,"max_degree":7,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:1901001","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0090529","count":3}]},{"hash":"2044922359480928445","title":"Unknown","description":"The cluster\u2019s terms are highly diverse, spanning development, transcription regulation, ncRNA-mediated silencing, and various DNA-related processes, with no clear shared pathway or cohesive function (and no edges/triangles to reinforce a common theme). Therefore, there is no interpretable single function to label the cluster.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000721","count":1},{"id":"GO:0060157","count":1},{"id":"GO:1990683","count":1},{"id":"GO:0097070","count":1},{"id":"GO:2000587","count":1}]},{"hash":"1702382418320733907","title":"Amino acid metabolism and pyridoxine biosynthesis","description":"The top GO terms are dominated by amino acid catabolic and biosynthetic processes (alanine, valine, serine) with additional catabolic pathways and a pyridoxine (vitamin B6) biosynthesis term, suggesting a coherent theme around amino acid metabolism and related cofactor biosynthesis rather than a single signaling or structural function.","confidence":"High","size":24,"edges":45,"triangles":40,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0042853","count":11},{"id":"GO:0009097","count":11},{"id":"GO:0046392","count":9},{"id":"GO:0009099","count":9}]},{"hash":"1296118160697014945","title":"Translation and ER-Golgi vesicle trafficking","description":"This cluster centers on translation and ribosome-related processes (translation and ribosome disassembly) but also includes multiple vesicle trafficking and Rab/Rap GTPase\u2013regulated terms (COPII cargo loading, intracellular transport, plasma membrane to endosome, recycling endosome to Golgi, Rab signaling). The co-occurrence suggests proteins that participate in or regulate both protein synthesis and intracellular transport, potentially coordinating translation with trafficking. ","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032790","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0032486","count":2},{"id":"GO:0090110","count":2},{"id":"GO:0090630","count":2}]},{"hash":"1413423535987704757","title":"Unknown","description":"The top GO terms are highly diverse and scarcely overlapping (corneocyte development, GPI anchor biosynthesis, phosphatidylinositol dephosphorylation, peptide hormone response, visual perception, DNA recombination, cell cycle regulation, mRNA stability, and more), with only single representations. This lack of a unifying biological theme among the terms suggests no coherent function characterizes this cluster.","confidence":"","size":23,"edges":42,"triangles":18,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0003335","count":1},{"id":"GO:2000327","count":1},{"id":"GO:0046856","count":1},{"id":"GO:0006506","count":1},{"id":"GO:0071375","count":1}]},{"hash":"1853708561693490282","title":"Neural patterning and transcriptional regulation","description":"The cluster combines GO terms for RNA polymerase II transcription and DNA-templated transcription with diverse nervous system development processes (left/right pattern formation, spinal cord neuron and motor neuron cell fate specification, somite formation, cerebral cortex interneuron differentiation, bronchiole development). This points to a cohesive module of transcriptional regulators driving neural development and regional patterning.","confidence":"High","size":23,"edges":182,"triangles":772,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0060972","count":3},{"id":"GO:0021530","count":3},{"id":"GO:0043433","count":3}]},{"hash":"1124119184330718783","title":"RNA Methylation and Processing","description":"This cluster is enriched for methylation-related GO terms across RNA species (tRNA, rRNA, mRNA capping) and protein methylation, suggesting a cohesive role for methyltransferases in RNA maturation and modification, with some links to arginine methylation and related pathways.","confidence":"High","size":23,"edges":131,"triangles":347,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":10},{"id":"GO:0046690","count":10},{"id":"GO:0019919","count":10},{"id":"GO:0009236","count":10},{"id":"GO:0016049","count":10}]},{"hash":"1120677172083887733","title":"Unknown","description":"This cluster has no edges and no GO terms to guide labeling; 23 proteins with no shared functional signal. Although 20 proteins were re-added by ReCIPE, there is no network connectivity or common pathway to define a theme, so a specific label cannot be assigned. Therefore Unknown.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"62571666575929384","title":"Xenobiotic detoxification and redox metabolism","description":"Dominated by GO terms tied to detoxification and redox balance, including cellular oxidant detoxification, glutathione metabolism/derivatives, and xenobiotic catabolic processes, which together point to a glutathione-driven detox/redox maintenance cluster; included lipid-signaling and calcium-regulation terms likely reflect broader metabolic connections but do not override the core theme.","confidence":"High","size":23,"edges":56,"triangles":97,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098869","count":10},{"id":"GO:0001516","count":9},{"id":"GO:0045454","count":7},{"id":"GO:0009636","count":6},{"id":"GO:0006749","count":6}]},{"hash":"596228500411530275","title":"Membrane Transporters for Ions and Nutrients","description":"Most of the top GO terms describe transmembrane transport of diverse substrates (nitrate/nitrite, arabinose, sialic acid, phosphate, potassium, vitamins), indicating a cluster of membrane transporter proteins that shuttle nutrients and ions across membranes. The inclusion of a term about neurotransmitter loading into synaptic vesicles suggests a broader transporter/vesicle-related function, but the dominant theme is membrane transport activity across a variety of substrates.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":7},{"id":"GO:0015739","count":7},{"id":"GO:0015751","count":6},{"id":"GO:0035435","count":6},{"id":"GO:0071805","count":6}]},{"hash":"183165831615885346","title":"Mitochondrial energy production and p53-mediated stress response","description":"The cluster\u2019s top GO terms cluster around mitochondrial function: mitochondrial targeting and protein processing, assembly of respiratory chain and ATP synthase complexes, phospholipid transport, and regulation of cytochrome c release, plus DNA damage response signaling via p53. Together these imply a cohesive role in mitochondrial energy metabolism and p53-linked stress/apoptosis pathways, justifying a mitochondria-centric functional label.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":1},{"id":"GO:0045332","count":1},{"id":"GO:0090201","count":1},{"id":"GO:0033108","count":1},{"id":"GO:2001140","count":1}]},{"hash":"2072547755595679504","title":"Nutrient-responsive transcription regulators","description":"This cluster is dominated by GO terms tied to DNA-templated transcription and positive regulation of transcription from RNA Pol II in response to various carbon sources (nonfermentable carbon sources, oleic acid) and metabolic pathways (pyrimidine, lysine, proline biosynthesis; cellular respiration). The common thread is transcriptional regulation in response to nutrient/metabolic signals, suggesting these proteins are transcription factors or regulators modulating gene expression based on metabolic state.","confidence":"High","size":23,"edges":39,"triangles":17,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0035959","count":5},{"id":"GO:0061414","count":5},{"id":"GO:2001158","count":5},{"id":"GO:1900399","count":5}]},{"hash":"1079856458033865017","title":"Neural development and RNA metabolism","description":"The cluster is enriched for RNA processing and ribosome-related processes (ribosome biogenesis, translation initiation, mRNA splicing, transcription) along with signaling regulation (TORC1, GTPase activity), plus neural development terms (forebrain development, neural tube closure, neuron apoptotic process). This combination suggests a module tying RNA metabolism and protein synthesis machinery to neural development contexts.","confidence":"Medium","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0001731","count":6},{"id":"GO:0042254","count":6},{"id":"GO:0000398","count":6},{"id":"GO:0030900","count":5},{"id":"GO:1904263","count":5}]},{"hash":"1495639374254173206","title":"Bacterial central carbon metabolism and catabolism","description":"This cluster centers on core bacterial carbon processing, highlighted by the TCA cycle and acetyl-CoA\u2013related metabolism, along with multiple catabolic pathways for diverse organic acids and sugars (e.g., D-galactarate, glucarate, phenylacetate). The coexistence of these varied carbon-utilization terms suggests a group of proteins dedicated to broad energy generation and metabolic versatility in bacteria.","confidence":"High","size":23,"edges":182,"triangles":771,"max_degree":22,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0046392","count":4},{"id":"GO:0006107","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0043427","count":3}]},{"hash":"1214274023726124153","title":"Fungal Carbohydrate Catabolism and Cell Wall Remodeling","description":"This cluster centers on degradation of plant cell wall polysaccharides (cellulose, mannan, xylan) and a fungal-specific cell wall remodeling process, including disassembly related to cellular fusion. The co-occurrence of nutrient response and sulfate assimilation terms supports a metabolic program linked to growth on polysaccharides and fungal cellular dynamics. Together, these functions point to a cohesive role in fungal carbohydrate catabolism and cell wall remodeling.","confidence":"High","size":23,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0007584","count":4},{"id":"GO:0000103","count":3},{"id":"GO:0006809","count":3},{"id":"GO:0042493","count":3}]},{"hash":"240369341668414054","title":"Bacterial polysaccharide and LPS biosynthesis","description":"The top GO terms cluster around biosynthetic pathways for polysaccharides and glycoconjugates, including colanic acid and O antigen, and sugar donor pathways (dTDP-rhamnose, ADP-L-glycero-beta-D-manno-heptose). This points to bacterial cell-surface polysaccharide assembly and LPS biosynthesis, with supportive carbohydrate metabolism terms; thus the label reflects the dominant function of the cluster.","confidence":"High","size":23,"edges":244,"triangles":1594,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":21},{"id":"GO:0042619","count":17},{"id":"GO:0009718","count":15},{"id":"GO:0006012","count":15},{"id":"GO:0009242","count":15}]},{"hash":"884052438917004008","title":"Membrane Transport of Ions and Nutrients","description":"The top GO terms cluster around various transmembrane transport processes\u2014sugars like glucose and arabinose, multiple ions (sodium, potassium, phosphate, nitrate), and neurotransmitter loading into vesicles\u2014pointing to a cohesive role in membrane transport and nutrient uptake across substrates. This label succinctly captures the shared function of the proteins in the cluster.","confidence":"High","size":22,"edges":47,"triangles":57,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0044381","count":17},{"id":"GO:0015751","count":17},{"id":"GO:0070715","count":17},{"id":"GO:0035435","count":17},{"id":"GO:0052106","count":17}]},{"hash":"1986456409516821497","title":"Unknown","description":"The cluster has only sparse, weak GO term signals (uracil catabolic process, nitrogen utilization, and an obsolete oxidation-reduction term) with no edges or interactions linking the proteins. There is no clear shared function or pathway across the 22 proteins, so a specific, cohesive label cannot be determined.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006212","count":1},{"id":"GO:0019740","count":1},{"id":"GO:0055114","count":1}]},{"hash":"221322129315091753","title":"Cardiac muscle contraction and sarcomere organization","description":"This cluster is dominated by GO terms tied to heart muscle function, including cardiac muscle contraction, sarcomere organization, and regulation of heart rate by epinephrine, suggesting a cohesive theme around cardiac muscle function and sarcomere assembly, with a few metabolism-related terms appearing as potential noise.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":2},{"id":"GO:0017000","count":2},{"id":"GO:1902455","count":1},{"id":"GO:0034609","count":1},{"id":"GO:1904753","count":1}]},{"hash":"448588818965449722","title":"Diverse Membrane Transporters","description":"The top GO terms are dominated by transmembrane transport activities across a wide range of substrates\u2014ions (potassium, sodium, cadmium), xenobiotics, sugars (arabinose, fucose), vitamins, and nitrate\u2014along with a vesicular transport role (neurotransmitter loading). This pattern suggests a cluster of membrane transporter proteins with broad substrate specificity rather than a single, narrow function. Confidence in this labeling is Medium.","confidence":"","size":22,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":6},{"id":"GO:0070574","count":6},{"id":"GO:0006855","count":5},{"id":"GO:0015751","count":5},{"id":"GO:0042128","count":5}]},{"hash":"1268502988574098515","title":"Organelle assembly and homeostasis","description":"These terms cluster around the maintenance and assembly of organelles (ER targeting, mitochondrial complex IV assembly and translation, vacuolar ATPase assembly) plus supporting processes like lipid catabolism and iron homeostasis, and a stress response. This pattern suggests a theme of organelle biogenesis/maintenance and inter-organelle protein trafficking rather than a single pathway.","confidence":"Medium","size":22,"edges":59,"triangles":62,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0045047","count":2},{"id":"GO:0006465","count":2},{"id":"GO:0033617","count":1},{"id":"GO:0070131","count":1},{"id":"GO:0070072","count":1}]},{"hash":"747988208955015063","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000466","count":9},{"id":"GO:0000463","count":9},{"id":"GO:0000480","count":9},{"id":"GO:0000472","count":9},{"id":"GO:0000447","count":9}]},{"hash":"880881217100909389","title":"Cannabinoid biosynthesis proteins","description":"The top GO terms include olivetolic acid biosynthetic process and cannabinoid biosynthetic process, indicating a shared role in cannabinoid biosynthesis. Several other terms (developmental processes, DNA binding) seem incidental or noisy annotations, but the cannabinoid-related terms dominate the signal, making this a cannabinoid biosynthesis\u2013associated cluster.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901697","count":1},{"id":"GO:1901696","count":1},{"id":"GO:0006306","count":1},{"id":"GO:0043388","count":1},{"id":"GO:0030900","count":1}]},{"hash":"2012404125259119245","title":"Golgi trafficking and glycosylation","description":"The cluster\u2019s GO terms largely point to intracellular transport involving the Golgi/ER (retrograde endosome-to-Golgi transport, Golgi retention) and post-translational processing (dolichol-linked oligosaccharide biosynthesis), along with associated nutrient transport (glucose, amino acids) within the cell. A few terms like grooming behavior or lens development may be unrelated or species-specific noise. Overall, a coherent theme around Golgi/ER trafficking and glycosylation emerges.","confidence":"Medium","size":22,"edges":9,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007625","count":2},{"id":"GO:0034488","count":2},{"id":"GO:0006488","count":2},{"id":"GO:0080144","count":2},{"id":"GO:1904659","count":2}]},{"hash":"1618158221284348221","title":"Mitosis and Spindle Assembly","description":"The cluster\u2019s dominant GO terms point to mitotic processes, particularly chromosome alignment/segregation and spindle interactions with microtubules (mitotic metaphase chromosome recapture, mitotic sister chromatid biorientation, positive regulation of microtubule polymerization, attachment of spindle microtubules to kinetochore). There are a few autophagy and DNA repair terms, but they are less prominent, making a mitosis-centric label most representative for this group.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990942","count":1},{"id":"GO:1990758","count":1},{"id":"GO:0031116","count":1},{"id":"GO:0051987","count":1},{"id":"GO:1905185","count":1}]},{"hash":"1220714064187326603","title":"Cell Cycle Regulation and Transcription","description":"The top GO terms are dominated by mitotic cell cycle processes (G1/S transition, re-entry into mitosis, syncytial blastoderm mitotic cycle) and DNA-templated transcription, indicating a cluster of proteins involved in cell cycle control and transcriptional regulation. While there are outliers related to viral interactions and metabolic processes, the strongest and most cohesive signal is cell cycle regulation paired with transcriptional activity.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":2},{"id":"GO:0000320","count":1},{"id":"GO:0060153","count":1},{"id":"GO:1990069","count":1},{"id":"GO:0016242","count":1}]},{"hash":"740680482027394251","title":"Paraxial/Axial Mesoderm Development","description":"The top GO terms are dominated by mesoderm-related processes (axial mesoderm development, paraxial mesoderm development, somitogenesis) and related tissue formation like circulatory system development, suggesting a core theme of early embryonic mesoderm patterning. Some other terms (e.g., rhabdomere development, cellulose catabolic process) appear as noise or cross-species annotation artifacts, but the mesoderm development signal is strongest and representative of the cluster.","confidence":"Medium","size":22,"edges":113,"triangles":219,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":4},{"id":"GO:0045227","count":3},{"id":"GO:0048318","count":2},{"id":"GO:0001756","count":2},{"id":"GO:0048339","count":2}]},{"hash":"1942481327030761550","title":"Meiosis and oocyte development","description":"The most represented terms point to meiotic recombination and chromosome pairing (double-strand break repair in meiotic recombination, heteroduplex formation, synaptonemal complex assembly), cohesion during female meiosis, and ovarian follicle development, indicating a cluster of proteins involved in oocyte meiosis and germline development. The translation terms are likely generic housekeeping signals and do not override the clear meiotic/oogenic theme.","confidence":"High","size":22,"edges":18,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0009636","count":1},{"id":"GO:1990918","count":1},{"id":"GO:0001541","count":1},{"id":"GO:0007066","count":1}]},{"hash":"399644017079494260","title":"Hypoxia-Associated ECM Remodeling and Adhesion","description":"The cluster centers on hypoxia response together with extracellular matrix remodeling activities: cell adhesion, proteolysis, and regulation of collagen catabolism, including integrin-mediated adhesion. This suggests a cohesive module for ECM remodeling under low oxygen. Some peripheral terms (behavioral, plant/catabolic) appear incidental but do not derail the core theme. ","confidence":"Medium","size":22,"edges":75,"triangles":110,"max_degree":18,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0001666","count":4},{"id":"GO:0007155","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0035641","count":2},{"id":"GO:0010710","count":2}]},{"hash":"888388983384591041","title":"Neural development and dendrite morphogenesis","description":"The cluster includes GO terms for nervous system and hippocampus development, and dendrite morphogenesis, along with calcium-dependent exocytosis and ERK signaling regulation, pointing to neuronal differentiation and synaptic maturation as the core theme.","confidence":"High","size":22,"edges":20,"triangles":3,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":15},{"id":"GO:0034198","count":15},{"id":"GO:0051893","count":14},{"id":"GO:0045956","count":14},{"id":"GO:0021766","count":14}]},{"hash":"2143567295002944321","title":"Sphingolipid metabolism and GPI anchor biosynthesis","description":"The cluster is dominated by lipid-related GO terms, especially sphingolipid metabolism (sphingosine, sphinganine-1-phosphate) and regulation of sphingolipid signaling, plus GPI anchor biosynthesis and phospholipid biosynthesis, suggesting a cohesive lipid biosynthesis/signaling theme. Some terms are peripheral, but the core pattern supports a lipid-centric label.","confidence":"High","size":21,"edges":17,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":2},{"id":"GO:0015760","count":2},{"id":"GO:0009395","count":2},{"id":"GO:0035233","count":2},{"id":"GO:0044328","count":2}]},{"hash":"1141779270871636288","title":"Unknown","description":"The top GO terms cover DNA repair, various developmental processes (kidney development, spermatogenesis, stem cell proliferation), signaling pathways, and metabolic regulation, with no single cohesive function linking them. The absence of edges and the broad, disparate functions suggest there is no unified module to label, so a single interpretable name cannot be assigned.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0001822","count":1},{"id":"GO:0007283","count":1},{"id":"GO:1901896","count":1},{"id":"GO:0072089","count":1}]},{"hash":"215253541884888921","title":"Sperm capacitation and membrane potential regulation","description":"Based on the top GO terms, the strongest signals are regulation of membrane potential and sperm capacitation, which together suggest a reproductive signaling context involving electrical changes in gamete biology. The remaining terms mainly reflect diverse metabolic and regulatory processes, which may be ancillary or reflect pleiotropy. Overall, the cluster appears anchored around reproductive signaling with membrane potential changes, hence the label.","confidence":"Low","size":21,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042391","count":3},{"id":"GO:0048240","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0009636","count":2},{"id":"GO:0006212","count":2}]},{"hash":"1377941778395932052","title":"Ion and Metabolite Transmembrane Transporters","description":"The proteins in this cluster are linked to a range of transmembrane transport GO terms (xenobiotic, arabinose, potassium, nitrate, sodium, vitamin, fucose transport) and even neurotransmitter loading into synaptic vesicles, pointing to a common role as membrane transporters moving ions and small metabolites across membranes. This transporter-centric theme best explains the shared function among the cluster members.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":11},{"id":"GO:0015751","count":11},{"id":"GO:0071805","count":11},{"id":"GO:0042128","count":11},{"id":"GO:0006004","count":11}]},{"hash":"1501662604120273611","title":"Transmembrane Transporters","description":"Proteins in this cluster are enriched for transmembrane transport functions across a diverse set of substrates, including xenobiotics, ions (K+, Na+), sugars (arabinose, fucose), and vitamins, and even vesicular neurotransmitter loading. This repeated annotation to membrane transport supports a coherent theme of transporter activity rather than unrelated metabolic roles.","confidence":"High","size":21,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":13},{"id":"GO:0015751","count":12},{"id":"GO:0071805","count":12},{"id":"GO:0042128","count":12},{"id":"GO:0006004","count":12}]},{"hash":"1861175807049138573","title":"Unknown","description":"The GO terms are highly diverse, including mitotic cell cycle and cell population proliferation (cell division), intracellular signaling and GPCR pathway regulation, various developmental contexts (lateral root development, eye photoreceptor development, gastrulation-related polarity), pheromone signaling, and even a behavioral cue (proboscis extension reflex). This spread across species and processes suggests there is no single cohesive function or theme tying the cluster together, so a specific, representative name cannot be confidently assigned.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0035556","count":1},{"id":"GO:0071380","count":1},{"id":"GO:0048527","count":1},{"id":"GO:0000750","count":1}]},{"hash":"55308098128683103","title":"Glycolysis and Gluconeogenesis Core Metabolism","description":"The cluster is dominated by GO terms for glycolysis, gluconeogenesis, fructose metabolism, carbohydrate phosphorylation, and pentose phosphate pathway regulation, pointing to central sugar metabolism and energy production. A few outliers (cobalamin biosynthesis, mitophagy regulation, and other non-metabolic terms) are present but do not override the central carbohydrate metabolism signal.","confidence":"Medium","size":21,"edges":162,"triangles":709,"max_degree":20,"top_function":"autophagy","top_go_terms":[{"id":"GO:0046835","count":7},{"id":"GO:0006094","count":6},{"id":"GO:0006096","count":5},{"id":"GO:0043456","count":5},{"id":"GO:0006000","count":5}]},{"hash":"2248153058518686201","title":"Ubiquitin-dependent proteolysis and cell cycle control","description":"Top GO terms point to ubiquitin-proteasome\u2013mediated degradation (ERAD, SCF, APC) and cell-cycle processes (mitotic control, anaphase-promoting complex\u2013dependent catabolic processes). Chromatin organization and transcription, plus DNA repair, suggest integration of proteostasis with genome maintenance during the cell cycle. This cohesive theme justifies a label focused on ubiquitin-dependent proteolysis coupled to cell-cycle regulation.","confidence":"High","size":21,"edges":71,"triangles":87,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0031146","count":5},{"id":"GO:0031497","count":4},{"id":"GO:0070059","count":4},{"id":"GO:0000724","count":4}]},{"hash":"2053450233948987781","title":"Stress-Responsive Secretory Trafficking","description":"The top GO terms cluster around the secretory pathway (ER to Golgi vesicle transport) and lipid transport (sphingoid long-chain base), both of which tie into vesicle trafficking. A general stress response term is also enriched, suggesting these proteins may coordinate lipid trafficking and secretory processes under stress. While metabolism and signaling terms appear, the dominant pattern is secretory trafficking coupled to lipid transport and stress response, supporting this label.","confidence":"Medium","size":21,"edges":20,"triangles":5,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006950","count":2},{"id":"GO:1905329","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006006","count":1},{"id":"GO:0033499","count":1}]},{"hash":"66950437409966310","title":"Starch, glycogen, and trehalose metabolism","description":"The cluster shows enrichment across both synthesis and breakdown of storage carbohydrates (starch, glycogen, trehalose) and related polysaccharide digestion, indicating a cohesive role in storage polysaccharide metabolism.","confidence":"High","size":21,"edges":33,"triangles":8,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0005993","count":5},{"id":"GO:0005980","count":5},{"id":"GO:0010021","count":5},{"id":"GO:0030980","count":5},{"id":"GO:0019252","count":5}]},{"hash":"156687650330714060","title":"RNA Processing and Splicing Regulation","description":"The terms cluster around mRNA splicing, spliceosome function, mRNA export, stability, modification, and RNA silencing, indicating a group of proteins involved in post-transcriptional RNA processing and regulation of gene expression.","confidence":"High","size":21,"edges":109,"triangles":259,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":11},{"id":"GO:0000381","count":11},{"id":"GO:0045292","count":11},{"id":"GO:0016556","count":10},{"id":"GO:0006406","count":10}]},{"hash":"1309599843904983451","title":"RNA processing and transcriptional regulation","description":"This cluster is enriched for RNA processing (spliceosome-mediated mRNA splicing and polyadenylation), transcriptional regulation (RNA Pol II control, chromatin organization, DNA-templated transcription), and ribosome biogenesis/translation initiation, suggesting a broad program coordinating gene expression from RNA processing to protein synthesis.","confidence":"High","size":21,"edges":209,"triangles":1311,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000398","count":4},{"id":"GO:0035264","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0030433","count":3}]},{"hash":"88668168057588734","title":"Spliceosome-Mediated mRNA Processing and RNA Silencing","description":"This cluster is dominated by post-transcriptional RNA regulation: many proteins are linked to splicing via the spliceosome (cis/splice site recognition and regulation of alternative splicing), mRNA export and modification, and RNA silencing pathways (miRNA- and ncRNA-mediated gene silencing). The strongest terms\u2014regulatory ncRNA-mediated gene silencing, regulation of mRNA splicing via spliceosome, and miRNA-mediated silencing\u2014together point to coordinated control of gene expression at the RNA level, particularly processing and silencing mechanisms.","confidence":"High","size":21,"edges":208,"triangles":1293,"max_degree":20,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":12},{"id":"GO:0048026","count":12},{"id":"GO:0045292","count":9},{"id":"GO:0016556","count":8},{"id":"GO:0006406","count":8}]},{"hash":"84801108473578311","title":"Chromatin and genome maintenance","description":"The cluster\u2019s top GO terms cluster around nuclear processes: telomere maintenance, establishment of protein localization to chromatin, regulation of rRNA processing, and single-strand break repair, all pointing to chromatin organization and genome maintenance. A few terms relate to membrane targeting (SRP-dependent cotranslational targeting), suggesting some multifunctional proteins or annotation noise, but the predominant pattern supports chromatin/genome maintenance. Confidence: Medium","confidence":"","size":21,"edges":30,"triangles":6,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006614","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0090180","count":1},{"id":"GO:2001172","count":1},{"id":"GO:1903212","count":1}]},{"hash":"128338173505430337","title":"Neuronal development and axon remodeling","description":"The top GO terms cluster around brain development and neuron differentiation (rhombomere 5 development, brain segmentation, olfactory bulb interneuron development) and include collagen sprouting of injured axon, plus neuron signaling (nitric oxide mediated signal transduction). While there are general processes like DNA-templated transcription and DNA repair present, the strongest theme is neural development and axon remodeling, suggesting this cluster represents proteins involved in neuronal differentiation, brain patterning, and post-injury axon remodeling.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0021571","count":2},{"id":"GO:0035284","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0048674","count":1}]},{"hash":"1002796552040157338","title":"Mitochondrial translation and calcium handling","description":"These proteins cluster around mitochondrial functions: several terms point to assembly of the respiratory chain complex IV, multiple terms indicate mitochondrial translation, and others involve calcium import into mitochondria and regulation of mitochondrial calcium levels. A few DNA repair and genome maintenance terms appear, but they are peripheral to the dominant mitochondrial gene expression and calcium-related themes. Overall, the cluster seems to reflect mitochondrial protein synthesis together with calcium handling and respiratory chain assembly.","confidence":"High","size":21,"edges":17,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0036444","count":2},{"id":"GO:0051561","count":2},{"id":"GO:0000733","count":1}]},{"hash":"1785801513664455512","title":"Nutrient-responsive RNA Polymerase II transcription","description":"The top GO terms are centered on transcription by RNA Polymerase II and regulation of transcription from RNAP II promoters, including responses to carbon sources and metabolic cues. This suggests a cluster of proteins involved in transcriptional control linked to metabolic regulation, rather than enzymatic steps of metabolism themselves.","confidence":"High","size":21,"edges":150,"triangles":568,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035959","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0061414","count":5},{"id":"GO:2001158","count":5},{"id":"GO:1900399","count":5}]},{"hash":"1631071021709373201","title":"RNA Splicing and Post-transcriptional Regulation","description":"The cluster\u2019s top GO terms center on mRNA splicing by the spliceosome, mRNA processing steps (polyadenylation, export, modification), and RNA-mediated gene silencing (ncRNA and miRNA pathways), implying a cohesive group of proteins involved in post-transcriptional RNA processing and regulation of translation. The presence of IRES-dependent translation hints at broader RNA regulatory roles, reinforcing a splicing/processing-centric cluster theme.","confidence":"High","size":21,"edges":152,"triangles":562,"max_degree":19,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":7},{"id":"GO:0048026","count":7},{"id":"GO:0006378","count":7},{"id":"GO:0045292","count":6},{"id":"GO:0075522","count":6}]},{"hash":"1393398068181101725","title":"Autophagy and TORC1 signaling","description":"This cluster centers on autophagy- and nutrient-sensing processes. Key terms point to microautophagy (GO:0016237), the cytoplasm-to-vacuole targeting (Cvt) pathway (GO:0032258), cellular response to amino acid starvation (GO:0034198), and positive regulation of TORC1 signaling (GO:1904263), along with phosphatidylinositol-mediated signaling (GO:0048015). These collectively indicate a cohesive theme of nutrient-responsive membrane trafficking and autophagic regulation, despite a few peripheral terms related to cell cycle or development. Confidence: Medium","confidence":"","size":21,"edges":5,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0007409","count":3},{"id":"GO:0032258","count":2}]},{"hash":"1452214817531042549","title":"Plant nitrogen metabolism and plasmodesmata transport","description":"The cluster is enriched for plant-relevant metabolism terms (ureide, allantoin, purine catabolic, and oxalate metabolism) and the plasmodesmata-mediated intercellular transport term, pointing to nitrogen compound processing and cell-to-cell transport in plants. While there are a few outlier terms related to development or defense, the core theme centers on plant nitrogen metabolism and intercellular communication.","confidence":"High","size":21,"edges":33,"triangles":9,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0010136","count":2},{"id":"GO:0033609","count":2},{"id":"GO:0010497","count":2},{"id":"GO:0000256","count":2},{"id":"GO:0006145","count":2}]},{"hash":"1139877912503018672","title":"Mitochondrial respiration and protein import","description":"The top GO terms indicate mitochondrial electron transport (ubiquinol to cytochrome c), proton transmembrane transport, and proton motive force\u2013driven ATP synthesis, along with protein import into the mitochondrial matrix and protein targeting to mitochondrion. This suggests a cluster centered on mitochondrial energy production and the mitochondrial protein import machinery. Some vacuolar terms appear, but the core signal is mitochondrial bioenergetics and import. ","confidence":"High","size":21,"edges":189,"triangles":986,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":4},{"id":"GO:0007035","count":4},{"id":"GO:0042777","count":4},{"id":"GO:0006122","count":3},{"id":"GO:0006814","count":3}]},{"hash":"141807852702088565","title":"Diverse membrane transporters","description":"The GO terms show transmembrane transport of a variety of substrates (arabinose, phosphate, potassium, nitrate/nitrite, vitamins, sialic acid) and vesicular neurotransmitter loading, indicating a cluster of membrane transporter proteins with diverse substrates. The pattern is cohesive around transport activity, despite no interaction edges.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":4},{"id":"GO:0035435","count":4},{"id":"GO:0071805","count":4},{"id":"GO:0042128","count":4},{"id":"GO:0015706","count":4}]},{"hash":"876542063026789231","title":"Bacterial metabolism and metal ion transport","description":"The top GO terms cluster around carbohydrate and amino acid biosynthesis and general metabolism (lipopolysaccharide biosynthesis, serine and N-acetylglucosamine synthesis, glycolate and carbohydrate metabolism), together with metal ion transport and calcium homeostasis (zinc, copper, calcium). This combination suggests a functional grouping related to metabolic processing and ion transport characteristic of bacterial envelope biogenesis and nutrient handling, with a possible outlier term (response to testosterone) that may reflect cross-annotated or non-specific signals. Overall, the theme is metabolism coupled with metal ion transport.","confidence":"Medium","size":20,"edges":101,"triangles":243,"max_degree":15,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0009103","count":5},{"id":"GO:0006564","count":4},{"id":"GO:0006874","count":3},{"id":"GO:0071577","count":3},{"id":"GO:0033574","count":3}]},{"hash":"347246472748540474","title":"Metabolism and xenobiotic response","description":"The cluster\u2019s top terms cluster around core metabolic processes (glycolysis, 2-oxoglutarate and lipoate metabolism, polyamine catabolism) and detox/xenobiotic response, suggesting a metabolic/detoxification theme rather than a single specific pathway. Some terms are obsolete, but the remaining terms point to energy metabolism and xenobiotic processing as the shared function among these proteins.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0017198","count":2},{"id":"GO:0006598","count":2},{"id":"GO:0006096","count":1}]},{"hash":"741908245083901740","title":"Cardiac Muscle Development and Endosomal Transport","description":"The cluster centers on heart development, cardiac muscle contraction, and striated muscle differentiation, indicating a cardiovascular/muscle focus. Additional terms point to vesicle trafficking and membrane dynamics (endosomal transport, negative regulation of membrane tubulation) and signaling processes (PI3K/AKT) plus sterol biosynthesis, suggesting a link between muscle biology, lipid metabolism, and intracellular trafficking.","confidence":"Medium","size":20,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903526","count":3},{"id":"GO:0016197","count":2},{"id":"GO:0060716","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0060048","count":2}]},{"hash":"1146840662707091372","title":"Chromatin regulation and cell cycle control","description":"This cluster is enriched for DNA-templated transcription and histone methylation (H3K4/H3K79), along with ubiquitin-dependent proteolysis and mitotic spindle assembly. These terms point to a nuclear program that links chromatin state and gene expression with chromosome segregation and cell division, consistent with development-related growth signals. A secondary connection to membrane signaling (PI3P biosynthesis) may support growth, but the core theme is chromatin/transcription coupled to cell-cycle regulation.","confidence":"Medium","size":20,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0035948","count":3},{"id":"GO:0034729","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0042787","count":2}]},{"hash":"1150949806885245978","title":"Membrane Biogenesis and Metal Ion Stress","description":"Top GO terms suggest a theme tying membrane-related processes (nuclear envelope organization, GPI anchor attachment, rhabdomere membrane biogenesis) with metal ion handling (heme oxidation, iron ion homeostasis, cadmium response). The immune-related terms are sparse and likely incidental; overall, the cluster seems to coalesce around membrane biology and responses to metal ion stress. Confidence: Medium.","confidence":"","size":20,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006998","count":2},{"id":"GO:0016255","count":1},{"id":"GO:0045313","count":1},{"id":"GO:0006788","count":1},{"id":"GO:0032764","count":1}]},{"hash":"1145844218519122246","title":"Mitotic spindle dynamics and chromosome alignment","description":"Top GO terms point to mitosis: positive regulation of microtubule polymerization, attachment of spindle microtubules to kinetochores, and mitotic sister chromatid biorientation. These co-occur with one outlier term on stem cell maintenance, which does not define the core function.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031116","count":1},{"id":"GO:0051987","count":1},{"id":"GO:1990758","count":1},{"id":"GO:1902455","count":1}]},{"hash":"146650063952423382","title":"Innate Immune Activation and IFN-\u03b2 Production","description":"The cluster is enriched for innate-immune terms: antibacterial humoral response, innate immune response in mucosa, macrophage activation involved in immune response, and positive regulation of interferon-beta production, suggesting a set of proteins involved in mucosal defense and antiviral signaling. While some terms touch on translation, transcription regulation, and piRNA processing, these appear peripheral; the dominant theme is innate immune activation and interferon signaling.","confidence":"Medium","size":20,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0019731","count":1},{"id":"GO:0002227","count":1},{"id":"GO:0043388","count":1},{"id":"GO:0045578","count":1}]},{"hash":"603767779655583222","title":"Neurodevelopment and ribosome biogenesis","description":"The cluster shows strong neural development signals (forebrain development, neural tube closure, neuron apoptotic process) alongside ribosome biogenesis (maturation of SSU-rRNA) and signaling regulation (TORC1, GTPase activity, transcription), suggesting a set of proteins coordinating neural development with protein synthesis and signaling pathways.","confidence":"Medium","size":20,"edges":114,"triangles":289,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000462","count":6},{"id":"GO:0008584","count":5},{"id":"GO:0030900","count":4},{"id":"GO:1904263","count":4},{"id":"GO:0051402","count":4}]},{"hash":"154001490395241996","title":"DNA Damage Response and Cell Cycle Regulation","description":"The cluster centers on DNA-centric processes: DNA replication, DNA repair, replication checkpoints, and cellular responses to ionizing radiation, along with mitotic/meiotic cell cycle activity, which together point to a coordinated DNA damage response coupled to cell cycle control. Some translation initiation terms and apoptotic/aging associations may reflect broader stress or downstream effects but do not override the core theme. ","confidence":"High","size":20,"edges":14,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0006281","count":2},{"id":"GO:0000076","count":2},{"id":"GO:0071479","count":2},{"id":"GO:0051321","count":2}]},{"hash":"284883326835259813","title":"Amino acid biosynthesis and redox metabolism","description":"The cluster shows enrichment for biosynthetic processes of valine, isoleucine, and lysine, indicating a focus on amino acid production. Additional terms for one-carbon metabolism and NADPH regeneration point to redox-balanced biosynthesis. The sporulation term suggests a possible stress-response context typical of Bacillus-like organisms.","confidence":"Medium","size":20,"edges":156,"triangles":699,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":12},{"id":"GO:0009097","count":9},{"id":"GO:0009099","count":6},{"id":"GO:0030435","count":6},{"id":"GO:0046392","count":5}]},{"hash":"1271845177167833300","title":"DNA Repair and Cell Cycle Cluster","description":"Top terms cluster around DNA repair (DNA repair, double-strand break repair), meiotic cell cycle, and centrosome duplication, pointing to roles in genome maintenance and cell division. Apoptotic and hormone-response terms are related but secondary. A few neural development terms appear, likely reflecting broader roles in development, but the dominant theme is DNA damage response and cell-cycle regulation.","confidence":"High","size":20,"edges":24,"triangles":8,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0051298","count":2},{"id":"GO:0043433","count":2}]},{"hash":"2135393721482623833","title":"Steroid and lipid biosynthesis","description":"The top GO terms are strongly dominated by lipid-related biosynthetic processes (fatty acid elongation, very long-chain fatty acid, sphingolipid biosynthesis) and steroid hormone production (C21-steroid metabolism, estrogen and glucocorticoid biosynthesis). This pattern points to a cluster centered on lipid metabolism and steroid biosynthesis, with some regulatory or ancillary processes like transcription regulation and pigment biosynthesis becoming less central. ","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030497","count":19},{"id":"GO:0008207","count":19},{"id":"GO:0006704","count":19},{"id":"GO:0042438","count":19},{"id":"GO:0031427","count":19}]},{"hash":"1296668547181220412","title":"RNA processing and transcription regulation","description":"These proteins are enriched for RNA-related processes: mRNA capping (7-methylguanosine), RNA guanine-N7 methylation, and tRNA wobble uridine modification, along with regulation of DNA-templated transcription. This constellation points to RNA processing and transcription control as the cluster's core function. A couple of outlier terms (antibiotic biosynthesis, nodulation) are less connected to this core, suggesting peripheral associations.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001300","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0017000","count":2}]},{"hash":"259536466087134715","title":"Mitochondrial respiration and redox homeostasis","description":"This cluster shows strong enrichment for mitochondrial electron transport, aerobic respiration, cytochrome complex assembly, and proton transport, along with cellular redox homeostasis and detoxification of reactive oxygen species, all pointing to a cohesive role in oxidative phosphorylation and redox balance. Although a couple of terms are obsolete, the dominant theme remains mitochondrial respiration and redox management.","confidence":"High","size":20,"edges":123,"triangles":368,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0030416","count":3},{"id":"GO:0019430","count":3},{"id":"GO:0017004","count":3}]},{"hash":"2177246849013659956","title":"Cell Cycle and Protein Processing","description":"The terms point to core roles in cell division/mitotic cycle (cell division, mitotic cell cycle) and in protein handling (ribosomal export, ER membrane targeting, unfolded protein response) suggesting coordination between cell cycle progression and protein processing/quality control. Peripheral terms such as responses to lead ion or morphine appear as ancillary stress signals, not defining the cluster\u2019s primary function. This supports labeling as Cell Cycle and Protein Processing with Medium confidence.","confidence":"Medium","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0016576","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0010288","count":2},{"id":"GO:0000278","count":2}]},{"hash":"137610983372836452","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":148,"triangles":580,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006310","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0000462","count":2}]},{"hash":"660535228415590804","title":"Regulatory Signaling and Apoptosis","description":"Top GO terms point to modulation of diverse cellular processes, with a common thread of signaling regulation and apoptosis control (growth factor response, ubiquitination, lipidation, transcription factor import, mRNA modification, and extrinsic muscle cell apoptosis). The lack of edges suggests a loosely connected regulatory set rather than a single pathway, supporting a label that reflects broader regulatory functions in signaling and cell death.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071364","count":1},{"id":"GO:0090083","count":1},{"id":"GO:0010763","count":1},{"id":"GO:0031397","count":1},{"id":"GO:2001145","count":1}]},{"hash":"207354749344214071","title":"Nucleolar ribosome biogenesis and rRNA processing","description":"The top GO terms cluster around ribosome biogenesis and rRNA maturation (SSU/LSU/5.8S), with several terms for ribosome assembly and rRNA processing, plus supportive nuclear/nucleolar activities like chromatin remodeling and nucleosome assembly, indicating a cohesive role in ribosome production within the nucleus/nucleolus.","confidence":"High","size":19,"edges":169,"triangles":935,"max_degree":18,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042273","count":5},{"id":"GO:0000462","count":4},{"id":"GO:0000390","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0043044","count":3}]},{"hash":"356945372221436582","title":"Lamellipodium assembly and cell migration","description":"The top terms converge on actin-driven protrusion, lamellipodium assembly, cell polarity, spreading, and chemotaxis, indicating proteins that coordinate cytoskeleton remodeling and adhesion during cell movement. Some terms are obsolete, but the core theme is consistent with motility and lamellipodium dynamics.","confidence":"High","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:1990441","count":3},{"id":"GO:0043552","count":3},{"id":"GO:2000769","count":3},{"id":"GO:0002408","count":3},{"id":"GO:0060124","count":3}]},{"hash":"1739669336627705673","title":"MAPK-Driven Growth and Cell Cycle","description":"The top terms center on MAPK signaling cascades (p38MAPK and ERK1/ERK2) and growth/division processes such as mitotic cell cycle, pseudohyphal/invasive growth, and responses to growth stimuli (PMA, GM-CSF). Structural and polarity-related terms (septin ring organization, ER polarization) further tie signaling to cell proliferation and morphogenesis. Overall, the cluster appears to reflect MAPK-mediated regulation of growth and cell cycle progression.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:1904628","count":2},{"id":"GO:0038066","count":2},{"id":"GO:0070371","count":2},{"id":"GO:0001403","count":2}]},{"hash":"566505562755898321","title":"Protein prenylation (farnesylation and geranylgeranylation)","description":"GO terms strongly point to protein farnesylation and geranylgeranylation as a shared function, i.e., lipid modification of proteins that modulates signaling and can influence cell-cycle regulation; this cohesiveness justifies the label.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010035","count":1},{"id":"GO:0018344","count":1},{"id":"GO:0008285","count":1},{"id":"GO:0018343","count":1},{"id":"GO:0048146","count":1}]},{"hash":"1579053842889826527","title":"Nucleotide and Cofactor Biosynthesis","description":"The proteins cluster around nucleotide phosphorylation and biosynthesis (ADP, CDP, purine ribonucleotides) and cofactor production (NAD+, CoA), pointing to a cohesive role in nucleotide and coenzyme metabolism. The brain development term is present but appears peripheral to the main metabolic theme.","confidence":"High","size":19,"edges":134,"triangles":539,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0015937","count":7},{"id":"GO:0016310","count":7},{"id":"GO:0046939","count":6},{"id":"GO:0046940","count":6},{"id":"GO:0009435","count":4}]},{"hash":"2069158833638885010","title":"ER-Golgi Trafficking and Protein Processing","description":"This cluster is dominated by GO terms related to ER-to-Golgi vesicle transport and post-translational targeting to the ER membrane, plus translocation to membranes, indicating a shared role in the secretory pathway and protein processing within the ER-Golgi system. A few sugar metabolism terms are present but appear secondary to the trafficking/processing theme, so the overall signal points to ER-Golgi trafficking functions.","confidence":"Medium","size":19,"edges":64,"triangles":91,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0006620","count":2},{"id":"GO:0031204","count":2},{"id":"GO:0009750","count":1}]},{"hash":"192254641194381410","title":"Endocrine Development and Hormone Signaling","description":"The cluster shows a clear emphasis on endocrine processes: regulation of blood pressure via renin-angiotensin, thyroid hormone generation, adeno-hypophysis morphogenesis, and response to cAMP. These terms suggest a coherent theme around hormone signaling and endocrine development, with other items like otolith development and metal ion transport appearing as peripheral or context-dependent associations. Confidence: Medium","confidence":"","size":19,"edges":162,"triangles":828,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0003081","count":6},{"id":"GO:0048840","count":6},{"id":"GO:0006590","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0015677","count":6}]},{"hash":"125895223751071953","title":"Amino acid and vitamin biosynthesis","description":"This cluster is dominated by GO terms for biosynthetic processes of amino acids (tyrosine, phenylalanine, lysine, alanine) and cofactors like biotin and cobalamin, as well as heme precursor synthesis (protoporphyrinogen IX). Together these point to a core theme of metabolic biosynthesis. The Notch signaling and DNA-templated transcription terms appear more as broader annotations rather than core drivers of this cluster. ","confidence":"Medium","size":19,"edges":138,"triangles":585,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":9},{"id":"GO:0009102","count":9},{"id":"GO:0006782","count":9},{"id":"GO:0042853","count":8},{"id":"GO:0097053","count":8}]},{"hash":"1594835345312365391","title":"Intracellular trafficking and membrane transport","description":"The terms cluster around vesicle- and transporter-mediated movement within the cell\u2014ER-Golgi transport and reverse, endocytosis, anterograde trafficking to the membrane, and nuclear import\u2014plus GTPase regulation which governs vesicle trafficking and membrane dynamics. Glucose transporter trafficking in response to insulin also aligns with this theme. A few cell division terms appear but do not dominate, so the main signal is intracellular transport processes. ","confidence":"High","size":19,"edges":78,"triangles":163,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0007076","count":3},{"id":"GO:0006897","count":3}]},{"hash":"1048108266142869528","title":"Golgi-to-vacuole and endomembrane trafficking","description":"This cluster is dominated by vesicle transport terms between the Golgi, ER, endosomes, and vacuoles (Golgi organization; Golgi to vacuole transport; retrograde Golgi-ER and endosome-Golgi transport; endocytic recycling; Cvt pathway; exocyst localization), indicating a cohesive role in intracellular trafficking within the secretory and endocytic pathways. A few mitosis-related terms are present but less represented, so the primary theme is vesicle trafficking, not cell division.","confidence":"High","size":19,"edges":139,"triangles":533,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006896","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0007112","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0032258","count":3}]},{"hash":"366027491731971789","title":"Ubiquitin-Proteasome\u2013Mediated Cell Cycle Regulation","description":"The cluster is enriched for ubiquitination and proteasome-related processes (proteasomal degradation, SCF-dependent ubiquitin tagging, and polyubiquitination) along with mitotic G1 DNA damage checkpoint signaling and G1/S transcription regulation, pointing to a core role in protein turnover governing cell cycle control. Also notes of metal stress responses (cadmium, methylmercury) and circadian regulation fit with ubiquitin-mediated regulation, reinforcing the central theme of ubiquitin\u2013proteasome\u2013driven cell cycle control.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031571","count":6},{"id":"GO:0071276","count":6},{"id":"GO:0000083","count":5},{"id":"GO:0000209","count":5},{"id":"GO:0042787","count":5}]},{"hash":"1009176354076650625","title":"Unknown","description":"The GO terms are diverse (ER organization, mitochondrial inner-m membrane insertion, iron/arsenate transport, serine biosynthesis, dephosphorylation, secretion, and transepithelial water transport), with no clear dominant function linking the proteins.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071786","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0033215","count":1},{"id":"GO:1901684","count":1},{"id":"GO:0006827","count":1}]},{"hash":"2034244784657666943","title":"Cell wall and polysaccharide metabolism","description":"GO terms show polysaccharide catabolism (xylan, raffinose) and cell envelope biosynthesis (lipopolysaccharide, lipid A, spore wall) plus biofilm formation and antibiotic response, indicating a theme around carbohydrate utilization and cell-wall/envelope construction in microbial adaptation.","confidence":"Medium","size":19,"edges":58,"triangles":54,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":4},{"id":"GO:0046677","count":2},{"id":"GO:0034232","count":2},{"id":"GO:0019428","count":2},{"id":"GO:0042710","count":2}]},{"hash":"1256658015466597082","title":"Unknown","description":"The top GO terms are highly diverse, including plant cell wall processes (xylan catabolic and cutin biosynthetic), lipid biosynthesis/remodeling (phosphatidylcholine remodeling, ether lipid and triglyceride biosynthesis, PC biosynthesis regulation), immune signaling (interleukin-2 production, T cell activation-induced cell death regulation), and mitochondrial energy metabolism, with no clear shared pathway or function across the proteins; there are no edges or coherent theme to bind the cluster. ","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":2},{"id":"GO:0006663","count":1},{"id":"GO:0070970","count":1},{"id":"GO:0036151","count":1},{"id":"GO:0019432","count":1}]},{"hash":"959112331086894657","title":"Vacuolar amino acid transport and starvation response","description":"The top GO terms point to lysine transport into and out of the vacuole and alanine transport, complemented by cellular responses to potassium ion starvation and nitrogen starvation, suggesting a coherent theme around vacuolar amino acid transport and nutrient stress adaptation. Some transcription-related terms appear, but they are less representative of the dominant pattern focused on vacuolar amino acid movement and starvation responses.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045842","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0045078","count":2},{"id":"GO:0015808","count":2}]},{"hash":"1542743279978778703","title":"Glycosphingolipid biosynthesis","description":"Two strongly represented GO terms are globoside biosynthetic process and mannosyl-inositol phosphorylceramide biosynthetic process, both indicating glycosphingolipid pathways. While some other terms touch on broader carbohydrate metabolism or are obsolete, the dominant signal is lipid glycosylation and sphingolipid assembly, suggesting the cluster centers on glycosphingolipid biosynthesis or related lipid metabolism.","confidence":"High","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001576","count":1},{"id":"GO:0051999","count":1},{"id":"GO:0036210","count":1},{"id":"GO:0006006","count":1},{"id":"GO:0042952","count":1}]},{"hash":"1249170342265945761","title":"Plant seed membrane transport and metabolism","description":"The top GO terms show a mix of membrane transport across the plasma membrane (glutathione, amino acids, calcium), membrane dynamics (phospholipid translocation), and core metabolic processes (NADP/NAD+, polyphosphate) together with seed development. This suggests a theme around plant seed-specific transport and metabolic regulation at the membrane, rather than a single tightly defined function. However, the connections are not strongly cohesive (no edges), so the label is tentative.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051515","count":2},{"id":"GO:0098709","count":2},{"id":"GO:0061091","count":2},{"id":"GO:0048316","count":2},{"id":"GO:0032973","count":1}]},{"hash":"1250193635929385652","title":"Phosphoinositide signaling and autophagy","description":"The top GO terms cluster around phosphatidylinositol phosphate biosynthesis and PI lipid signaling (GO:0046854, GO:1902635), endomembrane system organization (GO:0010256), and autophagosome assembly regulation (GO:2000786), which together point to a membrane-centric module governing lipid signaling and autophagy. Some terms are more contextually distant (sporulation, myelin, megakaryocyte development), but the core signal supports a membrane dynamics/autophagy theme.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0010256","count":1},{"id":"GO:0031321","count":1},{"id":"GO:0046854","count":1},{"id":"GO:1902635","count":1}]},{"hash":"882699579093871961","title":"Sugar and aldehyde metabolism cluster","description":"This cluster\u2019s top GO terms center on catabolic processes for sorbitol, formaldehyde, ethanol, galactose, and furaldehyde, with a related fructose biosynthesis term. The common thread is metabolism of various carbohydrates and aldehydes, suggesting proteins involved in sugar/aldehyde processing rather than a single precise pathway. Confidence: Medium","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006062","count":1},{"id":"GO:0046294","count":1},{"id":"GO:0000947","count":1},{"id":"GO:0045777","count":1},{"id":"GO:0006068","count":1}]},{"hash":"92875071614716666","title":"Cerebellar Glial Differentiation Signaling","description":"The cluster is dominated by terms tied to cerebellar development, notably cerebellar cortex formation and Bergmann glial cell differentiation, suggesting a role in cerebellar glia development. Supporting terms include neural development signaling and cell migration, with additional signaling pathway annotations (insulin and T cell receptor signaling) that may reflect broader signaling proteins in this cluster. Some cell-cycle regulation terms imply developmental control of proliferation, aligning with differentiation processes. Overall, a cerebellar glial differentiation\u2013centric function best fits the combined GO terms.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2001275","count":4},{"id":"GO:0008286","count":4},{"id":"GO:0097011","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0021697","count":3}]},{"hash":"349288312681951829","title":"Unknown","description":"The top GO terms are diverse (translation, transport, freezing response, peroxisome autophagy) with only 1 hit each and no interactions, so there is no clear shared function or pathway to define a meaningful label. Therefore Unknown with confidence None.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0006810","count":1},{"id":"GO:0050826","count":1},{"id":"GO:0030242","count":1}]},{"hash":"1072396717968126515","title":"Glycosylation and carbohydrate metabolism in insect follicle cells","description":"Most of the top GO terms point to carbohydrate metabolism and protein glycosylation (glycogen biosynthesis, galactose metabolism, O-linked glycosylation). Several terms (follicle cell adhesion, maintenance of polarity of follicular epithelium) indicate a role in Drosophila ovarian follicle cells during oogenesis, where glycosylation of extracellular proteins and metabolic support are important. Taken together, the cluster appears to represent glycosylation- and carbohydrate-metabolism\u2013related activities in insect follicle cells.","confidence":"High","size":18,"edges":105,"triangles":327,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":6},{"id":"GO:0071555","count":5},{"id":"GO:0075015","count":4},{"id":"GO:0001744","count":4},{"id":"GO:0007299","count":4}]},{"hash":"1488590597072379096","title":"Actin Cytoskeleton Dynamics and GTPase Signaling","description":"This cluster is enriched for actin-related processes (filament polymerization/organization, cortical patch assembly) and small GTPase\u2013mediated signaling, indicating coordinated actin cytoskeleton remodeling driven by GTPase activity. The presence of dendritic spine morphogenesis and cell polarity terms further supports a theme of cytoskeletal dynamics affecting cell shape and morphology; a couple of outliers may reflect broader annotation noise but do not change the dominant pattern.","confidence":"High","size":18,"edges":132,"triangles":568,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0030041","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0007264","count":3},{"id":"GO:0030036","count":3},{"id":"GO:0007015","count":3}]},{"hash":"91721240199197760","title":"Unknown","description":"The GO terms are diverse, spanning immune signaling (TLR3, IL-2 production), neuronal synaptic regulation, mitochondrial inheritance, lipid regulation, and development, with several obsolete entries. There is no clear, single biological function or pathway tying these terms together, suggesting either a multi-function or noisy cluster rather than a coherent theme.","confidence":"","size":18,"edges":150,"triangles":769,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:1903044","count":1},{"id":"GO:0052547","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0070584","count":1},{"id":"GO:0000001","count":1}]},{"hash":"2087381551554306994","title":"Galactose-responsive metabolism and transcription","description":"This cluster centers on galactose-related processes: galactose metabolism, galactitol and D-galacturonate pathways, and especially transcriptional regulation influenced by galactose, including positive regulation of RNA Pol II transcription by galactose. While other metabolic terms (lipid/isoprenoid biosynthesis, threonine/methionine biosynthesis) appear, the strongest cohesive signal is carbohydrate/galactose metabolism linked to transcriptional control, suggesting a theme of galactose-driven metabolic regulation.","confidence":"Medium","size":18,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":3},{"id":"GO:0009088","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006468","count":2},{"id":"GO:0061623","count":2}]},{"hash":"390436282664065665","title":"Ubiquitin-regulated protein turnover and trafficking","description":"This cluster prominently features ubiquitination-related processes (autoubiquitination, deubiquitination, ubiquitin-dependent ERAD) and regulation of endocytosis, pointing to a theme of protein quality control and intracellular trafficking. Some terms also touch on neuronal growth and mitochondrial dynamics, but the core signals center on ubiquitin-mediated turnover and trafficking.","confidence":"Low","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0010636","count":1},{"id":"GO:0097237","count":1}]},{"hash":"584003881290116697","title":"Nuclear DNA replication and chromatin remodeling","description":"This cluster centers on core nuclear processes: DNA replication and DNA unwinding, transcription, and RNA splicing, with chromatin-related terms like subtelomeric heterochromatin formation and nucleosome mobilization. The presence of tissue-development GO terms (e.g., substantia nigra and seminiferous tubule development) alongside male meiosis hints at germline-related gene expression programs, reinforcing a theme of nuclear DNA management and chromatin dynamics across development.","confidence":"Medium","size":18,"edges":150,"triangles":769,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0021762","count":3},{"id":"GO:0006348","count":3},{"id":"GO:0042766","count":3},{"id":"GO:0072520","count":3}]},{"hash":"1873814509290148506","title":"Fungal transcriptional regulation of metabolism","description":"This cluster centers on GO terms about transcriptional regulation (DNA-templated transcription and RNA Pol II\u2013dependent transcription) and regulation of metabolic pathways (lysine and leucine biosynthesis, cellular respiration), with fungus\u2011specific processes like aflatoxin and ergosterol biosynthesis, suggesting proteins involved in controlling fungal metabolism and secondary metabolism.","confidence":"Medium","size":18,"edges":14,"triangles":2,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001196","count":3},{"id":"GO:0035961","count":3},{"id":"GO:0061429","count":3},{"id":"GO:0035948","count":3},{"id":"GO:0043457","count":3}]},{"hash":"1174808816094422190","title":"Diverse membrane transporters","description":"This cluster's GO terms are dominated by transmembrane transport activities across a variety of substrates (nitrite, nitrate, arabinose, phosphate, potassium, vitamin, sialic acid) and vesicular neurotransmitter loading, indicating proteins that function primarily in moving substrates across membranes rather than a single specialized substrate. The diversity suggests a broad transporter role or a transporter family with multiple substrates.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":6},{"id":"GO:0015751","count":5},{"id":"GO:0035435","count":5},{"id":"GO:0071805","count":5},{"id":"GO:0042128","count":5}]},{"hash":"416668046905277830","title":"ER protein folding and ER stress response","description":"The cluster is dominated by GO terms tied to the endoplasmic reticulum: post-translational targeting to membrane, protein folding in ER, and ER stress\u2013responsive translation initiation. It also includes regulation of protein kinase activity and cellular heat response, aligning with ER quality control and the unfolded protein response. A few terms (e.g., DNA replication) are less connected, but the strongest signals point to ER protein folding/quality control and stress response.","confidence":"High","size":18,"edges":140,"triangles":635,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0031204","count":14},{"id":"GO:0006260","count":14},{"id":"GO:0045454","count":14},{"id":"GO:0090084","count":14},{"id":"GO:0070389","count":14}]},{"hash":"919673206201856993","title":"Germline development and spermatogenesis","description":"The cluster is dominated by germline-focused processes: piRNA processing, male meiotic nuclear division, spermatid differentiation, and DNA-templated transcription, with supporting signals from splicing regulation in germ cells, pointing to a coherent theme of germline gene expression during spermatogenesis.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0034587","count":3},{"id":"GO:0043046","count":3},{"id":"GO:0007140","count":3},{"id":"GO:0035021","count":3}]},{"hash":"1128224212441397236","title":"Chromatin Modification and Actin Remodeling in Neural Development","description":"The top terms show histone acetylation (H4 and H3) pointing to chromatin modification, plus Arp2/3 complex\u2013mediated actin nucleation and barbed-end capping indicating actin cytoskeleton remodeling; vesicle transport (ER to Golgi) and development terms (forebrain, seminiferous tubule, neuron apoptotic process) alongside TORC1 signaling suggest coordinated regulation of gene expression, cytoskeleton dynamics, and trafficking during neural development.","confidence":"Medium","size":18,"edges":130,"triangles":501,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0043982","count":5},{"id":"GO:0043981","count":5},{"id":"GO:0034314","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0043966","count":4}]},{"hash":"661342717219415370","title":"Redox-regulated embryonic growth and apoptosis","description":"The terms cluster around redox-related processes (glutathione metabolism, response to oxidative stress) together with cell proliferation and apoptosis, including in utero embryonic development. This suggests a role in redox-sensitive regulation of cell fate during development, balancing growth and programmed cell death. The low connectivity (1 edge, 0 triangles) indicates the terms are related but not tightly interconnected, consistent with a broad developmental redox theme rather than a single tightly defined pathway.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0006749","count":2}]},{"hash":"852723511599650705","title":"Organelle Protein Import and Targeting","description":"The cluster is enriched for GO terms related to importing proteins into mitochondria (matrix and inner membrane) and chloroplasts (stroma), as well as ER localization/exit site and ER-to-cytosol retrograde transport. This points to a cohesive theme of protein targeting and trafficking to organelles and membranes, despite a few unrelated terms that may be incidental annotations.","confidence":"High","size":18,"edges":60,"triangles":70,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":3},{"id":"GO:0045039","count":2},{"id":"GO:0032094","count":2},{"id":"GO:0000002","count":2},{"id":"GO:0045037","count":2}]},{"hash":"1110843905138858993","title":"Diverse Membrane Transporters","description":"The top GO terms are dominated by various transport activities across membranes for different substrates (glucose, trehalose, urate, DHA, xenobiotics, organic cations, etc.), indicating a core theme of solute transport. A few terms touch on postsynaptic density clustering or epithelial maintenance, but the prevailing signal is transporter function; thus the label \"Diverse Membrane Transporters\" captures the cluster.","confidence":"High","size":18,"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:0044381","count":1},{"id":"GO:0070715","count":1},{"id":"GO:0052106","count":1}]},{"hash":"484474132954222261","title":"Mitotic DNA Replication Machinery","description":"The top GO terms are dominated by mitotic DNA replication processes: initiation, preinitiation complex assembly, elongation, and GINS complex assembly, indicating a module of proteins involved in initiating and carrying out DNA replication specifically during mitosis. Some terms are obsolete, but the core signal points to replication machinery operating in cell division rather than general transcription or metabolism.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":1},{"id":"GO:0033585","count":1},{"id":"GO:0032508","count":1},{"id":"GO:1902983","count":1},{"id":"GO:1902977","count":1}]},{"hash":"1023991721235604575","title":"Alcohol and Retinoid Metabolism","description":"The cluster is dominated by GO terms for retinol and retinal metabolism, along with multiple alcohol and aldehyde catabolic/oxidation processes (ethanol catabolic/oxidation, formaldehyde catabolic, sorbitol catabolic, and related Ehrlich pathway activity), plus a broader redox/oxidation-reduction theme and even related biosynthetic metabolism. This suggests a cohesive function in detoxification and metabolism of alcohols and retinoids, rather than unrelated processes.","confidence":"High","size":18,"edges":95,"triangles":240,"max_degree":17,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0042572","count":12},{"id":"GO:0055114","count":11},{"id":"GO:0006068","count":9},{"id":"GO:0006069","count":9},{"id":"GO:0042574","count":7}]},{"hash":"2300024160070406450","title":"Unknown","description":"The GO terms are highly diverse, spanning nucleotide and inositol metabolism, stress responses, lipid and proteoglycan biosynthesis, and signaling/development. There is no single dominant function or pathway linking the proteins, so the cluster appears functionally heterogeneous or uncharacterized, warranting an Unknown label.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006144","count":1},{"id":"GO:0032958","count":1},{"id":"GO:0016036","count":1},{"id":"GO:0071454","count":1},{"id":"GO:0006020","count":1}]},{"hash":"1942763801883040325","title":"Unknown","description":"The top GO terms are a mix of unrelated processes (glucose response, insulin secretion, ammonia assimilation, promoter binding, epithelial proliferation, plasminogen activation) and several obsolete terms, with no clear shared function or interaction pattern tying the proteins together. Given the apparent heterogeneity and lack of connectivity, there isn\u2019t a coherent, representative label to assign.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044044","count":1},{"id":"GO:0009749","count":1},{"id":"GO:0090295","count":1},{"id":"GO:1904797","count":1},{"id":"GO:0010756","count":1}]},{"hash":"1489036852686136414","title":"Lipid Droplet Biogenesis and Storage","description":"Based on the top GO terms, the proteins are enriched for lipid droplet organization, lipid storage, and seed oilbody biogenesis, with related lipid metabolism activities (e.g., diacylglycerol catabolic process, arachidonate metabolism) and some vesicle trafficking terms. This pattern points to a function in lipid droplet formation and storage rather than a single enzymatic activity.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034389","count":1},{"id":"GO:0019915","count":1},{"id":"GO:0010344","count":1},{"id":"GO:0042122","count":1},{"id":"GO:1903507","count":1}]},{"hash":"2234254336092905741","title":"Unknown","description":"The GO terms cover diverse processes (cell division stages, development in plants/fungi, nucleolar maintenance, membrane transport, and lipid/phospholipid regulation) with no single dominant function. Because no coherent theme emerges among the top terms, a specific functional label cannot be confidently assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000022","count":1},{"id":"GO:0044339","count":1},{"id":"GO:0051515","count":1},{"id":"GO:0098709","count":1},{"id":"GO:0061091","count":1}]},{"hash":"796355602344986143","title":"Organogenesis and tissue homeostasis","description":"This cluster contains GO terms tied to development of multiple organs (heart, placenta, liver) and maintenance of tissue states (hepatocyte homeostasis, satellite cell maintenance), along with regulatory processes like differentiation and retinoic acid signaling. While it also includes generic cellular processes (protein transport, autoprocessing), the dominant pattern points to organogenesis and tissue maintenance rather than a single specific pathway.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0016540","count":2},{"id":"GO:0043516","count":1},{"id":"GO:0010424","count":1},{"id":"GO:0014834","count":1}]},{"hash":"1149989606759076967","title":"Carbohydrate Biosynthesis and Metal Ion Transport","description":"The GO terms cluster around carbohydrate biosynthetic processes (N-acetylglucosamine, N-acetylneuraminate, L-serine biosynthesis) and metal ion transport/homeostasis (cadmium and copper transport, calcium ion homeostasis), suggesting a theme of metabolic biosynthesis intertwined with metal ion handling. However, the presence of diverse terms and no known interactions means the link is partial rather than cohesive. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0070574","count":3},{"id":"GO:0006874","count":3},{"id":"GO:0006825","count":3},{"id":"GO:0005975","count":3},{"id":"GO:0006045","count":3}]},{"hash":"1409915144354648923","title":"Actin Protrusion and Rho-JNK Signaling","description":"The Top Terms reveal cytoskeletal remodeling via filopodium and microspike assembly, together with regulation of Rho signaling and the JNK cascade. Ubiquitination hints at coordinated protein turnover during remodeling, supporting a module focused on actin-based protrusions governed by Rho-JNK signaling; other terms like peroxisome autophagy or meiosis appear less central to this core function.","confidence":"High","size":17,"edges":6,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0046328","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0030035","count":2}]},{"hash":"2002390793321023985","title":"Lipid Metabolism and Membrane Trafficking","description":"The cluster shows enrichment for lipid-related processes (phospholipid catabolic process, phosphatidylglycerol biosynthesis, sphingolipid metabolism and signaling, GPI anchor attachment) and vesicle transport from the ER to the Golgi, suggesting roles in membrane lipid homeostasis and trafficking; a few terms appear peripheral (e.g., certain signaling/germ cell terms) and may be noise. ","confidence":"High","size":17,"edges":98,"triangles":285,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0016255","count":2},{"id":"GO:0015760","count":2},{"id":"GO:0009395","count":2},{"id":"GO:0035233","count":2}]},{"hash":"1359570158652529174","title":"MAPK and Hormone Receptor Signaling","description":"Top GO terms indicate regulation of MAPK/ERK signaling (GO:0070374) and signaling involving hormone receptors (growth hormone receptor signaling pathway GO:0060396; insulin receptor signaling pathway GO:0046626). There is also positive regulation of GTPase activity (GO:0043547) and involvement in apoptotic processes (GO:0006915), suggesting broader modulation of cell signaling and fate decisions. While a couple terms (e.g., visual perception GO:0007601) are less connected and may be incidental, the cluster is predominantly enriched for signaling regulation related to kinase cascades and hormone receptor pathways, justifying a label focused on MAPK and endocrine signaling.","confidence":"Medium","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0051534","count":2},{"id":"GO:0070374","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0032092","count":2}]},{"hash":"1944278879306957145","title":"NAD/Nucleotide and Core Metabolism","description":"The top GO terms cluster around nicotinamide/NAD metabolism (nicotinate nucleotide salvage, nicotinamide metabolic process), glycolysis, and related catabolic nutrient processes, plus nitrogen utilization, pointing to a core energy and nucleotide metabolism theme. A few terms like brain development and negative regulation of DNA amplification are less directly connected and may reflect broader annotation noise, but the dominant signal supports a metabolic focus.","confidence":"Medium","size":17,"edges":125,"triangles":537,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006212","count":3},{"id":"GO:0019740","count":3},{"id":"GO:0019358","count":3},{"id":"GO:0002047","count":3},{"id":"GO:0006769","count":3}]},{"hash":"2198282092845923635","title":"Actin Cytoskeleton Organization and Centrosome Dynamics","description":"The cluster is dominated by terms related to actin cytoskeleton organization (cortical actin, actin reorganization) and centrosome-related processes (protein localization to microtubules, centrosome separation, regulation of protein localization to centrosome) as well as vesicle docking. This suggests proteins that coordinate cytoskeletal architecture with centrosome/microtubule functions and trafficking, particularly during cell division. Some minor terms (like mRNA processing) are less connected but do not override the main theme of cytoskeletal and centrosomal regulation.","confidence":"Medium","size":17,"edges":13,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:2000251","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0030866","count":2},{"id":"GO:0035372","count":2},{"id":"GO:0006977","count":2}]},{"hash":"1514949280100995887","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000781","count":2},{"id":"GO:0016077","count":2},{"id":"GO:1901911","count":2},{"id":"GO:2000233","count":2},{"id":"GO:0046656","count":2}]},{"hash":"958756579823135946","title":"Plant cell cycle and stress response","description":"The GO terms cluster around cell cycle control (cell division; re-entry into mitotic cell cycle) and transcription, with concurrent stress-related processes (response to hypoxia; cellular oxidant detoxification) and metabolism (one-carbon metabolism); the presence of stomatal opening hints at a plant-specific context, suggesting these proteins coordinate cell cycle progression with environmental stress responses in plants.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0006730","count":2}]},{"hash":"1755908355158238131","title":"Unknown","description":"The top GO terms cover very different biological areas (RNA processing/splicing, peroxisome organization and dynamics, brown fat differentiation, oocyte maturation, and flight behavior) with only single-term support each, giving no clear, cohesive functional theme for the cluster. Therefore, no specific representative function can be assigned.","confidence":"","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008380","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0007629","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0044375","count":1}]},{"hash":"519614744986799847","title":"Nucleic acid metabolism and genome maintenance","description":"The top GO terms point to RNA processing and tRNA modification (tRNA processing, isopentenyl adenine biosynthesis, tRNA locus-associated regulation) alongside DNA metabolic processes (DNA replication, Okazaki fragment processing in mitotic replication, single-strand break repair) and genome rearrangement activities (immunoglobulin V(D)J recombination, isotype switching). This mix suggests a shared theme around nucleic acid metabolism, genome maintenance, and rearrangement rather than a single, narrow function. The terms collectively indicate involvement in RNA maturation and DNA replication/repair pathways, supporting a broad nucleic-acid-centric cluster label rather than a more specific function. ","confidence":"Medium","size":17,"edges":17,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":1},{"id":"GO:0034265","count":1},{"id":"GO:0061587","count":1},{"id":"GO:0000012","count":1},{"id":"GO:0090298","count":1}]},{"hash":"1383346617338280096","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":132,"triangles":624,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0000480","count":4},{"id":"GO:0000466","count":4}]},{"hash":"162305759876846609","title":"Diverse amino acid and small-molecule metabolism","description":"The top GO terms point to catabolic and biosynthetic processes for GABA, putrescine, L-proline, lysine, biotin, protoporphyrinogen IX, ethanol, and even antibiotic biosynthesis. This mix indicates a cluster centered on metabolism of amino-acid\u2013derived and other small molecules (cofactors and pigments) rather than a single specific pathway, suggesting a broad metabolic theme.","confidence":"Medium","size":17,"edges":135,"triangles":665,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0009450","count":9},{"id":"GO:0009447","count":9},{"id":"GO:0055129","count":9},{"id":"GO:0009089","count":7},{"id":"GO:0017000","count":6}]},{"hash":"2293711638568724050","title":"Unknown","description":"The terms span DNA repair, translation, tRNA wobble modification and mitochondrial tRNA aminoacylation, plus diverse biosynthetic and developmental processes (cobalamin and phylloquinone biosynthesis, viral processes, brain development, and telomere maintenance), with no clear single theme tying the proteins together. A concise, representative label cannot be confidently assigned.","confidence":"","size":17,"edges":55,"triangles":89,"max_degree":12,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0009236","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0042372","count":2}]},{"hash":"1382540900437622671","title":"Mitochondrial protein import and respiration","description":"Several top GO terms cluster around mitochondrial function: import of proteins into the mitochondrial matrix, mitochondrial translation, aerobic respiration, and proton transport, which together point to mitochondria-centric energy metabolism and protein handling. The presence of autophagy-related terms and minor outliers likely reflect ancillary roles or overlapping annotations, but the dominant signal supports a mitochondrial metabolism module.","confidence":"High","size":17,"edges":122,"triangles":498,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":2},{"id":"GO:1902987","count":2},{"id":"GO:0019878","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0009060","count":2}]},{"hash":"1281335105834606588","title":"Cell Cycle and Protein Trafficking Cluster","description":"Dominant terms center on cell division and the mitotic cell cycle, with additional signals for ER-to-Golgi vesicle transport, ubiquitin-dependent protein degradation, and vacuolar targeting, suggesting a group of proteins coordinating cell-cycle progression with protein processing and turnover.","confidence":"Medium","size":17,"edges":34,"triangles":14,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0006888","count":3},{"id":"GO:0008283","count":2},{"id":"GO:0006412","count":2}]},{"hash":"1833633552334073048","title":"Ribosomal RNA Maturation","description":"The cluster\u2019s top terms are maturation of 5.8S rRNA and maturation of LSU-rRNA, both core steps in ribosome biogenesis, indicating enrichment for ribosomal RNA processing. Other GO terms (DNA repair, development, immune response) are present but less representative of the main function, so the dominant signal points to rRNA maturation.","confidence":"High","size":17,"edges":86,"triangles":185,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0000466","count":2},{"id":"GO:0006297","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0006288","count":2},{"id":"GO:0051402","count":2}]},{"hash":"100010134345012363","title":"RNA Splicing Machinery","description":"Top terms are dominated by RNA processing and splicing, including nuclear-transcribed mRNA decay, snoRNA splicing, and spliceosome-mediated mRNA splicing, indicating the proteins mainly participate in RNA maturation. A few outliers (steroid hormone receptor assembly, interferon response, development) are at low frequency and likely incidental.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":2},{"id":"GO:0034247","count":2},{"id":"GO:0008380","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0006463","count":1}]},{"hash":"1649514451008968284","title":"DNA Replication and Genome Maintenance","description":"The cluster centers on DNA replication and genome maintenance, with strong signals for DNA replication, mitotic checkpoint signaling, and UV-damage excision repair. Supporting terms include cell division, oxidative stress response, and protein quality control (proteasome assembly and autophagy) as well as peroxisomal protein import, suggesting a broad module linking genome replication with DNA damage response and cellular stress management.","confidence":"High","size":17,"edges":109,"triangles":382,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019079","count":8},{"id":"GO:0006260","count":8},{"id":"GO:0034599","count":8},{"id":"GO:0070682","count":7},{"id":"GO:0000733","count":7}]},{"hash":"14525636858667354","title":"Thiamine biosynthesis and central carbon metabolism","description":"Top GO terms show enrichment for thiamine biosynthetic processes and thiamine diphosphate biosynthesis, along with central carbon metabolism pathways (pentose-phosphate shunt, glycolysis, TCA cycle). This points to a cohesive set of proteins involved in producing the thiamine-derived cofactor and integrating it into core metabolism, rather than unrelated functions. The strong, related metabolic themes justify a confident label.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0006098","count":5},{"id":"GO:0009229","count":4},{"id":"GO:0006096","count":4}]},{"hash":"1410891364903809500","title":"Cardiac development and calcium signaling","description":"The top terms point strongly to cardiac biology: heart development, cardiac muscle hypertrophy in response to stress, and calcium ion transport, suggesting the proteins cluster around cardiac development and calcium signaling pathways. Other terms (DNA repair, transcription) appear less central to the core theme, so the label reflects the dominant cardiac-related functions. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0014898","count":2},{"id":"GO:0006816","count":2}]},{"hash":"1767867838058210459","title":"Ribosome biogenesis and translation","description":"The dominant GO terms are about ribosomal subunit maturation, export, and cytoplasmic translation, plus related cell cycle and DNA replication initiation processes. This suggests the proteins cluster around ribosome assembly and protein synthesis, with some links to cell cycle regulation, hence the label.","confidence":"High","size":17,"edges":11,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:1903833","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000463","count":1},{"id":"GO:0000027","count":1}]},{"hash":"1326159873950021915","title":"Chaperone-assisted Protein Folding and Maturation","description":"I chose this name because the dominant GO terms center on chaperone activity, protein refolding/maturation (including Fe-S cluster\u2013related maturation), and suppression of aggregation, pointing to proteostasis and quality control of proteins. ATP-dependent activity and redox homeostasis further support an energy-assisted folding/maintenance role; a few terms (e.g., DNA replication) appear peripheral to the main theme. ","confidence":"High","size":17,"edges":49,"triangles":69,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045454","count":8},{"id":"GO:0006469","count":7},{"id":"GO:0031204","count":6},{"id":"GO:0051259","count":6},{"id":"GO:0006260","count":6}]},{"hash":"198936603324552598","title":"Meiosis- and Spermatogenesis-Related Proteostasis","description":"The GO terms point to a module centered on meiosis and spermatogenesis, with emphasis on protein turnover (ubiquitination, proteasome assembly, protein destabilization) and meiotic processes (spermatocyte growth, meiosis cytokinesis). Some peroxisome-related and RNA catabolic terms may be less central background annotations, but the core signal is proteostasis during male germ cell development.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":2},{"id":"GO:0070682","count":2},{"id":"GO:0006401","count":1},{"id":"GO:0010381","count":1},{"id":"GO:0048147","count":1}]},{"hash":"1480059738374405889","title":"GTPase-regulated endosomal trafficking","description":"This cluster's prominent GO terms center on endomembrane trafficking and GTPase signaling: positive regulation of GTPase activity, receptor recycling, regulation of endosome size, and vesicle fusion processes. While terms for cell cycle and ribosome biogenesis also appear, the strongest and most consistent signal is vesicle trafficking and membrane recycling governed by small GTPases.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0000747","count":2}]},{"hash":"1112912724796763990","title":"Diverse substrate membrane transporters","description":"The terms are dominated by various transmembrane transport processes across substrates like arabinose, phosphate, potassium, nitrate/nitrite, sialic acid, vitamins, and even vesicular loading of neurotransmitters, plus an antibiotic transport note. This suggests a cluster of proteins functioning primarily as transporters across membranes with diverse substrate specificities.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":5},{"id":"GO:0035435","count":5},{"id":"GO:0071805","count":5},{"id":"GO:0042128","count":5},{"id":"GO:0015706","count":5}]},{"hash":"534841347410351267","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0019433","count":2},{"id":"GO:0055114","count":2},{"id":"GO:2000134","count":2},{"id":"GO:0019310","count":1}]},{"hash":"1389528209854900989","title":"Polysaccharide catabolism and cell wall remodeling","description":"The cluster shows enrichment for pectin catabolic process, polysaccharide catabolic process, cell wall organization, and related sugar transport terms (arabinose, glucose, organic cation transport). This points to a shared function in carbohydrate metabolism and cell-wall remodeling, typical of plant processes, with a few nucleic-acid catabolism and transport terms likely representing peripheral noise.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":2},{"id":"GO:0042121","count":1},{"id":"GO:0090503","count":1},{"id":"GO:0006308","count":1},{"id":"GO:0000272","count":1}]},{"hash":"1226046346886276095","title":"Unknown","description":"The GO terms are spread across metabolism (glucose homeostasis, carbohydrate phosphorylation), gene regulation (transcription elongation and chromatin silencing), DNA replication initiation, development (left/right pattern formation), and plant signaling (abscisic acid response), with no clear single functional theme connecting the proteins. The lack of cohesive function and lack of interaction edges support labeling this cluster as Unknown.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042593","count":2},{"id":"GO:0034244","count":2},{"id":"GO:0090055","count":2},{"id":"GO:1903468","count":2},{"id":"GO:0090419","count":2}]},{"hash":"763735866051633970","title":"Nutrient-Driven Transcriptional Regulation","description":"This cluster's top GO terms center on positive regulation of transcription from RNA polymerase II promoter under various nutrient cues (nitrogen catabolite activation, carbon source signals, glyoxylate cycle influence, amino acid and nucleotide biosynthesis). The recurring theme is transcriptional activation in response to metabolic/nutrient states, suggesting the proteins are transcription factors or regulators coordinating metabolic gene expression.","confidence":"High","size":16,"edges":51,"triangles":99,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":14},{"id":"GO:1901714","count":13},{"id":"GO:0035959","count":13},{"id":"GO:0001080","count":13},{"id":"GO:1901717","count":13}]},{"hash":"1530560187385472505","title":"Neural development and brain morphogenesis","description":"The top GO terms strongly point to neural development and brain-related processes, including pyramidal neuron development, brain morphogenesis, and cerebrospinal fluid secretion, with another term linked to behavior (locomotory exploration). While a few terms relate to general cellular maintenance (autophagosome maturation, peroxisome organization, pH regulation), the neural development theme dominates, justifying this label as a representative description of the cluster's function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032581","count":1},{"id":"GO:0097352","count":1},{"id":"GO:0051452","count":1},{"id":"GO:0043588","count":1},{"id":"GO:0033326","count":1}]},{"hash":"1075492872173904466","title":"Mitochondrial metabolism and autophagic turnover","description":"The terms are dominated by mitochondrial-focused processes: mitochondrial respiratory chain complex IV assembly, heme biosynthesis and redox activity, and several autophagy-related terms (autophagosome assembly, aggrephagy). These collectively point to mitochondrial energy metabolism with cellular quality control via autophagy, despite a couple outliers likely representing noise. ","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0006590","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0035786","count":1},{"id":"GO:0071668","count":1}]},{"hash":"839874752064075015","title":"Polysaccharide Metabolism and Secreted Glycoproteins","description":"The cluster is characterized by GO terms for polysaccharide catabolism (xylan, arabinan, L-arabinose) alongside extracellular and glycosylation-related processes (extracellular matrix secretion; O-linked glycosylation). This points to a group of secreted glycoproteins involved in processing or remodeling carbohydrate-rich substrates, possibly in cell wall or ECM contexts. Immunoglobulin production and translation regulation terms are less central but may reflect a subset of proteins with immune-like domains or regulatory roles. Overall, a coherent theme around secreted, glycosylated proteins linked to carbohydrate metabolism.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":4},{"id":"GO:0002378","count":2},{"id":"GO:0031221","count":2},{"id":"GO:0017148","count":2},{"id":"GO:0046373","count":2}]},{"hash":"1298273006157848417","title":"DNA Repair and Proteostasis","description":"This cluster centers on DNA damage response and chromatin regulation (nucleotide-excision repair and heterochromatin formation) and includes components of protein turnover (deneddylation, proteasome assembly) and cell-cycle control (G2/M). The presence of nuclear mRNA surveillance and mRNA binding regulation suggests a broader role in RNA and protein quality control, with germline development terms hinting at functions during oogenesis. Overall, these terms converge on genome maintenance coupled with proteostasis and cell cycle regulation.","confidence":"Medium","size":16,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000715","count":2},{"id":"GO:0090054","count":1},{"id":"GO:0010972","count":1},{"id":"GO:0060625","count":1},{"id":"GO:0043248","count":1}]},{"hash":"2260690518289756479","title":"Unknown","description":"The top GO terms are broad and scattered across diverse processes (tRNA methylation, rRNA processing, DNA repair, telomere maintenance, heme and iron metabolism, cobalamin biosynthesis, APP biosynthetic regulation, etc.), with no single shared function evident among the proteins. The absence of edges and a unifying pathway suggests there isn\u2019t a coherent cluster theme to name beyond Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0006479","count":1},{"id":"GO:0006364","count":1},{"id":"GO:0006281","count":1}]},{"hash":"140934823172380748","title":"Inflammatory eicosanoid biosynthesis","description":"The GO terms clustered here repeatedly point to lipid mediator production, including leukotriene and prostaglandin biosynthesis (and production) and related inflammatory responses, supported by the lipoxygenase pathway. Additional terms related to calcium signaling and oxidative stress fit with inflammatory signaling dynamics. A couple of terms (GPI anchor biosynthetic process, ER protein folding) may reflect general membrane/protein maturation context rather than core function of the cluster, but the dominant theme is inflammatory lipid mediator biosynthesis.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":3},{"id":"GO:0034975","count":1},{"id":"GO:0019370","count":1},{"id":"GO:0002544","count":1},{"id":"GO:0071277","count":1}]},{"hash":"1003954280101056897","title":"Fungal sterol and aflatoxin biosynthesis regulation","description":"The top GO terms include ergosterol biosynthesis and aflatoxin biosynthetic process, plus transcriptional regulation from RNA polymerase II promoters and other metabolism-related regulation (e.g., lysine biosynthesis in fungi). This points to a cluster of proteins involved in regulating fungal metabolism, especially sterol/secondary metabolism, through transcriptional control. ","confidence":"High","size":16,"edges":12,"triangles":1,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001196","count":4},{"id":"GO:0035961","count":4},{"id":"GO:1901714","count":4},{"id":"GO:0061429","count":4},{"id":"GO:0035948","count":4}]},{"hash":"1034453483271391534","title":"Transmembrane Transporters (Ions and Metabolites)","description":"The top GO terms are dominated by transmembrane transport for a wide range of substrates (arabinose, phosphate ion, potassium, nitrate/nitrite, sialic acid, vitamins) and related transporter activity, plus a neuronal vesicle loading term, which together point to a cluster of membrane transporter proteins handling diverse ions and metabolites.","confidence":"High","size":16,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":7},{"id":"GO:0035435","count":7},{"id":"GO:0071805","count":7},{"id":"GO:0042128","count":7},{"id":"GO:0015706","count":7}]},{"hash":"420731705450038484","title":"Regulated Intramembrane Proteolysis (RIP) Signaling","description":"The GO terms center on membrane-associated proteolysis (ectodomain and intracellular domain proteolysis) and membrane trafficking (Golgi to plasma membrane, ER-to-cytosol), suggesting regulated intramembrane proteolysis events that generate signaling fragments. The presence of terms related to NFAT signaling and immune regulation supports a signaling role downstream of RIP-like proteolysis. A few phosphate transport terms appear as less central context but do not undermine the main RIP-signaling theme.","confidence":"Medium","size":16,"edges":72,"triangles":125,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006893","count":1},{"id":"GO:0006509","count":1},{"id":"GO:1904211","count":1},{"id":"GO:0031293","count":1},{"id":"GO:0051533","count":1}]},{"hash":"115756767112323831","title":"DNA Replication and Chromatin Silencing","description":"Top GO terms point to DNA replication and chromatin regulation, including replication initiation, pre-replicative complex assembly, mitotic chromosome condensation, and heterochromatin formation at telomeres and silent mating-type loci. While a few terms seem organism-specific or unrelated, the dominant signal is nuclear processes governing DNA replication and chromatin structure. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046331","count":1},{"id":"GO:0009744","count":1},{"id":"GO:0031938","count":1},{"id":"GO:0007076","count":1},{"id":"GO:0006270","count":1}]},{"hash":"1788703324465762741","title":"Copper Transport and Homeostasis","description":"The top GO terms center on copper ion import, intracellular copper ion homeostasis, regulation of copper transport, and related xenobiotic transport, suggesting a cluster of proteins dedicated to copper acquisition, distribution, and maintenance across membranes. A few terms like cellular response to cisplatin and oxidative stress appear but are secondary to copper handling, making this a cohesive copper-centered transport module.","confidence":"High","size":16,"edges":94,"triangles":273,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0098705","count":2},{"id":"GO:0015680","count":2},{"id":"GO:1902311","count":2},{"id":"GO:0072719","count":2}]},{"hash":"1295794550985776423","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000480","count":8},{"id":"GO:0000472","count":8},{"id":"GO:0043044","count":7},{"id":"GO:0000466","count":7},{"id":"GO:0031047","count":7}]},{"hash":"503517951684721381","title":"Ribosome biogenesis, translation, and cell division","description":"These proteins cluster around ribosome biogenesis and translation machinery, with strong signals for the formation of translation initiation complexes and translation reinitiation, alongside RNA processing complexes (snoRNP and spliceosomal assembly). The concurrent hints of mitotic cell cycle regulation and cell division suggest a link between protein synthesis capacity and cell-cycle progression, justifying a label that emphasizes ribosome/translation biology in the context of mitosis.","confidence":"High","size":16,"edges":18,"triangles":7,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3}]},{"hash":"1207956548566684554","title":"Chloroplast ribosome biogenesis and translation","description":"This cluster is dominated by GO terms for translation (cytoplasmic and general), ribosome biogenesis, ribosomal subunit export, and tRNA modification, with an additional plastid transcription term. Together these indicate a shared role in ribosome assembly and protein synthesis, including plastid-related (chloroplast) processes; a few cell division terms are present but appear peripheral to the main theme.","confidence":"High","size":16,"edges":57,"triangles":69,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0042793","count":2},{"id":"GO:0002181","count":1}]},{"hash":"958814057631828012","title":"Mitochondrial translation and Fe-S cluster biogenesis","description":"The top GO terms are dominated by mitochondrial-specific processes: mitochondrial translation and translation-related terms, protein insertion into the mitochondrial membrane, and cristae formation, plus iron-sulfur (Fe-S) cluster assembly and maturation. This points to a module centered on mitochondrial protein synthesis and Fe-S biogenesis essential for mitochondrial enzyme function and inner membrane organization, with apoptosis as a downstream association. A lone term on potassium ion homeostasis is less central but can reflect mitochondrial ion regulation. ","confidence":"High","size":16,"edges":22,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0051204","count":1},{"id":"GO:0030007","count":1},{"id":"GO:0042407","count":1},{"id":"GO:0070131","count":1}]},{"hash":"842069998026497697","title":"Unknown","description":"The GO terms cover a broad, non-overlapping mix of functions (fungal growth and invasive growth, tRNA modification, urmylation, cell cycle and centrosome dynamics, axonogenesis, DNA repair, inflammatory cytokine regulation, and pain perception), providing no single coherent theme to define the cluster.","confidence":"","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007124","count":2},{"id":"GO:0032447","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0002143","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1348067351016737540","title":"Nuclear DNA Damage Response and RNA Processing","description":"This cluster centers on nuclear processes: regulation of double-strand break repair by homologous recombination, regulation of DNA damage checkpoints, spindle checkpoint control, and histone methylation, alongside transcription (DNA-templated) and mRNA processing. The co-occurrence of DNA repair, cell-cycle control, chromatin-related processes, and RNA processing suggests a cohesive theme of genome maintenance coupled with gene expression regulation and protein quality control within the nucleus. Some terms (like misfolded protein response and chromatin-related methylation) reinforce this nuclear quality control/epigenetic context, while a few terms appear as annotation noise.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010569","count":1},{"id":"GO:2000002","count":1},{"id":"GO:1901300","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0090231","count":1}]},{"hash":"2152748501200202121","title":"Chromatin remodeling and transcription regulation","description":"The cluster shows multiple terms tied to chromatin dynamics and transcription control (e.g., chromatin remodeling, DNA-templated transcription, histone deacetylation regulation) and RNA processing (snoRNP assembly, snoRNA localization), suggesting an epigenetic regulation theme with associated RNA processing. Some outlier terms exist, but the dominant signal is chromatin-based gene expression regulation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031063","count":2},{"id":"GO:0016330","count":2},{"id":"GO:0000492","count":1},{"id":"GO:0006338","count":1},{"id":"GO:0048254","count":1}]},{"hash":"1583686823502945088","title":"Unknown","description":"The top GO terms are scattered, including mRNA surveillance (exon-exon junction complex disassembly, nonsense-mediated decay) alongside diverse processes like spindle checkpoint signaling, Rho signaling, endosomal transport, lysosome targeting, and myelin assembly. The cluster has no interactions (edges 0) and no coherent shared function, so there isn\u2019t a single interpretable theme to label.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903259","count":1},{"id":"GO:0000184","count":1},{"id":"GO:0032515","count":1},{"id":"GO:0032516","count":1},{"id":"GO:0007094","count":1}]},{"hash":"1849971915003359535","title":"Ubiquitin-mediated trafficking and signaling","description":"The top GO terms cluster around ubiquitination (autoubiquitination, K63-linked ubiquitination, ubiquitin-dependent catabolic processes) and ER-to-Golgi vesicle transport, pointing to a group of proteins involved in ubiquitin-regulated turnover and vesicle trafficking. Regulatory links to GTPase activity and the JNK cascade further suggest involvement in signaling connected to protein modification and trafficking; a few outliers (like subtelomeric heterochromatin formation) appear peripheral.","confidence":"High","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0043162","count":2}]},{"hash":"1105499236611534881","title":"Detoxification and xenobiotic catabolism","description":"GO terms in this cluster point to diverse metabolic breakdown and detoxification activities, including cellular oxidant detoxification, chlorophyll catabolism, beta-ketoadipate pathway, and degradation of halogenated and other xenobiotics, alongside menaquinone biosynthesis and even plant-specific development signals. The unifying theme is metabolism-driven detoxification and catabolism across organisms, though the terms span multiple biology areas, making the link broad but coherent enough to justify a detoxification/metabolic-catabolism label.","confidence":"Medium","size":16,"edges":72,"triangles":150,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":7},{"id":"GO:0019433","count":6},{"id":"GO:0015996","count":6},{"id":"GO:0009234","count":6},{"id":"GO:0009636","count":5}]},{"hash":"152597934384252099","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":53,"triangles":69,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":2},{"id":"GO:0034965","count":1},{"id":"GO:0000294","count":1},{"id":"GO:0001682","count":1},{"id":"GO:0000447","count":1}]},{"hash":"832207208101445232","title":"ER Protein Folding and Membrane Targeting under Stress","description":"Cluster centers on ER-associated protein folding and targeting to membranes, supported by chaperone-related terms and redox homeostasis, indicating a proteostasis and stress-response theme. While DNA replication and tRNA modification appear, the dominant signal is chaperone-assisted folding and membrane translocation in the secretory pathway, with negative regulation of heat response suggesting nuanced regulation under stress.","confidence":"Medium","size":16,"edges":16,"triangles":8,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0031204","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0034975","count":4},{"id":"GO:0090084","count":4}]},{"hash":"1351024560428823080","title":"Unknown","description":"The GO terms are diverse (development, cell movement, neural differentiation, metabolism, reproduction, and stress responses) with only singleton associations and no shared enriched function; zero edges mean no cohesive pathway links, so a single representative function cannot be identified. ","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031214","count":1},{"id":"GO:0006935","count":1},{"id":"GO:0030505","count":1},{"id":"GO:0030334","count":1},{"id":"GO:0048714","count":1}]},{"hash":"188550652333183353","title":"Unknown","description":"This cluster has only one connection and no enriched GO terms, indicating no evident shared function among the 15 proteins; therefore a meaningful label cannot be inferred.","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"778442992315616882","title":"Growth signaling and proliferation control","description":"The cluster shows enrichment for growth-regulating and signaling terms, including negative regulation of cell proliferation, mitotic cell cycle, Wnt signaling modulation, apoptosis, KIT signaling, and related signaling processes (NF-kappaB/STAT), plus cell migration and endocytosis; together these suggest a cohesive module governing proliferation, survival, and movement rather than structural functions.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008285","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0090090","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0043065","count":5}]},{"hash":"1179430070457427019","title":"Diverse substrate membrane transporters","description":"Top GO terms indicate transmembrane transport across diverse substrates (xenobiotics, arabinose, fucose, nitrates, vitamins) and ion transport (K+, Na+), plus neurotransmitter loading into synaptic vesicles. This convergence on membrane transport across multiple substrates suggests a cluster of transporter proteins with broad specificity. The name reflects this transporter-centric theme.","confidence":"Medium","size":15,"edges":71,"triangles":189,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0042128","count":2}]},{"hash":"807409358765771992","title":"Mitosis, Translation Initiation, and ER-Golgi Trafficking","description":"Top GO terms indicate coordination between cell cycle progression (mitotic spindle assembly, neural tube closure, cell proliferation), translation initiation and reinitiation, and vesicle trafficking between the ER and Golgi (including retrograde transport) with related proton/vacuolar acidity. This combination suggests a cohesive cluster where cell division, protein synthesis initiation, and secretory pathway dynamics are intertwined. Confidence: Medium","confidence":"Medium","size":15,"edges":11,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2}]},{"hash":"1320251863449465380","title":"Heart development and actin cytoskeleton remodeling","description":"The cluster centers on heart development and actin cytoskeleton processes, with prominent terms for heart formation, actin filament assembly, and adhesion-dependent cell spreading. Signaling terms (PDGF, retinoic acid, Ras) further tie into cytoskeletal dynamics and developmental signaling, supporting a cohesive theme of cardiac development coupled with cytoskeletal remodeling. Some neuronal or immune signals appear, but they are secondary to the core heart/cytoskeleton theme.","confidence":"Medium","size":15,"edges":99,"triangles":392,"max_degree":14,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:2000251","count":6},{"id":"GO:0034446","count":6},{"id":"GO:0007507","count":5},{"id":"GO:0043552","count":5},{"id":"GO:0051017","count":5}]},{"hash":"2098502072260933747","title":"Skeletal Muscle Development and Differentiation","description":"The GO terms show strong signals for skeletal muscle tissue development, muscle fiber development, and muscle cell differentiation, pointing to a muscle-specific gene program. Transcription-related terms suggest regulation of this program, while peripheral terms like circadian rhythm regulation and ubiquitination may modulate muscle biology rather than define it. Together, they support a muscle development/differentiation theme for this cluster.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007519","count":1},{"id":"GO:0036268","count":1},{"id":"GO:0031397","count":1},{"id":"GO:0031591","count":1}]},{"hash":"555185895749928150","title":"Plant gametogenesis and meiosis with actin dynamics","description":"The cluster combines meiosis-related processes (sister chromatid cohesion, double-strand break repair, reciprocal meiotic recombination) with plant reproductive development (embryo sac and pollen development) and cytoskeletal actin dynamics (Arp2/3-mediated nucleation, actin patch assembly), plus mitochondrial inheritance. This suggests a cohesive module in plants linking gametogenesis and meiotic events to actin-driven cytoskeletal organization.","confidence":"Medium","size":15,"edges":19,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":2},{"id":"GO:0007064","count":2},{"id":"GO:0006302","count":1},{"id":"GO:0007131","count":1},{"id":"GO:0009553","count":1}]},{"hash":"445942160824779367","title":"Metabolic Pathways with Transcriptional Regulation","description":"The top GO terms show a mix of metabolic processes (lysine biosynthesis via diaminopimelate, galactose and sorbitol-related metabolism, inositol catabolism, heme catabolic activity) and regulatory processes (negative regulation of kinase activity; transcription by RNA polymerase II). This suggests a cluster of proteins involved in metabolism with some regulatory roles, rather than a single cohesive pathway. ","confidence":"Low","size":15,"edges":71,"triangles":194,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0009089","count":12},{"id":"GO:0042167","count":11},{"id":"GO:0006012","count":11},{"id":"GO:0033673","count":11},{"id":"GO:0019877","count":11}]},{"hash":"1566217795653793058","title":"DNA Restriction-Modification System Proteins","description":"GO:0009307 clearly points to DNA restriction-modification systems (restriction enzymes and methyltransferases) as the core function; the obsolete term is not informative. The cluster\u2019s label encapsulates a cohesive theme around bacterial DNA defense mechanisms, even though no interaction edges are detected. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090305","count":1},{"id":"GO:0009307","count":1}]},{"hash":"1613396147059926553","title":"Nutrient-Responsive Transcription Regulation","description":"Most terms cluster around DNA-templated transcription and positive regulation of transcription from RNA polymerase II promoter, tied to metabolic and nutrient cues such as nitrogen catabolite activation, carbon-source signaling, and regulation of proline, pyrimidine, urea, and GABA catabolic processes. This points to a group of factors governing transcription in response to nutrient availability rather than a single metabolic pathway; a couple of terms (cadmium response, redox) appear ancillary. Confidence: High","confidence":"","size":15,"edges":25,"triangles":5,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0035959","count":4},{"id":"GO:0061414","count":4},{"id":"GO:2001158","count":4},{"id":"GO:1900399","count":4}]},{"hash":"442466466371316655","title":"Nucleocytoplasmic RNA Export and Centrosome Cycle","description":"This cluster is driven by RNA export functions: mRNA export from the nucleus, ribosomal large subunit export, and ncRNA export, collectively pointing to nucleocytoplasmic transport and RNA processing. The presence of the centrosome cycle term reinforces a link to cell-cycle coordination. Periphery terms include stress response, Wnt signaling regulation, spermatogenesis, and sphingoid base transport, which are less central to the core theme. ","confidence":"Medium","size":15,"edges":21,"triangles":14,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006950","count":2},{"id":"GO:1905329","count":2},{"id":"GO:0070208","count":1},{"id":"GO:0007283","count":1},{"id":"GO:0000055","count":1}]},{"hash":"961956149505054515","title":"Chromatin remodeling and heterochromatin maintenance","description":"This cluster is strongly enriched for chromatin-related processes: transcription initiation-coupled chromatin remodeling, heterochromatin formation (pericentric and rDNA), DNA replication-dependent chromatin assembly, and regulation of transcription by RNA polymerase II. These collectively point to proteins involved in establishing and maintaining chromatin structure and transcriptional control, including heterochromatin formation on sex chromosomes. Based on this cohesive theme, the label reflects the cluster\u2019s core function.","confidence":"High","size":15,"edges":32,"triangles":13,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0033128","count":4},{"id":"GO:0030466","count":4},{"id":"GO:0045815","count":4},{"id":"GO:0051290","count":4},{"id":"GO:0000122","count":4}]},{"hash":"796528883928557675","title":"Alcohol and aldehyde catabolism","description":"The top GO terms cluster around catabolic processing of alcohol- and aldehyde-containing compounds (sorbitol, ethanol, formaldehyde, furaldehyde) and related sugar metabolism (fructose biosynthesis), with supportive references to the Ehrlich pathway and NADH oxidation. This coherence suggests a cohesive set of proteins involved in processing alcohol- and aldehyde-derived metabolites, with a drug-response term present but not central to the cluster\u2019s function.","confidence":"High","size":15,"edges":91,"triangles":364,"max_degree":13,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0097327","count":14},{"id":"GO:0006062","count":14},{"id":"GO:0046294","count":14},{"id":"GO:0000947","count":14},{"id":"GO:0045777","count":14}]},{"hash":"1880003937904857390","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":78,"triangles":234,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":3},{"id":"GO:0002931","count":3},{"id":"GO:0044205","count":3},{"id":"GO:0006207","count":3},{"id":"GO:0006526","count":3}]},{"hash":"75274246389387250","title":"Neurodevelopment and Actin Dynamics","description":"The cluster's terms cluster around neural development (spinal cord and forebrain development, neural tube closure) and neuron-specific processes (neuron apoptotic process), suggesting a neurodevelopmental theme. Additionally, regulation of Arp2/3-mediated actin nucleation and GTPase activity points to cytoskeletal remodeling during neural development, with TORC1 signaling and transcription-related terms indicating growth and gene regulation contexts in the developing nervous system.","confidence":"High","size":15,"edges":40,"triangles":35,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0043547","count":9},{"id":"GO:0021510","count":8},{"id":"GO:0034316","count":8},{"id":"GO:0030900","count":7},{"id":"GO:1904263","count":7}]},{"hash":"758095526542684735","title":"Mitochondrial Energy Metabolism and Transport","description":"The cluster centers on mitochondrial processes: NAD and CoA transmembrane transport, the malate-aspartate shuttle, mitochondrial membrane fission and permeability, and adaptive thermogenesis. These terms tie fatty acid response and glucose-triggered insulin secretion to cellular energy status, suggesting a cohesive module of mitochondrial energy production and metabolite transport that underpins thermogenesis and metabolic signaling.","confidence":"High","size":15,"edges":11,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0061179","count":6},{"id":"GO:0035352","count":5},{"id":"GO:1990845","count":5},{"id":"GO:0070542","count":5},{"id":"GO:0035349","count":5}]},{"hash":"1388439077928098427","title":"Ion transport and energy metabolism","description":"The top GO terms centre on ion transport (sodium ion transport) and energy generation (proton motive force-driven ATP synthesis), indicating a core theme of membrane energetics and ion homeostasis. Supporting terms point to amino acid homeostasis (histidine, lysine) and protein handling (proteasome storage granule assembly), aligning with metabolic regulation. Some outliers (DNA transcription regulation and osteoblast differentiation) may reflect annotation noise or multifunctional proteins rather than a single cohesive function. Overall, this label captures the central theme with acknowledgement of heterogeneity.","confidence":"Medium","size":15,"edges":96,"triangles":354,"max_degree":14,"top_function":"lipid metabolic process","top_go_terms":[{"id":"GO:0006814","count":3},{"id":"GO:0006933","count":3},{"id":"GO:0090464","count":3},{"id":"GO:1902906","count":3},{"id":"GO:0042777","count":3}]},{"hash":"232465723416417478","title":"Ectoine and fatty acid metabolism","description":"The cluster shows strong representation of ectoine biosynthetic (GO:0019491) and catabolic (GO:0042400) processes, plus several fatty acid metabolic terms (methyl-branched fatty acid metabolic process and fatty acid alpha-oxidation). This points to a core metabolic theme centered on osmoprotectant-related pathways and lipid processing. Additional terms for translation regulation and virus response appear less central, so the primary signal is ectoine and lipid metabolism.","confidence":"Medium","size":15,"edges":31,"triangles":11,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0042400","count":2},{"id":"GO:0019491","count":2},{"id":"GO:0097089","count":2},{"id":"GO:1902181","count":2}]},{"hash":"970674573038123772","title":"Embryogenesis and Morphogenesis","description":"This cluster\u2019s top GO terms cluster around developmental processes, including blastocyst development, semicircular canal morphogenesis, and vestibular reflex, suggesting a developmental/morphogenetic theme. Other terms point to general cellular activities (DNA replication, cell division, ER-to-Golgi transport) that commonly occur during development. The lack of strong network connectivity (no edges) indicates a diffuse association, best captured by a developmental/morphogenesis label rather than a single specific pathway. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001824","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0010719","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006260","count":2}]},{"hash":"2293376652838365661","title":"Unknown","description":"The terms span immune defense, development, transcription/DNA processes, and specific host-symbiont interactions, with no single cohesive function dominating the cluster, so a precise, representative label cannot be assigned.","confidence":"","size":15,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":2},{"id":"GO:0018107","count":2},{"id":"GO:0007118","count":2},{"id":"GO:0060324","count":2},{"id":"GO:0006351","count":2}]},{"hash":"683872255988419412","title":"Diverse Membrane Transporters","description":"The cluster\u2019s top GO terms are all transmembrane transport-related, covering xenobiotic, vitamin, arabinose, potassium, sodium, and nitrate transport, plus a vesicular neurotransmitter loading term, indicating a group of membrane transport proteins with diverse substrates. This cohesive signal supports labeling as membrane transporter proteins rather than a miscellaneous set.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":12},{"id":"GO:0035461","count":12},{"id":"GO:0015751","count":11},{"id":"GO:0071805","count":11},{"id":"GO:0042128","count":11}]},{"hash":"1923756807414522461","title":"Mitochondrial beta-oxidation and ETC assembly","description":"The cluster is driven by mitochondrial energy metabolism, with strong representation of fatty acid beta-oxidation (long-chain transport, carnitine-linked steps, acyl-CoA oxidase) and assembly of ETC complexes I and II (NADH to ubiquinone), indicating roles in mitochondrial fatty acid metabolism and oxidative phosphorylation.","confidence":"High","size":15,"edges":76,"triangles":173,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0001547","count":1},{"id":"GO:0032000","count":1},{"id":"GO:0051791","count":1},{"id":"GO:0008292","count":1},{"id":"GO:0015909","count":1}]},{"hash":"1981954790480078922","title":"Membrane Solute Transporters","description":"This cluster centers on transmembrane transport of diverse solutes and ions (arabinose, phosphate, potassium, nitrate/nitrite, sialic acid, vitamins) and vesicular neurotransmitter loading, suggesting a general transporter function across membranes rather than a single substrate. The shared theme is membrane transport activity across multiple substrates, though some terms reflect specialized vesicular transport. Therefore, \u201cMembrane Solute Transporters\u201d is a concise and representative label.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0015706","count":2}]},{"hash":"2010007133159259624","title":"RNA Processing and Splicing Regulation","description":"The GO terms cluster around post-transcriptional RNA handling: splicing regulation and spliceosome involvement, mRNA export, splice site recognition, mRNA modification, and mRNA stability under stress, along with miRNA and regulatory ncRNA\u2013mediated gene silencing. Together they point to proteins coordinating RNA processing, splicing, export, modification, and silencing pathways.","confidence":"High","size":15,"edges":87,"triangles":279,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000381","count":7},{"id":"GO:0006406","count":7},{"id":"GO:1901407","count":7},{"id":"GO:0016556","count":6},{"id":"GO:0035278","count":6}]},{"hash":"1208545554544653938","title":"Cholesterol Homeostasis and Lipid Modification","description":"The cluster shows strong signals for cholesterol handling (cholesterol homeostasis, cholesterol efflux, regulation of plasma lipoprotein particle levels) and lipid biosynthesis/modification (triglyceride biosynthetic process, cholesterol esterification, protein palmitoylation/palmitoleylation). Macrophage foam cell differentiation ties lipid uptake to immune cells, while smoothened signaling and N-palmitoylation reflect lipid-modified signaling components. Together, these terms indicate a cohesive lipid metabolism and cholesterol management function.","confidence":"High","size":14,"edges":88,"triangles":331,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0019432","count":2},{"id":"GO:0007224","count":2},{"id":"GO:0097006","count":2},{"id":"GO:0018009","count":2},{"id":"GO:0042986","count":2}]},{"hash":"1716669905500810845","title":"Nutrient-Responsive Transcription Regulation (Fungi)","description":"This cluster centers on positive regulation of transcription from RNA polymerase II promoter in response to various nutrients (carbon and nitrogen) and related catabolic/biosynthetic processes, indicating a group of transcriptional regulators coordinating nutrient signaling in fungi.","confidence":"High","size":14,"edges":33,"triangles":50,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035959","count":14},{"id":"GO:0006351","count":14},{"id":"GO:0061414","count":14},{"id":"GO:2001158","count":14},{"id":"GO:1900399","count":14}]},{"hash":"1594635675668014202","title":"Unknown","description":"The GO terms across the cluster are heterogeneous and do not converge on a single biological function. They include xenobiotic and herbicide responses, alternative splicing via spliceosome, peptide catabolic processes and proteolysis, some obsolete terms, defense response to bacteria, and even cerebral cortex development, which together suggest no clear, shared function for this protein group.","confidence":"","size":14,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0000380","count":3},{"id":"GO:0043171","count":2},{"id":"GO:0006508","count":2}]},{"hash":"514469072048169576","title":"RNA processing and vesicle trafficking in epithelial morphogenesis","description":"This cluster shows enrichment for RNA processing and spliceosome-related terms (RNA splicing, spliceosomal assembly, mRNA processing) alongside vesicle trafficking and Golgi-related terms (COPII-coated vesicle cargo loading, Golgi organization), plus morphogenesis terms for wing discs and follicular epithelium. The combination suggests a link between post-transcriptional gene expression control and secretory pathway activity during epithelial development. Confidence: Medium","confidence":"","size":14,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043161","count":2},{"id":"GO:0008380","count":1},{"id":"GO:0000244","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0007472","count":1}]},{"hash":"2184459532602694635","title":"Unknown","description":"There are no shared GO terms or interaction signals in this cluster (Edges 0, Triangles 0, Max Degree 0) and no Top Terms to guide labeling. The note that 20 proteins were re-added by ReCIPE does not reveal a common function, so I cannot assign a meaningful label. Unknown is the appropriate name with confidence None.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"35616660655302352","title":"B cell maturation and immunoglobulin diversification","description":"This cluster's top GO terms include positive regulation of isotype switching to IgG and IgA, and somatic hypermutation of immunoglobulin genes, which are classic markers of B cell maturation and antibody diversification. Additional terms related to cell cycle regulation and mitotic checkpoints suggest proliferation during immune activation, while oxidative phosphorylation reflects metabolic changes in activated cells. Some terms like germ cell development and aging are less directly related, but the immune-related functions dominate the cluster.","confidence":"Medium","size":14,"edges":18,"triangles":8,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0007568","count":3},{"id":"GO:0048304","count":3},{"id":"GO:0006119","count":3}]},{"hash":"1607260919522791915","title":"Ribosome Biogenesis and Translation Initiation","description":"The terms cluster around 90S preribosome assembly, rRNA processing, snoRNP assembly, and regulation/rewinitiation of translation, pointing to proteins involved in ribosome biogenesis and initiation control.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001731","count":5},{"id":"GO:0006378","count":4},{"id":"GO:0075525","count":4},{"id":"GO:0006446","count":4},{"id":"GO:0002188","count":4}]},{"hash":"2108687706451970311","title":"Unknown","description":"The GO terms are a mix of purine metabolism (urate catabolic, allantoin biosynthesis, purine nucleobase metabolism) and unrelated processes (cell growth regulation, spermatocyte-related development, protein turnover) with no evident shared function or pathway, and there are no edges linking proteins, so a coherent label cannot be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019628","count":1},{"id":"GO:0019428","count":1},{"id":"GO:0006144","count":1},{"id":"GO:0001560","count":1},{"id":"GO:0010381","count":1}]},{"hash":"740254435129286942","title":"Unknown","description":"The GO terms cover several distinct processes, including GPI anchor biosynthesis and protein O-linked glycosylation, multiple catabolic pathways (quinolinate, tryptophan, allantoin, purine), ureide metabolism, zinc response, and phosphinothricin biosynthesis. There is no clear shared function connecting these proteins, and the network has no edges, so there isn't a coherent biological theme that ties them together. Therefore, this cluster is best labeled Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":1},{"id":"GO:0035269","count":1},{"id":"GO:0019805","count":1},{"id":"GO:0010136","count":1},{"id":"GO:0006569","count":1}]},{"hash":"2304996850245775923","title":"Mitochondrial respiratory chain assembly","description":"The top GO terms are dominated by assembly processes for mitochondrial respiratory chain complexes (e.g., complex IV assembly and respirasome assembly) and regulation of cytochrome c release, indicating a cohesive theme around mitochondrial electron transport and apoptosis control; other immune-related terms appear infrequently and are likely incidental.","confidence":"High","size":14,"edges":44,"triangles":54,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":3},{"id":"GO:0090201","count":2},{"id":"GO:0097250","count":2},{"id":"GO:0009306","count":1},{"id":"GO:0002315","count":1}]},{"hash":"1313025844161650427","title":"Calcium-Dependent Muscle and Neural Signaling","description":"The top GO terms cluster around calcium signaling and calcium-regulated processes, notably muscle contraction (sarcomere organization, cardiac muscle contraction regulation by Ca2+ release) and neural signaling (regulation of synaptic activity, epinephrine response, calcium transporters). A couple terms (ER protein exit, cell wall biosynthesis) seem less connected, but the dominant theme points to calcium-dependent regulation in muscle and nervous system.","confidence":"Medium","size":14,"edges":16,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0070863","count":2},{"id":"GO:0042546","count":2},{"id":"GO:0006078","count":2},{"id":"GO:0045214","count":2},{"id":"GO:1901896","count":2}]},{"hash":"202522630663136285","title":"Ubiquitin-Proteasome System and Antiviral Defense","description":"Core theme is ubiquitin-dependent proteolysis (SCF proteasome, ERAD, K63-linked ubiquitination), with a coordinating role in innate antiviral defense and TNF signaling; vitamin D response is present but peripheral.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0000083","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0033280","count":2}]},{"hash":"1988469827737492075","title":"Calcium signaling in bone formation","description":"This cluster is characterized by GO terms centered on calcium signaling and bone development, including chondrocyte proliferation, osteoblast development, store-operated calcium channel activity, and positive regulation of the calcineurin-NFAT pathway. These collectively point to calcium-dependent signaling pathways driving bone and cartilage formation. Some terms seem unrelated or obsolete (e.g., plant hormone signaling) and may reflect annotation noise, but the core theme remains calcium-mediated bone formation. ","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035988","count":1},{"id":"GO:0035584","count":1},{"id":"GO:0051533","count":1},{"id":"GO:0032237","count":1},{"id":"GO:0042136","count":1}]},{"hash":"1734959105489433710","title":"Ubiquitin-Dependent Degradation and Muscle Development","description":"The cluster shows enrichment for ubiquitin-related processes (ubiquitin-dependent protein catabolic process; negative regulation of protein ubiquitination; K33-linked ubiquitination) and skeletal muscle development/fiber development terms, suggesting a coherent theme of ubiquitin-mediated regulation in muscle biology; some immune-related terms appear noisy but do not override the dominant pattern.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0032764","count":1},{"id":"GO:0048294","count":1},{"id":"GO:0007519","count":1},{"id":"GO:0009958","count":1}]},{"hash":"1699230618175967782","title":"Unknown","description":"The GO terms across lipid biosynthesis (long-chain fatty acids, sphingolipids) and multiple signaling pathways (Rho, NF-kappaB, JNK), plus virus-related and mineralization terms, do not cohere into a single clear function or process for this cluster, so a unified, intuitive label isn\u2019t supported. ","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042761","count":1},{"id":"GO:0030497","count":1},{"id":"GO:0030148","count":1},{"id":"GO:0007266","count":1},{"id":"GO:0045070","count":1}]},{"hash":"1254548599077102619","title":"Unknown","description":"Top terms are widely dispersed across digestion/proteolysis, plant defense, hormonal regulation, and behavior, with no coherent shared function or interaction, and no edges linking members; thus no single functional theme emerges.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033619","count":2},{"id":"GO:0009627","count":2},{"id":"GO:0007586","count":2},{"id":"GO:0030163","count":2},{"id":"GO:0042985","count":2}]},{"hash":"1161137171042341436","title":"Glycolysis and TCA Core Metabolism","description":"Top terms cluster around glycolysis, the TCA cycle, glucose metabolism, gluconeogenesis, and regulation of pyruvate decarboxylation to acetyl-CoA, all central to mitochondrial energy production. A few terms (e.g., olfactory bulb development) appear unrelated and may reflect annotation noise, but the dominant themes point to core carbon metabolism and energy generation. Overall, the proteins seem to be central metabolic enzymes linking glycolysis to the TCA cycle.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0061732","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0061034","count":4}]},{"hash":"569626785476615350","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018063","count":1},{"id":"GO:0001682","count":1},{"id":"GO:0034414","count":1},{"id":"GO:1903225","count":1},{"id":"GO:0070208","count":1}]},{"hash":"300491773229633340","title":"Unknown","description":"The GO terms are highly diverse (immunoglobulin production, ECM secretion, plant polysaccharide metabolism, glycosylation, translation regulation, DNA ADP-ribosylation), with only single-term associations and no clear shared function, so there is no cohesive theme to assign a specific label.","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002378","count":1},{"id":"GO:0070278","count":1},{"id":"GO:0031221","count":1},{"id":"GO:0045493","count":1},{"id":"GO:0017148","count":1}]},{"hash":"1257568536387303229","title":"Vertebrate embryonic organogenesis","description":"This cluster centers on embryonic development across multiple organ systems\u2014heart morphogenesis, forebrain and facial development, olfactory pit formation, vascular and digestive tract development. The presence of retinoic acid signaling and neural metabolism terms (GABA catabolic process) supports a broad developmental theme rather than a single pathway. Overall, the proteins likely participate in vertebrate organogenesis and tissue morphogenesis.","confidence":"High","size":13,"edges":36,"triangles":48,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0036293","count":6},{"id":"GO:0003007","count":6},{"id":"GO:0030900","count":6},{"id":"GO:0060166","count":6},{"id":"GO:0060324","count":6}]},{"hash":"1362504467367556837","title":"Metabolite-regulated RNA Pol II transcription","description":"The terms are dominated by positive regulation of transcription from RNA polymerase II promoter in response to various metabolic cues (e.g., oleic acid, nonfermentable carbon sources), along with DFS-related transcription and DNA-templated transcription. This suggests a cohesive role in transcriptional regulation linked to cellular metabolic state, rather than a single biosynthetic or metabolic pathway. ","confidence":"High","size":13,"edges":71,"triangles":225,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035959","count":12},{"id":"GO:0006351","count":12},{"id":"GO:0061414","count":12},{"id":"GO:2001158","count":12},{"id":"GO:1900399","count":12}]},{"hash":"524726265703972469","title":"Diverse Membrane Transporters","description":"The proteins in this cluster are associated with multiple transmembrane transport processes across a range of substrates (xenobiotics, sugars like arabinose and fucose, various ions like potassium and sodium, nitrate, vitamins) and vesicular neurotransmitter loading, suggesting a coherent theme of membrane transporter functions with diverse substrates rather than a single substrate-specific role.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0006004","count":2}]},{"hash":"1847094589560876379","title":"Diverse Transmembrane Transport","description":"This cluster shows a coherent enrichment for broad membrane transport terms across multiple substrates\u2014ions (potassium, phosphate, nitrate/nitrite), sugars (arabinose), vitamins, and sialic acid\u2014along with related processes like neurotransmitter loading. The proteins appear to function primarily as transporters or transport-associated components across membranes, spanning various substrates rather than a single molecule.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":6},{"id":"GO:0015751","count":4},{"id":"GO:0035435","count":4},{"id":"GO:0042128","count":4},{"id":"GO:0015706","count":4}]},{"hash":"461266713514162087","title":"Centrosome and Mitosis Regulation","description":"The terms center on centriole replication, centrosome duplication, mitotic checkpoint signaling, and spindle/microtubule organization, plus ubiquitin-mediated proteolysis, all hallmark features of centrosome maintenance and mitotic control. A couple of terms (telomere maintenance via recombination, hemopoiesis) are less central but may reflect broader cell-cycle contexts. Overall, the cluster points to proteins coordinating centrosome function and mitosis.","confidence":"High","size":13,"edges":18,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007099","count":2},{"id":"GO:0030097","count":2},{"id":"GO:0051298","count":2},{"id":"GO:0031571","count":2},{"id":"GO:0051865","count":2}]},{"hash":"441258747522722887","title":"Membrane Transporters for Nutrients and Ions","description":"The Top Terms show diverse transmembrane transport activities for nitrate, nitrite, arabinose, phosphate, potassium, vitamins, and related nutrient assimilation, plus a transporter-related process (neurotransmitter loading) and cellular responses linked to nutrient availability. This cohesive pattern centers on membrane transport functions across multiple substrates, justifying a transporter-focused label.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":9},{"id":"GO:0042128","count":9},{"id":"GO:0042149","count":8},{"id":"GO:0015751","count":8},{"id":"GO:0035435","count":8}]},{"hash":"1164787790626553996","title":"Nucleolar RNA Processing and Chromatin Remodeling","description":"The cluster preferentially includes GO terms for box C/D snoRNP assembly and snoRNA localization, pointing to nucleolar RNA processing. It also shows chromatin-related terms such as chromatin remodeling and DNA-templated transcription, indicating coordination with chromatin state and transcription. Together, these terms suggest a central role in nucleolar RNA maturation linked to chromatin regulation in the nucleus. Some terms (ER unfolded protein response, cell cycle regulation, senescence) may reflect broader cellular stress responses or secondary effects rather than core functions of the cluster.","confidence":"Medium","size":13,"edges":15,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000492","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0031063","count":1},{"id":"GO:0006338","count":1}]},{"hash":"2190916034255808082","title":"Chloroplast gene expression and metabolism","description":"This cluster centers on plastid-related processes: chloroplast mRNA processing, chloroplast translation, and associated metabolic pathways like ubiquinone biosynthesis and the TCA cycle, suggesting plastid gene expression linked to core metabolism in plants. Some terms also reflect broader plant development and aging, but the plastid functions dominate.","confidence":"Medium","size":13,"edges":19,"triangles":13,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":3},{"id":"GO:0006099","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0010239","count":1},{"id":"GO:0043086","count":1}]},{"hash":"443757867667255132","title":"Clathrin-mediated endocytosis and mitochondrial dynamics","description":"The top GO terms cluster around vesicle trafficking via clathrin-dependent and receptor-mediated endocytosis, plus synaptic vesicle maturation. Several terms highlight mitochondrial dynamics (fusion), localization, and regulation of cytochrome c release, tying endocytic processes to mitochondrial function and apoptotic signaling. A few terms about myoblast fusion hint at shared membrane fusion machinery, but the dominant theme is endocytosis linked to mitochondrial dynamics and apoptosis. ","confidence":"Medium","size":13,"edges":10,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0072583","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0016188","count":2},{"id":"GO:0048260","count":2},{"id":"GO:0010636","count":2}]},{"hash":"1799192420439265549","title":"Golgi trafficking and SNARE-mediated vesicle fusion","description":"This cluster is dominated by GO terms for ER-to-Golgi and intra-Golgi vesicle transport, vesicle fusion with the Golgi, SNARE complex assembly, and regulation of Golgi organization, plus terms tied to delivering proteins to the plasma membrane and synaptic receptor exocytosis. The inclusion of long-term synaptic potentiation and postsynaptic receptor insertion points to neuronal vesicle trafficking delivering receptors to the synapse, all centered on Golgi- and SNARE-mediated processes.","confidence":"High","size":13,"edges":63,"triangles":162,"max_degree":12,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006888","count":9},{"id":"GO:0090161","count":9},{"id":"GO:0006891","count":8},{"id":"GO:0048280","count":8},{"id":"GO:0035493","count":7}]},{"hash":"1201510816415556349","title":"Multicellular Development and Gene Regulation","description":"Top GO terms center on broad developmental processes across tissues (forebrain/metencephalon, heart, eye, placenta, skeletal muscle) and on general gene regulation (RNA polymerase II transcription, chromatin remodeling), with insulin receptor signaling as a growth-related signal. This points to a cluster of proteins that coordinate multicellular development and transcriptional regulation rather than a single tissue function.","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0022037","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0007507","count":2}]},{"hash":"519313282799130490","title":"Translation initiation and preinitiation complex formation","description":"This cluster is dominated by GO terms related to starting protein synthesis, including formation of translation preinitiation complexes, IRES- and cap-dependent initiation, and regulation of translational initiation, suggesting a shared role in initiating translation. A few terms on RNA processing appear but the main signal centers on translation initiation machinery.","confidence":"High","size":13,"edges":71,"triangles":219,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0075525","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0042797","count":2}]},{"hash":"447546093809547081","title":"Cell-cycle control and differentiation signaling","description":"This cluster centers on key regulators of cell proliferation and fate decisions, with GO terms pointing to G1/S transition, keratinocyte and Schwann cell differentiation, growth-regulating pathways (Hippo, Wnt, PI3K-AKT), and processes like apoptosis. While diverse, the common thread is signaling that coordinates proliferation with differentiation and survival.","confidence":"Medium","size":13,"edges":7,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000082","count":4},{"id":"GO:0030216","count":4},{"id":"GO:0060044","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0035329","count":4}]},{"hash":"2038306906366036815","title":"Unknown","description":"Top GO terms span central metabolism, redox, amino acid and lipid/sterol biosynthesis, nitrate assimilation, and some tissue-specific processes, with several obsolete terms; the lack of a coherent, shared function across these terms suggests no single functional theme for the cluster.","confidence":"","size":13,"edges":63,"triangles":162,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0009097","count":4},{"id":"GO:0009853","count":4},{"id":"GO:0032443","count":4}]},{"hash":"730286682643283554","title":"GPI-Anchor Biosynthesis","description":"This cluster is dominated by GO terms for GPI anchor biosynthesis and dolichol-linked oligosaccharide biosynthesis, pointing to glycosylation and GPI-anchor formation as the core function. Five proteins map to GPI anchor biosynthesis and three to dolichol-linked glycosylation, suggesting a cohesive theme around glycoprotein maturation. Other terms (lipid storage, cholesterol homeostasis, immune signaling, pollen tube guidance, neuromuscular balance) are less consistent with this core and may reflect annotation noise or multifunctionality. Overall, the strongest signal supports a GPI-anchor biosynthesis role.","confidence":"Medium","size":13,"edges":30,"triangles":45,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":5},{"id":"GO:0010183","count":3},{"id":"GO:0006488","count":3},{"id":"GO:0042632","count":1},{"id":"GO:0031663","count":1}]},{"hash":"2072134278192639299","title":"Amino Acid Metabolism & Fe-S Cluster Assembly","description":"The cluster\u2019s top GO terms cluster around amino acid biosynthesis and degradation (pyruvate biosynthesis, alanine catabolism, kynurenine catabolism, lysine biosynthesis via diaminopimelate) and central carbon metabolism (glyoxylate pathway), plus [2Fe-2S] cluster assembly, suggesting a cohesive theme of amino acid turnover and cofactor biogenesis. The Notch signaling term appears as a minor outlier and may reflect annotation noise rather than a core function of the proteins. Confidence: High","confidence":"","size":13,"edges":36,"triangles":54,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0042866","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0097053","count":4},{"id":"GO:0007219","count":4},{"id":"GO:0019877","count":3}]},{"hash":"1028408336256571325","title":"Unknown","description":"The GO terms span several distinct biological processes\u2014spermatogenesis, RNA silencing, starvation and circadian regulation, jump response, and placenta development\u2014without a clear convergent function. This dispersion suggests there is no coherent functional theme tying the proteins into a single cluster.","confidence":"","size":13,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007283","count":2},{"id":"GO:0016246","count":2},{"id":"GO:0042595","count":2},{"id":"GO:0042321","count":2},{"id":"GO:0007630","count":2}]},{"hash":"2279283975624601731","title":"Stress-Responsive Metabolism and Detoxification","description":"The cluster shows enrichment for chemical and metal stress responses (cadmium, calcium, prostaglandin stimulus) and detoxification/metabolic processes (glutathione biosynthesis, daunorubicin metabolism, farnesol and arabinose catabolism, progesterone metabolism). This points to a cohesive theme of metabolic adaptation under chemical stress and detox pathways.","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0042448","count":13},{"id":"GO:0071799","count":13},{"id":"GO:0044597","count":13},{"id":"GO:0071276","count":13},{"id":"GO:0006750","count":13}]},{"hash":"1080912244843299405","title":"Aminoacyl-tRNA Synthetases and Translation","description":"This cluster is dominated by GO terms for protein synthesis: translation and multiple aminoacyl-tRNA synthetases (valyl-, leucyl-, methionyl-, isoleucyl-, tyrosyl-, and mitochondrial variants), plus a term for regulation of translational fidelity. The inclusion of mitochondrial tRNA charging terms supports a focus on cytosolic and mitochondrial translation machinery. The angiogenesis terms are minor and not central to the core theme. Confidence: High","confidence":"","size":13,"edges":61,"triangles":171,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0006438","count":6},{"id":"GO:0006429","count":5},{"id":"GO:0006431","count":5},{"id":"GO:0006428","count":4}]},{"hash":"1169859678239226346","title":"Ribosome Biogenesis and rRNA Processing","description":"This cluster is dominated by GO terms related to rRNA maturation and ribosome biogenesis, including SSU rRNA maturation, ribosomal subunit export from the nucleus, and nucleolus organization. The presence of multiple ribosome-related processes suggests a cohesive function in ribosome assembly and maturation within the nucleolus, with proteasome assembly appearing less prominently and development terms likely incidental. Confidence: High","confidence":"","size":13,"edges":31,"triangles":23,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0043248","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0000469","count":1},{"id":"GO:0042274","count":1}]},{"hash":"628624316135435083","title":"DNA replication and chromatin regulation","description":"The cluster is characterized by GO terms tied to DNA replication, DNA-templated transcription, and chromatin dynamics (chromatin remodeling and nucleosome mobilization), suggesting a shared function related to DNA metabolism coordinated by chromatin state and transcription control. Some terms (e.g., isotype switching, centrosome cycle, peroxisomal import, obsolete ubiquitination) appear peripheral or historical, but the core signal points to chromatin regulation during DNA-related processes.","confidence":"Medium","size":13,"edges":29,"triangles":12,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0045190","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0030433","count":3}]},{"hash":"794705232082842509","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0018013","count":1}]},{"hash":"940092017944730651","title":"Neuronal signaling and mitochondrial regulation","description":"The cluster\u2019s terms largely point to neural signaling and plasticity (neuron-neuron synaptic transmission, learning, fear response) with strong ties to mitochondrial function (calcium import into mitochondrion, mitophagy regulation, ROS control) and cilium-related regulation, suggesting a coordinated neuronal signaling module influenced by mitochondrial health; the glucan biosynthesis term appears as a potential outlier.","confidence":"Medium","size":13,"edges":51,"triangles":98,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006078","count":5},{"id":"GO:1902017","count":1},{"id":"GO:1903146","count":1},{"id":"GO:0006820","count":1},{"id":"GO:2000378","count":1}]},{"hash":"1244226483313480270","title":"Unknown","description":"The annotated terms are scattered and many are obsolete; a few reference post-translational modifications (N-terminal trimethyl/dimethylation, hydroxylation), but others describe cellular senescence, stress responses, viral membrane fusion, and metal ion responses. With no edges and no cohesive functional theme, there isn\u2019t a clear shared function for the cluster.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051770","count":2},{"id":"GO:0014070","count":2},{"id":"GO:0039654","count":1},{"id":"GO:0035902","count":1},{"id":"GO:0018012","count":1}]},{"hash":"727786980284597124","title":"Bacterial thiol biosynthesis and envelope lipid biosynthesis","description":"The cluster is strongly associated with thiol-based biosynthesis (bacillithiol and mycothiol) and with envelope-related lipid/glycosylation processes (glycolipid biosynthesis, GPI anchor biosynthesis, glycosylation). This suggests a cohesive function in redox homeostasis coupled to cell envelope construction/remodeling in bacteria. Additional stress-related terms (response to flooding, water deprivation) align with adaptive responses under osmotic conditions, reinforcing a stress-linked envelope/redox theme.","confidence":"High","size":13,"edges":48,"triangles":99,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0071793","count":6},{"id":"GO:0009413","count":6},{"id":"GO:0009744","count":6},{"id":"GO:0010555","count":6},{"id":"GO:0097502","count":6}]},{"hash":"26012440532753667","title":"Neural development and synaptic signaling","description":"The cluster\u2019s GO terms predominantly point to neural development (substantia nigra and Schwann cell development, skeletal muscle fiber development) and synaptic function (excitatory postsynaptic potential, calcineurin-NFAT signaling). Although a few terms are unrelated (cell cycle checkpoint, glycogen regulation, obsolete terms), the strongest pattern links neural differentiation and synaptic signaling pathways, suggesting proteins involved in neural development and neuronal communication.","confidence":"Medium","size":12,"edges":14,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0021762","count":2},{"id":"GO:0032516","count":1},{"id":"GO:0014044","count":1},{"id":"GO:0033173","count":1},{"id":"GO:0050774","count":1}]},{"hash":"2234821236895696667","title":"Meiotic and Mitotic Chromosome Condensation","description":"This cluster centers on chromosome condensation during meiosis and mitosis and other cell-division processes (meiotic condensation, mitotic condensation, microsporogenesis, and cell division), with secondary hints from nuclear transport and RNA-related processes (tRNA gene clustering, ribosomal protein import) and modest signals of stress granule disassembly and apoptotic signaling.","confidence":"Medium","size":12,"edges":63,"triangles":191,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010032","count":6},{"id":"GO:1903342","count":6},{"id":"GO:0070058","count":6},{"id":"GO:0007076","count":6},{"id":"GO:0051301","count":6}]},{"hash":"2295412489470257886","title":"Unknown","description":"The GO terms in this cluster are highly heterogeneous, ranging from innate immune response and polyadenylation to cytokinesis (contractile ring, septum), development (insect visual primordium, follicle cell adhesion), and chitin biosynthesis. This mix lacks a single cohesive biological theme, making it unclear what unites the proteins functionally.","confidence":"","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0098789","count":2},{"id":"GO:0000916","count":1},{"id":"GO:0075015","count":1}]},{"hash":"181625797136202429","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000304","count":1},{"id":"GO:0008614","count":1},{"id":"GO:0006543","count":1},{"id":"GO:0042823","count":1},{"id":"GO:0042128","count":1}]},{"hash":"1629687733574937005","title":"Diverse Autophagy Pathways","description":"The GO terms are dominated by autophagy-related processes: macroautophagy, autophagy of mitochondrion, Cvt pathway, and piecemeal microautophagy of the nucleus (nucleophagy). Additional terms for ufmylation and neddylation suggest regulatory layers of these pathways, with a few terms touching on defense or growth that can intertwine with autophagy in yeast. Overall, the common theme is involvement in multiple autophagic routes rather than a single specific function.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":1},{"id":"GO:0034727","count":1},{"id":"GO:1990592","count":1},{"id":"GO:0050832","count":1},{"id":"GO:0000422","count":1}]},{"hash":"2243636011219499700","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms for ribosome biogenesis, rRNA processing, and translation, including subunit biogenesis, ribosome assembly, tRNA modification, and initiation. The proteins likely form a ribosome assembly/translation machinery module, with a minor association to cell division. ","confidence":"High","size":12,"edges":57,"triangles":159,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0006400","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1811794322346607718","title":"Cell Growth and Division Coordination","description":"This cluster centers on cell cycle and growth-related processes, with terms spanning cell division, mitotic DNA replication, translation preinitiation complex formation, TORC1 signaling, and mRNA transport, plus ER-Golgi trafficking. These together suggest a coordinated module for cell proliferation and protein handling.","confidence":"Medium","size":12,"edges":41,"triangles":58,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051028","count":2}]},{"hash":"1817694309288713758","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000462","count":5},{"id":"GO:0000480","count":4},{"id":"GO:0000390","count":4},{"id":"GO:0000466","count":4},{"id":"GO:0031047","count":4}]},{"hash":"852795215460333197","title":"Bacterial lipid biosynthesis and cell wall assembly","description":"The GO terms most represented are fatty acid biosynthesis, lipid A biosynthesis, teichoic acid and lipoteichoic acid biosynthesis, and cell wall organization, which together point to a theme of envelope lipid metabolism and cell wall construction in bacteria. A few terms related to respiration and nonribosomal peptide biosynthesis appear but are less represented; nonetheless the primary signal is envelope lipid biosynthesis.","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006123","count":1},{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0006633","count":1},{"id":"GO:0071555","count":1}]},{"hash":"2279938086016561040","title":"Mitochondrial translation and tRNA aminoacylation","description":"The top GO terms point to mitochondrial protein synthesis, with direct signals for translation and several mitochondrial tRNA aminoacylation events (seryl-, glycyl-, prolyl-, threonyl- tRNA charging) as well as related processes like translational fidelity and selenocysteine biosynthesis. While some terms also touch on broader mitochondrial metabolism (e.g., ubiquinone biosynthesis), the common thread is mitochondrial translation machinery and tRNA charging. This makes a cohesive, specific label: mitochondrial translation and tRNA aminoacylation.","confidence":"High","size":12,"edges":24,"triangles":23,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0015966","count":1},{"id":"GO:0097056","count":1},{"id":"GO:0070158","count":1},{"id":"GO:0070150","count":1}]},{"hash":"1421841544634689536","title":"RNA Processing and Transcription Regulation","description":"This cluster centers on RNA metabolism and gene expression: transcription (DNA-templated), mRNA splicing, and mRNA decay processes (deadenylation/decapping), with additional signals pointing to nucleotide catabolism. Although there are a few terms related to GTPase signaling and Golgi maintenance, the dominant themes tie to transcription and RNA processing/ turnover.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0051684","count":2},{"id":"GO:1901919","count":1},{"id":"GO:0050850","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1211137747663460481","title":"Ubiquitin-dependent degradation and signaling regulation","description":"GO term analysis highlights autoubiquitination, various ubiquitin linkage-specific processes (K63, K6), ubiquitin-proteasome\u2013 and ERAD-related catabolic pathways, and regulation of signaling cascades (JNK, TNF). This suggests a cohesive role in ubiquitin-mediated protein turnover and modulation of signaling. ","confidence":"High","size":12,"edges":8,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:1903265","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0070534","count":4},{"id":"GO:0046328","count":4}]},{"hash":"904096491774893847","title":"Nuclear Spliceosome Assembly and RNA Processing","description":"The cluster is strongly enriched for spliceosome-related terms (spliceosomal complex assembly, snRNP assembly, mRNA splicing via spliceosome) and RNA processing (tRNA processing, histone mRNA metabolism) with a note of nuclear import, pointing to a cohesive module of nuclear RNA maturation and splicing; peripheral associations with stress and chromatin terms likely reflect broader regulatory connections.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000245","count":12},{"id":"GO:0000387","count":12},{"id":"GO:0008334","count":12},{"id":"GO:1990141","count":12},{"id":"GO:0051170","count":12}]},{"hash":"2061750416292658634","title":"Plant RNA silencing and ncRNA processing","description":"Dominant GO terms center on miRNA/siRNA pathways, RNA interference, and snoRNA processing, indicating a cluster of plant proteins involved in RNA silencing and ncRNA maturation, with additional connections to shoot apical meristem identity and polarity that reflect plant developmental regulation by RNA-based pathways.","confidence":"High","size":12,"edges":9,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035279","count":1},{"id":"GO:0009597","count":1},{"id":"GO:0009944","count":1},{"id":"GO:2000628","count":1},{"id":"GO:0010492","count":1}]},{"hash":"1508677810885883318","title":"Photosynthetic Bacteria Buoyancy","description":"This cluster is dominated by GO terms for photosynthesis, bacteriochlorophyll biosynthesis, and gas vesicle organization, pointing to photosynthetic bacteria and their buoyancy mechanisms (e.g., buoyant cyanobacteria or purple bacteria). The presence of core transcription/replication terms likely reflects general cellular growth, but the standout terms suggest a cohesive theme around light-driven energy capture and buoyancy structures. Some terms (like cilium movement and dense-core vesicle transport) may be annotation noise rather than core functions of these proteins.","confidence":"High","size":12,"edges":57,"triangles":142,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0030494","count":3},{"id":"GO:1990048","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006268","count":3}]},{"hash":"2140544096904489564","title":"Transcriptional Control of Metabolism","description":"Most terms cluster around transcriptional regulation (DNA-templated transcription and transcription from RNA polymerase II promoter) with several entries describing regulation by nutrients or signals (e.g., nitrogen catabolite activation, oleic acid). This is linked to various biosynthetic and metabolic pathways (lysine and ergosterol biosynthesis, gluconeogenesis, glyoxylate cycle, cellular respiration, aflatoxin biosynthesis), suggesting a theme of transcriptional control coordinating metabolic processes.","confidence":"Medium","size":12,"edges":30,"triangles":28,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0001080","count":3},{"id":"GO:0001892","count":3},{"id":"GO:2001196","count":2},{"id":"GO:0035961","count":2}]},{"hash":"878673567336381129","title":"Membrane Ion Transport and Homeostasis","description":"These proteins show enrichment for proton transmembrane transport, sodium and potassium ion movement across membranes, vacuolar acidification, and cell volume regulation, pointing to a shared role in maintaining ionic balance and membrane potential. A couple of terms (e.g., signaling pathway related to BDNF receptor) appear less central but do not override the dominant ion-transport theme.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031547","count":1},{"id":"GO:0051595","count":1},{"id":"GO:1903281","count":1},{"id":"GO:0007035","count":1},{"id":"GO:1902600","count":1}]},{"hash":"1693755824556513731","title":"Signaling and Transcription in Development","description":"The cluster shows enrichment for DNA-templated transcription and multiple signaling-related GO terms (PDGF, retinoic acid response, neurotrophin/TRK signaling, B cell receptor signaling, JUN phosphorylation) plus development-associated processes (heart development). This points to a core function in transcriptional regulation coupled with diverse cell signaling in developmental and immune/neuronal contexts, rather than a single narrow pathway.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0030838","count":2},{"id":"GO:0036120","count":2}]},{"hash":"1703813867844269423","title":"Proteasome-mediated protein turnover and immune signaling","description":"The cluster is dominated by proteasome-related terms (proteasomal ubiquitin-independent degradation, proteasome core complex assembly, deubiquitination) and includes key immune signaling pathways (non-canonical NF-kappaB, Fc-epsilon receptor, C-type lectin receptor). This combination suggests a functional module where proteasome activity intersects with immune signaling, with some supporting stress response terms (salt/ zinc) that can modulate these processes.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0010499","count":10},{"id":"GO:0010972","count":10},{"id":"GO:0038095","count":10},{"id":"GO:0038061","count":10},{"id":"GO:0016579","count":10}]},{"hash":"1133715042989125438","title":"Plant vacuolar proteolysis and iron homeostasis","description":"Proteins in this cluster point to iron handling (intracellular iron ion homeostasis, iron ion import) and vacuolar protein degradation (protein catabolic process in the vacuole), which together suggest a plant-specific coordination of iron metabolism with protein turnover. The presence of xenobiotic response signals and a note on inflorescence meristem growth further supports a broader plant stress and development context. Overall, the theme seems to be plant iron homeostasis coupled with vacuolar proteolysis.","confidence":"Medium","size":11,"edges":36,"triangles":51,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042135","count":3},{"id":"GO:0035609","count":3},{"id":"GO:0042493","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0010081","count":2}]},{"hash":"1476150286200389277","title":"Ubiquitin-Proteasome System Regulation","description":"The dominant GO terms point to regulation of protein turnover via the ubiquitin-proteasome system: deneddylation (COP9 signalosome), multiple deubiquitination activities (K11- and H2A K63-linked), proteasome storage granule assembly, and endopeptidase activity regulation, all of which connect to proteostasis. Some terms touch DNA repair and spliceosome dynamics, which can involve UPS-related regulation, supporting a cohesive theme of ubiquitin-mediated control of protein fate rather than a single isolated function.","confidence":"High","size":11,"edges":42,"triangles":79,"max_degree":10,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0010950","count":4},{"id":"GO:0006281","count":3},{"id":"GO:1902906","count":2},{"id":"GO:0045471","count":2},{"id":"GO:0000338","count":2}]},{"hash":"821012594036610569","title":"Ubiquitin/SUMO proteostasis and trafficking","description":"The top GO terms cluster around post-translational modification (sumoylation, ubiquitination, deubiquitination), protein quality control (ERAD), and regulation of endocytosis, with additional hints of broader effects on mitochondrial dynamics and transcription. This suggests a cohesive theme of ubiquitin/SUMO-mediated proteostasis coupled with intracellular trafficking. High","confidence":"","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":9},{"id":"GO:0033132","count":9},{"id":"GO:0010636","count":8},{"id":"GO:0097237","count":8},{"id":"GO:1901340","count":8}]},{"hash":"1582777055385213139","title":"DNA replication and cell cycle machinery","description":"The top GO terms cluster around DNA replication (including unwinding and recombination), DNA-templated transcription, the SOS response, and cell division, indicating a core set of replication- and cell-cycle\u2013related proteins. While a few terms touch on autophagy activation by symbionts or viral protein processing, the dominant theme is replication and division processes. ","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0032508","count":5},{"id":"GO:0009432","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0039520","count":4}]},{"hash":"1940322418833599714","title":"Vesicle trafficking and organelle transport","description":"The top GO terms cluster around intracellular cargo movement, including endocytosis, ER\u2013Golgi vesicle transport and retrograde Golgi\u2013ER transport, endosome-to-melanosome transport, and protein targeting to the vacuole. This indicates a cohesive function in vesicle trafficking and organelle communication. Some terms like cell polarity and development are related but broader and less central to the core theme. ","confidence":"High","size":11,"edges":50,"triangles":125,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071963","count":9},{"id":"GO:0021762","count":9},{"id":"GO:0000001","count":9},{"id":"GO:0010628","count":9},{"id":"GO:0006348","count":8}]},{"hash":"290768953194501331","title":"Chromatin remodeling and transcription regulation","description":"The set\u2019s most represented terms center on nucleosome positioning/maintenance, heterochromatin, histone modification regulation, and RNA polymerase II transcription termination, pointing to chromatin state as the shared function. A spliceosome-related term appears but overall these proteins seem linked to chromatin organization affecting transcription; several GO terms are labeled obsolete, but the core theme remains chromatin regulation.","confidence":"Medium","size":11,"edges":22,"triangles":10,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0060303","count":2},{"id":"GO:0016584","count":2},{"id":"GO:0042766","count":2},{"id":"GO:0070870","count":2}]},{"hash":"1157859921086686965","title":"Chaperone-driven proteostasis and microtubule organization","description":"The cluster is enriched for protein folding (GO:0006457), chaperone-related assembly (GO:0051131), and cytosolic quality control via ubiquitin-proteasome (GO:0071629), along with tubulin complex assembly and cortical microtubule organization (GO:0007021, GO:0043622). These together indicate a coordinated module for proteostasis and cytoskeletal (microtubule) organization, with transcription-related terms being less central. ","confidence":"Medium","size":11,"edges":29,"triangles":36,"max_degree":9,"top_function":"protein folding","top_go_terms":[{"id":"GO:0032968","count":3},{"id":"GO:0007021","count":3},{"id":"GO:0006457","count":3},{"id":"GO:0071629","count":2},{"id":"GO:0051131","count":2}]},{"hash":"1838664351014161357","title":"Transcription and Vesicle Trafficking Regulation","description":"The top terms include DNA-templated transcription and RNA Pol III transcription, alongside vesicle trafficking processes such as ER-to-Golgi transport, endocytosis, and synaptic vesicle maturation. TORC1 signaling and positive regulation of GTPase activity suggest growth- and signaling-driven control of these processes, with nuclear pore complex assembly linking to nucleocytoplasmic transport that supports transcription. Together, they point to a coordinated regulatory theme around transcription and intracellular trafficking.","confidence":"Medium","size":11,"edges":52,"triangles":141,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006915","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0045945","count":3},{"id":"GO:0051292","count":3}]},{"hash":"837769647692506048","title":"Regulation of Translation Initiation and Reinitiation","description":"This cluster centers on factors involved in starting translation and reinitiation, including formation of the translation preinitiation complex and IRES-dependent viral translation, indicating a cohesive theme of translational control. Ubiquitin-dependent protein turnover and developmental signals appear as supporting context, but the core signal is regulation of protein synthesis initiation; actin remodeling and transcription terms are less central. ","confidence":"High","size":11,"edges":44,"triangles":93,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":4},{"id":"GO:0006511","count":3},{"id":"GO:0001701","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0001731","count":3}]},{"hash":"50302547041307122","title":"Ubiquitin-mediated mitotic cell cycle control","description":"The dominant GO terms center on mitosis (cell division, mitotic cell cycle, metaphase/anaphase transition) and K11-linked ubiquitination, suggesting ubiquitin-dependent protein turnover during the mitotic process, likely APC/C-regulated. Plant-specific signals (cytokinin signaling, chlorophyll biosynthetic regulation) are present but do not define the core function; overall, the cluster appears to reflect ubiquitin-mediated control of mitotic progression.","confidence":"Medium","size":11,"edges":13,"triangles":7,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0070979","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0009736","count":3},{"id":"GO:1902325","count":3}]},{"hash":"124672709961290675","title":"Embryonic organogenesis and neural differentiation","description":"These proteins cluster around developmental processes spanning multiple organs and neural lineages. The top GO terms cover organ morphogenesis (ureteric bud, uterus, inner ear, pharyngeal system, bronchiole, gonad) and neuronal cell fate specification (forebrain, spinal cord oligodendrocyte and motor neuron differentiation), indicating a shared theme of embryonic development and tissue patterning rather than a single pathway.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0072107","count":2},{"id":"GO:0060065","count":2},{"id":"GO:0042472","count":2},{"id":"GO:0060037","count":2},{"id":"GO:0008584","count":2}]},{"hash":"679168096918680338","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000466","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0000747","count":4},{"id":"GO:0042254","count":4}]},{"hash":"1835961193423720539","title":"Microtubule Organization and Transport","description":"The cluster\u2019s GO terms are dominated by cytoskeletal and microtubule-related processes: tubulin complex assembly, cortical microtubule organization, spindle midzone assembly, plus-end microtubule depolymerization, and anterograde dendritic transport along microtubules. Additional terms on protein folding and quality control/chaperone assembly may reflect ancillary roles in maintaining cytoskeletal proteins. Overall, the shared theme is cytoskeletal dynamics and intracellular transport along microtubules.","confidence":"High","size":11,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":1},{"id":"GO:0007021","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0071629","count":1},{"id":"GO:0051131","count":1}]},{"hash":"206568539084089812","title":"Mesodermal development and Notch signaling","description":"The top GO terms cluster around embryonic mesoderm patterning, including axial and paraxial mesoderm development, somitogenesis, and circulatory system development, with additional support from Notch signaling regulation. This suggests the proteins may participate in signaling-guided mesoderm formation and tissue patterning. Some terms appear unrelated (e.g., certain metabolic or glycosylation terms), which may reflect annotation noise rather than core cluster function. Overall, the cluster appears to represent proteins involved in early mesoderm development and regulation of Notch signaling.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048318","count":2},{"id":"GO:0001756","count":2},{"id":"GO:0048339","count":2},{"id":"GO:0033577","count":2},{"id":"GO:0072358","count":2}]},{"hash":"246223408387315244","title":"Prenylated protein maturation and membrane trafficking","description":"The GO terms show a pattern around prenylation-related processes (CAAX-box protein processing, prenylated protein catabolic process), peroxisomal matrix import, and membrane-related organization and dynamics (nuclear envelope organization, mitochondrial fusion regulation, ergosterol biosynthesis). While some terms are obsolete or unrelated, the recurring theme centers on post-translational modification that targets proteins to membranes and their subsequent trafficking/maintenance, suggesting a membrane-associated maturation/trafficking cluster.","confidence":"Medium","size":11,"edges":25,"triangles":20,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0048137","count":2},{"id":"GO:0016558","count":2},{"id":"GO:0071586","count":2},{"id":"GO:0006998","count":2},{"id":"GO:0061077","count":2}]},{"hash":"507647248349290350","title":"Metabolic Versatility","description":"The top GO terms indicate multiple distinct metabolic and stress-related processes (retinol/retinal metabolism, ethanol and sorbitol catabolism, formaldehyde catabolism, PHB biosynthesis) along with sporulation and drug response. This suggests the cluster comprises proteins involved in diverse carbon-source utilization and general detox/stress responses rather than a single cohesive pathway, hence a broad label like Metabolic Versatility. ","confidence":"Medium","size":11,"edges":38,"triangles":66,"max_degree":9,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0042572","count":8},{"id":"GO:0055114","count":6},{"id":"GO:0042619","count":5},{"id":"GO:0006068","count":5},{"id":"GO:0006069","count":5}]},{"hash":"1217971270261005967","title":"DNA Damage Response and Homologous Recombination Repair","description":"The cluster is dominated by GO terms for cellular responses to gamma radiation and X-ray, plus mitochondrial double-strand break repair via homologous recombination and mitotic cell cycle, indicating a coherent theme of DNA damage sensing/repair and cell cycle control. Some terms like brain development and donor selection may reflect broader roles or annotation noise, but the core signal ties to genome maintenance through HR and related repair pathways.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071480","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0032508","count":2}]},{"hash":"985096688760220379","title":"Developmental organogenesis and tissue growth","description":"The top GO terms indicate multiple organ- and tissue-development processes (spinal cord, skin, seminiferous tubules, embryonic organs) and cell proliferation, pointing to a developmental/growth program across tissues. The inclusion of rRNA maturation terms may reflect a general need for ribosome biogenesis during growth rather than a single specific pathway. Overall, the cluster appears to group proteins involved in developmental processes and tissue expansion.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0007064","count":2},{"id":"GO:0072520","count":2}]},{"hash":"897650209734318211","title":"Neural development and transcriptional regulation","description":"The terms show a coherent neural development theme (forebrain development, neural tube closure, neuron apoptotic process) paired with gene regulation and signaling (DNA-templated transcription, histone modification, TORC1 and GTPase regulation). A minor outlier is the defense response term, but it does not dominate the set. This suggests a cluster of proteins involved in neural development with transcriptional and signaling regulation.","confidence":"Medium","size":10,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":2},{"id":"GO:0030900","count":1},{"id":"GO:1904263","count":1},{"id":"GO:0051402","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1662143835145650152","title":"Nutrient-responsive transcriptional activation","description":"The top GO terms point to positive regulation of transcription from the RNA polymerase II promoter in response to various nutrient- and carbon-source signals, along with related regulation of cellular respiration and biosynthetic processes. This suggests the proteins function as transcriptional regulators that activate gene expression in response to metabolic cues, forming a nutrient-responsive transcriptional module. Confidence: High","confidence":"","size":10,"edges":28,"triangles":56,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035959","count":10},{"id":"GO:0006351","count":10},{"id":"GO:0061414","count":10},{"id":"GO:2001158","count":10},{"id":"GO:1900399","count":10}]},{"hash":"1976261046458558075","title":"Cell Division and Intracellular Trafficking","description":"The set includes terms focused on cell division and mitotic checkpoint signaling, alongside processes related to intracellular transport and quality control (mRNA export, peroxisome protein import, late endosomal microautophagy). This mixture points to a broad theme of cell-cycle control together with protein/RNA trafficking and organelle maintenance, rather than a single narrow function.","confidence":"Medium","size":10,"edges":39,"triangles":81,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0061738","count":2},{"id":"GO:0033314","count":2},{"id":"GO:0018279","count":2},{"id":"GO:0001824","count":2}]},{"hash":"1059400072150303466","title":"Chromatin Regulation and Nuclear Organization","description":"The top GO terms point to control of transcription and chromatin state (negative regulation of transcription by RNA POL II, rDNA heterochromatin formation, histone modifications, and nucleus organization) and chromatin localization processes (establishment of protein localization to chromatin, dosage compensation, spermatogenesis). This suggests a cohesive cluster centered on chromatin remodeling and nuclear chromatin regulation, with a few peripheral terms (Rho signaling, innate mucosal immunity) likely reflecting broader roles or noise. Confidence: High","confidence":"","size":10,"edges":34,"triangles":54,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0000183","count":4},{"id":"GO:0043966","count":4},{"id":"GO:0007549","count":3},{"id":"GO:0035023","count":3}]},{"hash":"1290151267430894932","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:1990416","count":3},{"id":"GO:0000388","count":3},{"id":"GO:0071035","count":3},{"id":"GO:0071051","count":3}]},{"hash":"1803842735665466578","title":"Secretory Pathway Protein Maturation and Trafficking","description":"The top GO terms cluster around operations in the secretory/endomembrane system, including ER to Golgi transport, cotranslational targeting to membranes, GPI anchor attachment, and vacuolar protein processing, which together suggest proteins involved in maturation and trafficking along the secretory pathway. Some metabolism-related terms appear as outliers but do not define the main theme.","confidence":"Medium","size":10,"edges":43,"triangles":105,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0006613","count":1},{"id":"GO:0000103","count":1},{"id":"GO:1902358","count":1},{"id":"GO:0019344","count":1}]},{"hash":"1977190514552320845","title":"Membrane transporters and vesicle loading","description":"The top GO terms are dominated by transmembrane transport of various substrates (glucose, arabinose, nitrate, phosphate, potassium, sodium-coupled organic cation) and a function for loading neurotransmitters into synaptic vesicles, indicating a cluster of membrane transport proteins with vesicle trafficking roles; a term on intestinal epithelial maintenance is present but secondary. ","confidence":"High","size":10,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0044381","count":3},{"id":"GO:0015751","count":3},{"id":"GO:0070715","count":3},{"id":"GO:0035435","count":3},{"id":"GO:0052106","count":3}]},{"hash":"710095582160931994","title":"Protein turnover and transcription regulation","description":"The cluster combines proteins involved in protein homeostasis (COP9 signalosome assembly, protein deneddylation, K11- and H2A-K63-linked deubiquitination, proteasome-related assembly) with components of transcription and RNA processing (RNA Pol II preinitiation complex assembly and spliceosomal conformational changes). This suggests a cohesive theme of coordinating protein degradation pathways with transcription and RNA processing, despite some outliers such as ethanol response. ","confidence":"Medium","size":10,"edges":28,"triangles":35,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051123","count":2},{"id":"GO:1902906","count":1},{"id":"GO:0045471","count":1},{"id":"GO:0000338","count":1},{"id":"GO:0010387","count":1}]},{"hash":"591449083871902328","title":"Ribosome and Translation Machinery","description":"Most top GO terms in this cluster describe core translation processes (cytoplasmic translation, initiation, termination, and elongation) and ribosome dynamics, including mitochondrial translation and ribosome disassembly. Although a few terms like response to antibiotic and glial cell proliferation appear, the dominant signal is assembly and regulation of the protein synthesis machinery. Thus the cluster most plausibly represents ribosomal components and translational factors.","confidence":"High","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006413","count":3},{"id":"GO:0001514","count":3},{"id":"GO:0006415","count":3},{"id":"GO:0032790","count":3}]},{"hash":"778602522204645739","title":"Unknown","description":"The terms span immune signaling, development, cell death regulation, and DNA repair with only one annotation per term; there is no single cohesive function or pathway uniting the proteins, so a meaningful label cannot be inferred.","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0023035","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0060546","count":1},{"id":"GO:2000721","count":1},{"id":"GO:0060157","count":1}]},{"hash":"891838743609936291","title":"Fatty acid and sphingolipid biosynthesis","description":"This cluster centers on lipid metabolism, including fatty acid biosynthesis and sphingosine (sphingolipid) pathways, with additional signals for cholesterol esterification and tissue-specific lipid differentiation (skin/sebaceous glands and white fat) and CNS myelin maintenance. The common theme is lipid production and lipid-related cellular functions across tissues.","confidence":"High","size":9,"edges":31,"triangles":54,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0034435","count":5},{"id":"GO:0001949","count":5},{"id":"GO:0032286","count":5},{"id":"GO:0006675","count":5},{"id":"GO:0033561","count":4}]},{"hash":"1087462673867570895","title":"Unknown","description":"The top GO terms span metabolism (glycerol, phosphatidylglycerol, phosphate homeostasis) and broad developmental and cellular processes (guard cell morphogenesis, neural tube closure, apoptosis, GTPase regulation, histone deacetylation), with little overlap pointing to a single, coherent function. Therefore no clear, specific label fits the cluster, so it is Unknown.","confidence":"","size":9,"edges":17,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006071","count":2},{"id":"GO:0010442","count":2},{"id":"GO:0034478","count":2},{"id":"GO:0030643","count":2},{"id":"GO:0008283","count":2}]},{"hash":"434665270666625351","title":"Polyamine acetylation","description":"The cluster\u2019s top GO terms are dominated by polyamine acetylation: putrescine, spermidine, and spermine acetylation appear multiple times, indicating a coherent theme around polyamine modification. Other biosynthetic processes (ectoine, melatonin, glucosamine, mycothiol, arginine) are present but less consistently linked, so the strongest signal is polyamine acetylation and related small-molecule metabolism.","confidence":"Medium","size":9,"edges":14,"triangles":9,"max_degree":4,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0006348","count":7},{"id":"GO:0032920","count":4},{"id":"GO:0032919","count":4},{"id":"GO:0019491","count":4},{"id":"GO:0046208","count":4}]},{"hash":"116962142675920111","title":"Mitochondrial Fe-S cluster biogenesis and respiration","description":"The cluster has strong signals for mitochondrial electron transport (succinate to ubiquinone) and [2Fe-2S] cluster assembly, i.e., iron-sulfur cluster biogenesis linked to mitochondrial respiration. Although some terms are obsolete, the core theme points to Fe-S cluster maturation within mitochondria and oxidative phosphorylation. Additional terms reflect broader mitochondrial metabolism but do not override the central Fe-S/respiration connection.","confidence":"High","size":9,"edges":25,"triangles":30,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006121","count":2},{"id":"GO:0044571","count":2},{"id":"GO:0097428","count":2},{"id":"GO:1903026","count":2},{"id":"GO:0034396","count":2}]},{"hash":"1642674618457152960","title":"Developmental transcription and cell cycle regulation","description":"The cluster centers on DNA-templated transcription and DNA replication processes, with associated chromatin modification (histone H3 acetylation) and cell-cycle control (G2/M transition), plus development-related terms (skeletal muscle and multicellular organism development). This suggests a cohesive theme of coordinating gene expression with cell proliferation during development, so a label focusing on transcriptional regulation linked to development and the cell cycle fits. Confidence: Medium","confidence":"Medium","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0007519","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0000086","count":2}]},{"hash":"1732065136933295686","title":"Redox Homeostasis and Glutathione Metabolism","description":"The cluster is dominated by redox- and glutathione-related terms: cellular oxidant detoxification, glutathione metabolic process, protein glutathionylation, and cell redox homeostasis, plus regulation of mitochondrial membrane potential, all indicating a cohesive theme of managing oxidative stress and glutathione pathways. There are a few ancillary terms (chloride transport, NF-kappaB signaling, calcium channel regulation) that can be modulated by redox state, but the core signal is redox balance and glutathione metabolism.","confidence":"High","size":9,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":4},{"id":"GO:0035264","count":3},{"id":"GO:0010731","count":3},{"id":"GO:0006749","count":3},{"id":"GO:0051881","count":3}]},{"hash":"145862444760141276","title":"Neuronal development and synaptic morphogenesis","description":"The cluster is dominated by neural-development related terms\u2014dendritic spine morphogenesis, interneuron migration, apical protein localization, and calcium-dependent exocytosis\u2014along with cytoskeletal (tubulin) assembly and focal adhesion regulation. This combination points to neuronal morphogenesis and synaptic assembly rather than generic cellular processes.","confidence":"High","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006998","count":9},{"id":"GO:0061001","count":9},{"id":"GO:0032707","count":9},{"id":"GO:0051893","count":9},{"id":"GO:0007021","count":9}]},{"hash":"1920229084899546656","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000462","count":2}]},{"hash":"1336439772665827567","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":21,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":4},{"id":"GO:0034354","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0042493","count":3}]},{"hash":"2009782873875043045","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":33,"triangles":65,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0006367","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0001113","count":3}]},{"hash":"529751559321954619","title":"Golgi- and vesicle-trafficking","description":"The GO terms cluster around intracellular transport and Golgi function: Golgi localization and inheritance, Golgi to vacuole transport, protein targeting to vacuole, endocytosis, intracellular protein transport, and synaptic vesicle trafficking. This points to a cohesive theme of vesicle movement and Golgi-mediated protein routing, with related endocytic and presynaptic vesicle processes supporting the overall trafficking role. A few terms like response to virus or substrate adhesion-dependent spreading appear peripheral to the main theme. Confidence reflects the clear connectivity to vesicle trafficking and Golgi processes.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1900026","count":2},{"id":"GO:0006623","count":1},{"id":"GO:0006897","count":1},{"id":"GO:0051645","count":1},{"id":"GO:0048313","count":1}]},{"hash":"418903728167476256","title":"Muscle contraction and calcium handling","description":"The Top Terms cluster around muscle function and excitation-contraction coupling: regulation of fast-twitch skeletal muscle contraction, T-tubule organization, and calcium ion transport to the endoplasmic reticulum, as well as regulation of heart contraction. These points suggest the proteins are linked to muscle contraction and calcium signaling. A few terms (nerve formation, glycoside response, cadmium transport) are less directly related, but do not override the core muscle-centric theme.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006754","count":2},{"id":"GO:0031448","count":2},{"id":"GO:0021650","count":2},{"id":"GO:0033292","count":2},{"id":"GO:1903416","count":2}]},{"hash":"432368415398123163","title":"Galactose metabolism and isoprenoid biosynthesis","description":"The GO terms show multiple galactose-focused carbohydrate pathways (galactose glycolysis, galacturonate, galactitol, carbohydrate phosphorylation) alongside IPP/mevalonate\u2013related steps (isopentenyl diphosphate biosynthesis via MEP and mevalonate pathways, farnesyl diphosphate biosynthesis) and cholesterol biosynthesis, indicating a functional link between carbohydrate metabolism and isoprenoid biosynthesis in this cluster.","confidence":"Medium","size":9,"edges":14,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0061623","count":3},{"id":"GO:0046396","count":3},{"id":"GO:0019402","count":3},{"id":"GO:0019288","count":3},{"id":"GO:0006695","count":3}]},{"hash":"1269542770370946360","title":"Ciliary Axoneme Assembly and Motility","description":"Most of the top GO terms point to cilium/flagellum biology: flagellated sperm motility, sperm axoneme assembly, cilium movement, epithelial cilium movement, microtubule severing, and tubulin polyglycylation. A few terms about growth hormone and insulin signaling are less central to this cluster, which is dominated by ciliogenesis and motility. Thus the label emphasizes ciliary/axonemal structure and movement.","confidence":"High","size":9,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060396","count":2},{"id":"GO:0046626","count":2},{"id":"GO:2001307","count":1},{"id":"GO:0010914","count":1},{"id":"GO:1905419","count":1}]},{"hash":"2061761871876031634","title":"Nuclear transcription and RNA splicing machinery","description":"The top GO terms cluster around DNA-templated transcription, RNA polymerase II termination, mRNA splicing via spliceosome, spliceosomal complex and snRNP assembly, histone mRNA metabolism, and nuclear import, indicating a cohesive set of proteins involved in transcription and pre-mRNA processing within the nucleus; occasional ABA response and polar nucleus fusion terms seem context-specific rather than core to the cluster.","confidence":"High","size":9,"edges":30,"triangles":48,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1990141","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0006369","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0010197","count":2}]},{"hash":"930824154891291061","title":"Ribosome Biogenesis and Cell Cycle Regulation","description":"The cluster shows strong representation of translation and SSU-rRNA maturation, pointing to ribosome biogenesis, along with GO terms for cell cycle control, ubiquitin-proteasome regulation, and p53-mediated signaling, plus a stress response to actinomycin D, suggesting coordinated regulation of ribosome production with cell-cycle checkpoints and proteostasis under stress.","confidence":"High","size":9,"edges":28,"triangles":42,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0000462","count":3},{"id":"GO:0050821","count":2},{"id":"GO:0071157","count":2},{"id":"GO:2000059","count":2}]},{"hash":"338757394216584838","title":"Steroid and fatty acid biosynthesis","description":"This cluster is dominated by biosynthetic processes for lipids and steroids (fatty acid elongation, very long-chain fatty acid biosynthesis, estrogen and glucocorticoid biosynthesis), with a peripheral melanin biosynthesis term and a sporulation term suggesting broader biosynthetic capabilities. The overarching theme is biosynthesis of diverse biomolecules, especially lipids and steroids.","confidence":"Medium","size":9,"edges":16,"triangles":20,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030497","count":6},{"id":"GO:0008207","count":6},{"id":"GO:0006704","count":6},{"id":"GO:0042438","count":6},{"id":"GO:0030435","count":6}]},{"hash":"1456589406504613756","title":"Sterol and lipid biosynthesis","description":"This cluster is enriched for sterol biosynthetic processes (cholesterol via lathosterol, ergosterol) and related lipid metabolism (fatty acid biosynthesis, ether lipid metabolism), suggesting a common theme in membrane lipid production; a few immune/tissue terms appear less consistently and may reflect annotation noise.","confidence":"Medium","size":9,"edges":23,"triangles":29,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":2},{"id":"GO:0033490","count":2},{"id":"GO:0035754","count":2},{"id":"GO:0080065","count":2},{"id":"GO:0080064","count":2}]},{"hash":"390307543886661081","title":"Nuclear envelope and cytoskeletal organization","description":"Terms cluster around cellular structural organization: nuclear envelope, cytoskeleton (tubulin complex assembly), and vesicle trafficking (COPII), plus chromatin regulation (heterochromatin formation and H3-K36 dimethylation). A few tissue-development terms appear as broader annotations. Overall, the cluster seems to reflect cellular architecture and its regulation.","confidence":"Medium","size":8,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:1903709","count":3},{"id":"GO:0097676","count":3},{"id":"GO:1903699","count":3},{"id":"GO:0032635","count":3}]},{"hash":"1726939233270420447","title":"Neuronal development and proteostasis","description":"Major terms point to neuronal development (dendritic spine morphogenesis, hippocampus development) and cellular protein homeostasis (ribosomal subunit export, regulation of protein catabolic process, exosomal secretion, mitochondrial fission). These together suggest proteins involved in neuronal growth/structure maintenance and proteostasis; manganese response is a secondary cue. Medium","confidence":"","size":8,"edges":12,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0061001","count":3},{"id":"GO:0000056","count":3},{"id":"GO:0021766","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0045792","count":3}]},{"hash":"414175307540505949","title":"Lipid Biosynthesis and T Cell Regulation","description":"The cluster\u2019s top GO terms cluster around lipid metabolism and remodeling (triglyceride biosynthesis, platelet activating factor biosynthesis, phosphatidylcholine remodeling, ether lipid biosynthesis, CDP-diacylglycerol biosynthesis) with accompanying immune-related terms (interleukin-2 production, negative regulation of activation-induced T cell death). This suggests a functional theme where lipid metabolic processes intersect T cell signaling and survival, making the label representative. Some terms like cutin biosynthesis may be broader or cross-species annotations, but the dominant signal is lipid metabolism linked to immune function.","confidence":"Medium","size":8,"edges":13,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0019432","count":4},{"id":"GO:0006663","count":3},{"id":"GO:0070970","count":3},{"id":"GO:0036151","count":3},{"id":"GO:0008611","count":3}]},{"hash":"1489723526147195009","title":"Amino Acid and Vitamin Biosynthesis","description":"The top terms are dominated by biosynthetic and catabolic processes for multiple amino acids (lysine via aminoadipic acid, alanine, tyrosine, phenylalanine, aspartate, glutamate) and by biosynthesis of vitamins/cofactors (cobalamin/B12, biotin), with additional related metabolite production like kynurenic acid. Although a DNA-templated transcription term appears, the overall theme centers on amino acid metabolism and vitamin biosynthesis, justifying a cohesive label around these interconnected biosynthetic pathways.","confidence":"High","size":8,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":3},{"id":"GO:0042853","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0006571","count":1},{"id":"GO:0009236","count":1}]},{"hash":"1513163246689148371","title":"Plant hormone signaling and cell cycle control","description":"The terms include auxin-activated and ethylene-activated signaling pathways, development, and key cell cycle processes such as chromosome segregation and exit from mitosis, suggesting a link between plant hormonal signaling and cell division/organization. Other terms are diverse and less informative, so the overall pattern supports a moderate level of confidence.","confidence":"Medium","size":8,"edges":13,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":1},{"id":"GO:0060542","count":1},{"id":"GO:0007275","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0007035","count":1}]},{"hash":"639634892540689599","title":"Mitochondrial translation and energy metabolism","description":"The top GO terms center on mitochondrial protein synthesis (mitochondrial translation, tRNA modification/transamidation) and ATP generation via proton-motive force, indicating this cluster likely comprises mitochondrial translation machinery linked to oxidative phosphorylation and energy metabolism. A few outlier terms (e.g., nylon catabolic process, ER organization) may reflect annotation noise rather than true function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007029","count":1},{"id":"GO:0019876","count":1},{"id":"GO:0009062","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0070681","count":1}]},{"hash":"2015558505173509962","title":"Bacterial cell wall biosynthesis and antibiotic response","description":"The cluster shows enrichment for peptidoglycan biosynthesis and cell wall organization, plus an antibiotic response term, pointing to a module involved in cell envelope biogenesis and stress response in bacteria. Additional terms on metabolism and proton transport suggest supporting energy and membrane functions, but the strongest common theme centers on cell wall construction and antibiotic-related remodeling.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042853","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0008611","count":2},{"id":"GO:0009820","count":2}]},{"hash":"1017546626817420251","title":"Chromatin remodeling and transcription initiation","description":"The top GO terms cluster around chromatin dynamics and transcription regulation: chromatin remodeling (GO:0043044) and transcription initiation at RNA Pol II promoters (GO:0006367), with related terms like nucleosome positioning and histone exchange appearing as part of chromatin-associated regulation. Additional terms such as protein import and ribosomal RNA maturation suggest nuclear/nucleolar coordination, though some terms (e.g., mitotic spindle assembly, exploration behavior) are less directly tied and may reflect broader multifunctionality. Overall, the dominant theme is chromatin remodeling coupled with transcription initiation.","confidence":"Medium","size":8,"edges":23,"triangles":32,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0035640","count":2},{"id":"GO:0016584","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0000209","count":2}]},{"hash":"459209420443526783","title":"Ribosome biogenesis and translation initiation","description":"Dominant GO terms center on ribosome assembly and translation control, including formation of the translation preinitiation complex, translation reinitiation, maturation of SSU rRNA, and ribosome biogenesis. Additional terms like TORC1 signaling and GTPase regulation may reflect linked regulatory pathways, while neuron-related terms could be incidental or reflect shared components; overall the cluster is best described as a ribosome/translation-focused module.","confidence":"High","size":8,"edges":24,"triangles":36,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0030900","count":3}]},{"hash":"2099058776934671780","title":"Actin Cytoskeleton Assembly and Cell Polarity","description":"The frequent GO terms center on actin filament polymerization and assembly (filament and cortical patch), plus cell shape and polarity maintenance, pointing to a cohesive function in actin cytoskeleton organization and its role in cell polarity and morphology; chromatin-related terms appear as minor or peripheral signals.","confidence":"High","size":8,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":2},{"id":"GO:0043983","count":1},{"id":"GO:0006348","count":1},{"id":"GO:0000147","count":1},{"id":"GO:0016344","count":1}]},{"hash":"852724026318270559","title":"Polyamine acetylation","description":"This cluster is dominated by GO terms for acetylation of polyamines\u2014putrescine, spermidine, and spermine\u2014suggesting a shared role in polyamine modification. Other listed terms pertain to diverse biosynthetic and metabolic processes, which may reflect broader functional associations, but the strongest cohesive signal is polyamine acetylation.","confidence":"Medium","size":8,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032920","count":3},{"id":"GO:0006348","count":3},{"id":"GO:0032919","count":3},{"id":"GO:0019491","count":3},{"id":"GO:0046208","count":3}]},{"hash":"1314903268825885073","title":"Transmembrane transport of amino acids and ions","description":"The cluster is dominated by GO terms describing various transmembrane transport processes, including amino acids (methionine, D-alanine, GABA), polyamines, carnitine, ammonium, and rubidium, and by cell volume/osmotic regulation terms. This indicates a group of membrane transport proteins involved in nutrient uptake, ion/homeostasis, and osmoregulation.","confidence":"High","size":8,"edges":18,"triangles":23,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0071477","count":7},{"id":"GO:0098713","count":7},{"id":"GO:1902269","count":7},{"id":"GO:0035826","count":7},{"id":"GO:0006884","count":7}]},{"hash":"455449147913560879","title":"TCA Cycle and NADPH Metabolism","description":"The dominant GO terms point to central carbon metabolism\u2014tricarboxylic acid cycle and 2-oxoglutarate metabolism\u2014with supporting annotations for NADP+/NADPH biosynthesis and regeneration. This pattern suggests a cohesive core of enzymes focused on energy production and redox cofactor supply. A few outlier terms (e.g., certain biosynthetic or development annotations) are likely annotation noise and do not define the cluster\u2019s main function.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":5},{"id":"GO:0019878","count":4},{"id":"GO:1904465","count":3},{"id":"GO:0006103","count":3},{"id":"GO:0006537","count":3}]},{"hash":"1013318121801169793","title":"Zinc Transport and Homeostasis","description":"This cluster is dominated by GO terms related to zinc ion import, intracellular zinc ion homeostasis, detoxification of zinc ions, and zinc transmembrane transport, indicating a core function in zinc handling across membranes. A cadmium transport term appears but likely reflects metal transport in general; the zinc-centric terms best define the cluster. The limb development term seems incidental. ","confidence":"High","size":8,"edges":10,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":6},{"id":"GO:0010312","count":5},{"id":"GO:0006882","count":5},{"id":"GO:0060173","count":3},{"id":"GO:1903615","count":3}]},{"hash":"2130825168274002408","title":"Plant cell wall biosynthesis and glycosylation","description":"This cluster centers on plant cell wall construction and modification, with GO terms for homogalacturonan and glucuronoxylan biosynthesis, various protein glycosylation pathways, and mucilage/secondary wall biosynthesis, indicating a cohesive theme of wall biosynthesis and glycan modification.","confidence":"High","size":8,"edges":25,"triangles":40,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0016266","count":2},{"id":"GO:0010289","count":1},{"id":"GO:0006012","count":1},{"id":"GO:0035269","count":1}]},{"hash":"140265715533672688","title":"Mitochondrial import and ER-Golgi trafficking","description":"This cluster centers on protein trafficking to mitochondria and through the ER-Golgi pathway, as indicated by GO terms for import into the mitochondrial matrix and insertion into the mitochondrial inner membrane, plus endoplasmic reticulum to Golgi vesicle-mediated transport. Although a couple of older/obsolete terms appear, the current terms point to a shared function in targeting and integrating proteins into organelles and secretory compartments.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0006888","count":1},{"id":"GO:2000269","count":1},{"id":"GO:0001302","count":1}]},{"hash":"974134687429675721","title":"Mitochondrial Transport and Metabolism","description":"The top GO terms cluster around transport of diverse metabolites and ions (NAD, Mn, pyridoxal phosphate, deoxynucleotides, phosphate) and mitochondrial-associated processes (mitochondrial genome maintenance, fission-related localization, adaptive thermogenesis). Despite some obsolete annotations, the recurring theme is mitochondrial metabolite transport and energy metabolism.","confidence":"High","size":8,"edges":20,"triangles":22,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0097274","count":4},{"id":"GO:0000002","count":4},{"id":"GO:0006828","count":3},{"id":"GO:0035352","count":3},{"id":"GO:0090152","count":3}]},{"hash":"87613421477724567","title":"Transmembrane transport of ions and cofactors","description":"This cluster is enriched for multiple transmembrane transport functions, including manganese ion transport, NAD transmembrane transport, pyridoxal phosphate transport, phosphate ion transport, and deoxynucleotide transport, pointing to a shared theme of transporting ions and small molecules across membranes, with supporting links to mitochondrial/metabolic context (e.g., adaptive thermogenesis, insulin secretion regulation). ","confidence":"High","size":8,"edges":23,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0097274","count":7},{"id":"GO:0006828","count":6},{"id":"GO:0035352","count":6},{"id":"GO:0090152","count":6},{"id":"GO:0031921","count":6}]},{"hash":"1999098819347088693","title":"Chromatin regulation and mitotic cell cycle","description":"The cluster centers on DNA-templated transcription and histone methylation (H3-K79 and K27), together with mitotic cell cycle processes (cell division, APC-dependent catabolic process). This combination suggests proteins that regulate chromatin state and transcription while coordinating cell division. TORC1 signaling may reflect regulatory integration with growth signals. Overall, these proteins likely function as chromatin-modifying transcription regulators involved in mitosis.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:2001162","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0061087","count":4}]},{"hash":"631804808474527530","title":"Membrane transporters for ions and nutrients","description":"The prominent GO terms point to transmembrane transport of diverse substrates (arabinose, nitrate, sodium, potassium, xenobiotics, vitamins) across membranes, indicating a cluster of transporter proteins handling uptake/efflux of ions and nutrients. A couple of metabolic terms (L-arginine biosynthesis, fucose metabolism) appear but are less central, which can accompany transport roles in some proteins. Overall, the theme is membrane transporters for ions and nutrients.","confidence":"Medium","size":7,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006526","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0006855","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0071805","count":1}]},{"hash":"2216152274456983516","title":"Transmembrane Substrate Transporters","description":"This cluster is dominated by GO terms for transporting various substrates across membranes (vitamins, xenobiotics, sugars, ions, and other substrates). The recurring theme is membrane transporter activity handling diverse substrates, rather than a single substrate class, indicating a set of proteins that function as transmembrane transporters. ","confidence":"High","size":7,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":7},{"id":"GO:0042891","count":7},{"id":"GO:0006855","count":7},{"id":"GO:0044381","count":6},{"id":"GO:0015751","count":6}]},{"hash":"1247536953910157492","title":"Genome Maintenance: DNA Replication and Repair","description":"Top terms indicate strong involvement in DNA replication, nucleotide-excision repair, and translesion synthesis, pointing to genome maintenance and DNA damage tolerance as the core function of this cluster. While other terms suggest auxiliary processes like transcription and redox balance, the dominant theme is DNA replication/repair.","confidence":"High","size":7,"edges":10,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006808","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0070987","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006289","count":2}]},{"hash":"643385900890144484","title":"Transmembrane Transporters of Ions and Nutrients","description":"This cluster is driven by transmembrane transport terms across a wide range of substrates (xenobiotics, ions, sugars, nitrates, vitamins) and includes vesicular neurotransmitter loading, pointing to a membrane transport function as the shared theme. While a couple terms reflect metabolism, the transport components dominate, making 'Transmembrane Transporters of Ions and Nutrients' a precise label.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":6},{"id":"GO:0015751","count":6},{"id":"GO:0071805","count":6},{"id":"GO:0042128","count":6},{"id":"GO:0006004","count":6}]},{"hash":"1270163934246463220","title":"Unknown","description":"The top GO terms show a highly diverse mix: glycosphingolipid and sphingolipid (globoside, mannosyl-inositol phosphorylceramide) biosynthesis, plant-specific flavonoid biosynthesis, amino acid (tyrosine) biosynthesis, general metabolism, and potassium transport, with several obsolete terms. This lack of a clear, cohesive biological function or pathway makes it difficult to assign a precise, representative label to the cluster, so an Unknown label is most appropriate.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001576","count":2},{"id":"GO:0051999","count":2},{"id":"GO:0036210","count":2},{"id":"GO:0006626","count":1},{"id":"GO:0009813","count":1}]},{"hash":"468355533728314724","title":"Ribosome Biogenesis and Vesicle Trafficking","description":"This cluster centers on core protein synthesis (translation and ribosome biogenesis) and also on endomembrane trafficking processes (Golgi retention, intralumenal vesicle formation, MVB sorting, and exosomal secretion), suggesting a link between protein production and vesicle-mediated protein handling.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0045053","count":2},{"id":"GO:0070676","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1776705836992174303","title":"Neurodevelopment and Neural Tube Formation","description":"The most represented terms point to brain/forebrain development and neural tube closure, plus neuronal apoptotic processes, indicating involvement in neurodevelopment and neuronal differentiation. Supporting terms like DNA-templated transcription and regulators of TORC1 signaling and GTPase activity fit into regulatory steps commonly active during development. A few terms appear unrelated or incidental, suggesting annotation noise in a small subset. ","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0009442","count":2},{"id":"GO:0030900","count":1},{"id":"GO:1904263","count":1},{"id":"GO:0051402","count":1}]},{"hash":"557020227940668281","title":"Unknown","description":"The GO terms span autophagy-related vesicle transport, neural development, cell proliferation, thiamine biosynthesis, nuclear envelope organization, spine morphogenesis, immune regulation, focal adhesion, and microtubule assembly, with no single cohesive function linking all proteins. This suggests a heterogeneous set rather than a shared biological role.","confidence":"","size":7,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":4},{"id":"GO:0021766","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0009229","count":3},{"id":"GO:0009228","count":3}]},{"hash":"514897149508197257","title":"RNA Transcription and Ribosome Biogenesis","description":"The cluster's top GO terms are dominated by transcription-related processes (RNA polymerase II/III transcription, termination, RNA-templated transcription, tRNA transcription) and ribosome biogenesis, suggesting proteins involved in gene expression and ribosome assembly. A few rare terms (meiotic mismatch repair, placenta development, chemotaxis) are unlikely core functions but do not overwhelm the main theme.","confidence":"Medium","size":7,"edges":17,"triangles":21,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0071353","count":2},{"id":"GO:0042797","count":2},{"id":"GO:0006386","count":2},{"id":"GO:0001172","count":2}]},{"hash":"186252628467218081","title":"Central Carbon Metabolism and Energy Production","description":"The Top Terms are dominated by core carbon metabolism processes (TCA cycle, glycolytic process, gluconeogenesis, and pyruvate decarboxylation to acetyl-CoA) along with leucine and propionate catabolism, indicating a cohesive theme of energy generation and carbon flux. A couple of auxiliary terms (sucrose starvation response, sodium transport) are present but do not override the central metabolic signal. Therefore, this cluster is best described as central carbon metabolism and energy production.","confidence":"High","size":7,"edges":14,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":3},{"id":"GO:0019629","count":2},{"id":"GO:0006096","count":2},{"id":"GO:0043617","count":2},{"id":"GO:0006814","count":2}]},{"hash":"862592082767700950","title":"Plant stomatal development and CO2/light response","description":"The cluster is driven by GO terms about stomatal development regulation, response to CO2, and red/far-red light phototransduction, plus carbon utilization, pointing to a plant-specific module that links gas exchange with environmental light/CO2 signals. Some terms (iron-sulfur cluster maturation, placenta development, p53 signaling) seem unrelated or noisy, so confidence is limited.","confidence":"Low","size":7,"edges":11,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:2000122","count":2},{"id":"GO:0015976","count":2},{"id":"GO:0071244","count":2},{"id":"GO:0097428","count":1},{"id":"GO:0016226","count":1}]},{"hash":"1495261240413456622","title":"Neural development and transcriptional regulation","description":"The top GO terms are dominated by neural development (forebrain development, neural tube closure, multicellular organism development) and DNA-templated transcription, suggesting the proteins cluster around neural tissue formation and gene expression control. Additional terms point to stress and immune responses that can occur in developing tissues, but the core signal is neural development and transcriptional regulation.","confidence":"Medium","size":7,"edges":11,"triangles":6,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030900","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0001843","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0070059","count":5}]},{"hash":"1036843976615142876","title":"Mitochondrial respiration and Complex III assembly","description":"Predominant GO terms describe mitochondrial energy production, including proton transmembrane transport, mitochondrial respiratory chain complex III assembly, and electron transport from ubiquinol to cytochrome c, all core to oxidative phosphorylation and aerobic respiration. A few unrelated terms appear, likely due to multifunctionality or annotation noise, but the overarching theme remains mitochondrial respiration. Therefore, this cluster is best described as mitochondrial respiration and Complex III assembly.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":1},{"id":"GO:0034551","count":1},{"id":"GO:0009060","count":1},{"id":"GO:0006122","count":1},{"id":"GO:0006777","count":1}]},{"hash":"1121013887058966446","title":"BMP/TGF-\u03b2 Smad signaling regulators","description":"Cluster terms cluster around signaling and regulation of TGF-\u03b2/BMP pathways, including SMAD-mediated signaling, negative regulation of BMP signaling, and responses to TGF-\u03b2 stimulus. The presence of dephosphorylation terms (protein and peptidyl-threonine) suggests regulation by phosphatases, fitting phosphorylation-dependent control of this axis. While a few GO entries are obsolete, the core theme points to modulators of TGF-\u03b2/BMP/SMAD signaling.","confidence":"High","size":7,"edges":11,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000160","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0042006","count":1},{"id":"GO:0000173","count":1}]},{"hash":"614978743818424546","title":"Plant defense and root development","description":"The top GO terms include defense responses to virus and fungus, indicating immunity-related functions, and lateral root development, a clearly plant-specific growth process. While other terms reference general metabolism, the combination suggests a cluster of plant proteins involved in immunity and root growth rather than a single cohesive pathway. ","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":2},{"id":"GO:0030643","count":1},{"id":"GO:0010264","count":1},{"id":"GO:0048527","count":1},{"id":"GO:0051607","count":1}]},{"hash":"1668599499481592167","title":"RNA modification methyltransferases","description":"The top GO terms cluster around RNA methylation activities\u2014rRNA modification, RNA guanine-N7 methylation, tRNA wobble uridine modification, and 7-methylguanosine mRNA capping\u2014as well as related protein methylation. This points to a group of enzymes that transfer methyl groups to nucleic acids and, to some extent, to proteins. Some other terms (antibiotic biosynthesis, cobalamin biosynthesis) may reflect broader metabolic contexts in which methyltransferases operate, but the core signal is RNA methylation. Therefore, the label highlights the common function of methylation in RNA modification.","confidence":"High","size":7,"edges":14,"triangles":10,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000154","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0019919","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0046690","count":2}]},{"hash":"714541801405837137","title":"ER quality control and ER-to-Golgi retrograde transport","description":"The cluster's GO terms cluster around ER-associated degradation (ERAD), unfolded protein response, and retrograde transport from the Golgi to the ER, including proteolysis in retrograde transport and endosome localization. This points to a shared role in ER quality control and trafficking between the ER and Golgi, despite some unrelated terms present. ","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0042676","count":1},{"id":"GO:0010936","count":1},{"id":"GO:0030970","count":1},{"id":"GO:1904211","count":1}]},{"hash":"1972831782736061078","title":"Amino acid and cofactor biosynthesis","description":"These proteins cluster around multiple amino acid biosynthetic pathways (lysine, histidine, tyrosine, phenylalanine) and cofactor synthesis (heme via protoporphyrinogen IX; cobalamin), suggesting a metabolic module dedicated to building amino acids and essential cofactors. Some transcription-related terms and obsolete GO entries are present, but the dominant theme is biosynthesis.","confidence":"High","size":7,"edges":12,"triangles":7,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":4},{"id":"GO:0006782","count":4},{"id":"GO:0000105","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0006571","count":3}]},{"hash":"910066381207799367","title":"Chromatin Regulation and Mitosis","description":"The top GO terms center on chromatin modification (negative regulation of histone H3-K27 methylation; negative regulation of histone deacetylase activity; heterochromatin formation) and cell division processes (centrosome cycle; spindle assembly). This combination suggests proteins involved in epigenetic regulation that interfaces with mitotic apparatus and chromosome segregation, justifying a label that emphasizes both chromatin regulation and mitosis.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0061086","count":2},{"id":"GO:2000584","count":2},{"id":"GO:0060669","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0048513","count":2}]},{"hash":"151021927751474544","title":"Lipid biosynthesis and sphingolipid signaling","description":"Dominated by lipid metabolism terms: phosphatidylglycerol and phosphatidylcholine biosynthesis, ergosterol biosynthesis, phospholipid turnover, and sphingolipid-related processes (sphinganine-1-phosphate metabolism, sphingolipid signaling). This indicates a cluster of proteins involved in membrane lipid synthesis and sphingolipid signaling rather than other pathways.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006655","count":2},{"id":"GO:0006656","count":1},{"id":"GO:0006696","count":1},{"id":"GO:0015760","count":1},{"id":"GO:0009395","count":1}]},{"hash":"1239840998934903975","title":"Transmembrane Transporters for Ions and Small Molecules","description":"This cluster is dominated by GO terms describing transport across membranes for a variety of substrates (xenobiotics, arabinose, potassium, sodium, nitrate, vitamins) and a vesicular neurotransmitter loading process, indicating a common theme of membrane transporter activity handling diverse substrates and potentially vesicular packaging. While some metabolism terms appear, the overall pattern centers on transmembrane transport roles.","confidence":"High","size":6,"edges":9,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":5},{"id":"GO:0015751","count":5},{"id":"GO:0071805","count":5},{"id":"GO:0042128","count":5},{"id":"GO:0006004","count":5}]},{"hash":"2083381080264620943","title":"Unknown","description":"The terms mix neural development (CNS development, innervation, GDNF receptor signaling) with various tissue morphogenesis terms (colon epithelium, chondrocyte, glomerular basement membrane) and even bacterial biosynthetic processes (lipoteichoic acid, choline), with no clear shared function tying the cluster. Therefore no cohesive label can be assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070395","count":2},{"id":"GO:0040037","count":2},{"id":"GO:0042425","count":2},{"id":"GO:0007417","count":2},{"id":"GO:0035860","count":2}]},{"hash":"644356155605158291","title":"Innate Immunity and Cell Cycle Regulators","description":"The cluster is strongest in innate immune response terms (GO:0045087), with associated NF-kappaB regulation signals and proteasome-related protein turnover, plus links to mitotic cell cycle and microtubule localization. These together suggest a core theme of immune signaling connected to cell-cycle/cytoskeleton processes, with some noisy or unrelated terms present (e.g., placenta development, obsolete GO terms). Overall, the label captures the dominant connection with innate immunity and its relationship to cell-cycle machinery.","confidence":"Medium","size":6,"edges":8,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0051092","count":2},{"id":"GO:0032435","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0071276","count":2}]},{"hash":"2242054272509650781","title":"GTPase-regulated COPII vesicle budding","description":"The top GO terms emphasize positive regulation of GTPase activity and COPII-coated vesicle budding, pointing to a core theme of GTPase-controlled vesicle formation from the ER to the Golgi. Additional terms touch on protein stabilization, proteolysis, and some broader context (nutrient response, collagen catabolism, glomerular filtration) that may reflect auxiliary roles or incidental associations. Overall, the cluster seems centered on vesicle trafficking and related protein processing.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0090114","count":2},{"id":"GO:0030574","count":1},{"id":"GO:0050821","count":1}]},{"hash":"1168473334527660961","title":"Oocyte Meiosis and Chromosome Recombination","description":"The top GO terms center on meiotic recombination and chromosomal pairing in female meiosis, including double-strand break repair, synaptonemal complex assembly, sister chromatid cohesion, heteroduplex/joint molecule formation, and telomere-related circle formation, with an additional tie to ovarian follicle development. This set points to a cohesive role in oocyte meiosis and chromosome pairing, despite a few peripheral terms.","confidence":"High","size":6,"edges":11,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":2},{"id":"GO:1990918","count":2},{"id":"GO:0001541","count":2},{"id":"GO:0007066","count":2},{"id":"GO:0009949","count":2}]},{"hash":"1296441432329497783","title":"Nucleocytoplasmic transport and ribosome biogenesis components","description":"The top GO terms cluster around nuclear import/export processes, including ribosomal subunit export from the nucleus, ribosomal protein import, and mRNA export, plus nuclear pore complex assembly and hnRNP-related imports. These strongly suggest a shared role in nucleocytoplasmic trafficking and ribosome biogenesis, with some mitotic-related terms (astral microtubule organization, kinetochore localization) incidental to the broader transport/assembly theme.","confidence":"High","size":6,"edges":9,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":2},{"id":"GO:0042991","count":2},{"id":"GO:0006610","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0030953","count":2}]},{"hash":"549480716956260156","title":"Vesicle trafficking and GTPase signaling","description":"The top GO terms cluster around intracellular transport and membrane trafficking (intracellular protein transport; plasma membrane to endosome transport; COPII-coated vesicle cargo loading) and GTPase regulation (activation of GTPase activity; regulation of Rab protein signal transduction; Rap signaling), suggesting a core theme of vesicle trafficking and GTPase-mediated regulation. Some unrelated terms (e.g., siderophore biosynthesis, cilium assembly) appear as noise, but the dominant signal supports a trafficking/gTPase functional cluster.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009239","count":1},{"id":"GO:0019878","count":1},{"id":"GO:0042759","count":1},{"id":"GO:0032486","count":1},{"id":"GO:0090110","count":1}]},{"hash":"484976335628947275","title":"Cell cycle and division proteins","description":"The cluster is dominated by GO terms for cell division and cell cycle (and DNA replication), with additional related terms like mitotic nuclear membrane reassembly and DNA primer removal; overall, the proteins appear to participate in core cell-cycle progression and division.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0043137","count":1},{"id":"GO:0007084","count":1},{"id":"GO:0007283","count":1}]},{"hash":"82091876027167368","title":"Histone modification and chromatin regulation","description":"The term set centers on histone modifications (H3K4 trimethylation and H4 acetylation) and heterochromatin boundary formation, with additional signals for transcription elongation regulation by RNA Pol II, pointing to epigenetic chromatin regulation as the dominant theme.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0080182","count":3},{"id":"GO:0032968","count":3},{"id":"GO:0033696","count":3},{"id":"GO:0043983","count":2},{"id":"GO:0071392","count":2}]},{"hash":"1384069925447872162","title":"Bacterial cell wall remodeling and division","description":"The GO terms cluster around peptidoglycan turnover and biosynthesis, cell wall organization, cell shape regulation, and cell division, pointing to bacterial cell wall remodeling and division as the shared function; ancillary terms like cellulose catabolism and flocculation appear less central to the main theme.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009254","count":6},{"id":"GO:0030245","count":6},{"id":"GO:0009252","count":6},{"id":"GO:0007049","count":6},{"id":"GO:0071555","count":6}]},{"hash":"584142445839661755","title":"Translation and tRNA aminoacylation","description":"The dominant GO terms are tRNA processing and aminoacylation (methionyl-, phenylalanyl-, lysyl-) plus translation, indicating a cluster of protein-synthesis machinery; a few development-related terms appear but are secondary.","confidence":"High","size":6,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":2},{"id":"GO:0006431","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0048514","count":1},{"id":"GO:0006432","count":1}]},{"hash":"795873391864233097","title":"Neuronal development and synaptic function","description":"The terms cluster around neuronal biology: midbrain dopaminergic neuron differentiation, dendritic spine morphogenesis regulation, evoked neurotransmitter secretion, and regulation of long-term synaptic plasticity, with endocytosis aligning with synaptic vesicle cycling. While general proliferation terms appear, the dominant signals point to neuronal differentiation and synaptic regulation as the cluster\u2019s theme.","confidence":"High","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008283","count":4},{"id":"GO:0035264","count":4},{"id":"GO:0000755","count":3},{"id":"GO:0061670","count":3},{"id":"GO:0048169","count":3}]},{"hash":"2138376473500504085","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0060416","count":1},{"id":"GO:0055081","count":1},{"id":"GO:0010106","count":1},{"id":"GO:0071377","count":1}]},{"hash":"2240743255945814731","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0000480","count":3}]},{"hash":"1751556454537305859","title":"Unknown","description":"The Top Terms span developmental processes (skeletal muscle and nervous system development), immune signaling (B cell receptor signaling), endocrine signaling (growth hormone and insulin receptor pathways), cell cycle control, glucose-responsive invasive growth, and even tRNA modification, plus motility. This broad mix provides no clear, cohesive functional theme for a single intuitive label, so Unknown with None is most appropriate.","confidence":"","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007519","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0060396","count":2},{"id":"GO:0001403","count":2}]},{"hash":"1584346786675983784","title":"Transmembrane Transporters","description":"All top GO terms point to transport across membranes: xenobiotic, arabinose, potassium and sodium ions, nitrate, vitamin transport, and neurotransmitter loading into synaptic vesicles. This suggests a cluster of membrane transporter proteins with diverse substrate specificities rather than a single metabolic enzyme.","confidence":"High","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0071805","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0006004","count":1}]},{"hash":"1146846081665881677","title":"Neural Development and Brain Formation","description":"The top GO terms are dominated by brain and neural development (forebrain/brain development, neural tube closure) and DNA-templated transcription, suggesting the cluster centers on neural development and brain formation; other terms reflect broader stress or general cellular processes but do not override the neural theme.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030900","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0070059","count":3}]},{"hash":"1786653490366850684","title":"Mitotic spindle assembly and cytokinesis","description":"This cluster is dominated by terms related to cell division, particularly mitosis and cytokinesis, including FtsZ-dependent cytokinesis, mitotic spindle pole body duplication, spindle midzone assembly, cytoplasmic microtubule organization, and division site positioning. A couple of terms (e.g., translation regulation and touch sensation) seem less related and may be noise, but the core signal strongly points to mitotic spindle organization and cytokinesis.","confidence":"High","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1905789","count":2},{"id":"GO:0043093","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0031122","count":2},{"id":"GO:1903087","count":2}]},{"hash":"1446944041705999189","title":"Unknown","description":"The provided GO terms are highly heterogeneous, covering metabolic processes (sphingoid catabolic, dolichol-linked oligosaccharide biosynthesis, glucose transport), membrane trafficking (ER to Golgi), amino acid transport/homeostasis, and even organismal traits (grooming behavior, lens development). There is no clear, single biological theme linking all terms, so a cohesive label cannot be assigned. ","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046521","count":1},{"id":"GO:0007625","count":1},{"id":"GO:0034488","count":1},{"id":"GO:0006488","count":1},{"id":"GO:0080144","count":1}]},{"hash":"1473408001728723988","title":"Unknown","description":"The GO terms are diverse, spanning carbohydrate metabolism, sterol biosynthesis, mRNA capping, heme turnover, and regulatory processes, with several obsolete terms, and no clear single function tying all proteins together. Therefore, no specific, reliable label can be assigned.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006012","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0042167","count":1}]},{"hash":"1259411121256673615","title":"Heart Valve and Muscle Development","description":"The cluster shows GO terms tied to heart valve morphogenesis (tricuspid and pulmonary valve formation) and cardioblast migration, as well as skeletal muscle development (myoblast fusion and muscle fiber adaptation). Although neural development terms are present, the strongest shared theme is developmental processes governing heart valve formation and skeletal muscle formation, suggesting these proteins function in cardiovascular and muscle morphogenesis. ","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0003195","count":1},{"id":"GO:0003407","count":1},{"id":"GO:0045670","count":1},{"id":"GO:0043503","count":1},{"id":"GO:1901741","count":1}]},{"hash":"760541602988661566","title":"Detox and Redox Stress Response","description":"The terms point to a common theme of managing oxidative stress and detoxifying xenobiotics: pentose-phosphate shunt and glutathione biosynthesis support redox balance, while cadmium response, daunorubicin metabolism, and stress signaling indicate broad chemical-stress defense. Hormone-related responses (progesterone, prostaglandin) may reflect broader stress signaling, but the core pattern is detoxification and redox maintenance.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006098","count":2},{"id":"GO:0042448","count":1},{"id":"GO:0071799","count":1},{"id":"GO:0044597","count":1}]},{"hash":"2042143310725280655","title":"Ubiquitin-Driven Signaling and DNA Repair","description":"This cluster centers on ubiquitination-related processes (free ubiquitin chain polymerization, histone monoubiquitination, autoubiquitination) and DNA damage response (error-free postreplication repair, error-prone translesion synthesis), with additional signaling pathway terms such as Fc-epsilon receptor, BMP, and NF-kappaB. The shared theme is ubiquitin-mediated regulation of signaling and genome maintenance.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0010994","count":5},{"id":"GO:0010390","count":5},{"id":"GO:0038095","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0030509","count":5}]},{"hash":"1724728805950231218","title":"Endosomal Trafficking and Protein Transport","description":"The top GO terms cluster around endocytosis, endosome-to-vacuole transport, and general protein movement, indicating a common function in intracellular trafficking and sorting. Viral release and capsid terms may reflect interactions with host trafficking, but the core signal is endosomal transport, so the label focuses on that pathway.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019076","count":1},{"id":"GO:0048672","count":1},{"id":"GO:0046745","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0009838","count":1}]},{"hash":"1619469065172648849","title":"Ubiquitin signaling and chromatin regulation","description":"This cluster's top GO terms are dominated by ubiquitination-related processes\u2014free ubiquitin chain polymerization, histone monoubiquitination, and autoubiquitination\u2014indicating entities involved in ubiquitin-conjugation and chromatin modification. Additional terms touch DNA repair/tolerance (postreplication repair, translesion synthesis), which are known to be ubiquitin-regulated, and signaling pathways that can be modulated by ubiquitination. Together, they suggest a group of proteins coordinating ubiquitin-mediated regulation of signaling, chromatin state, and DNA repair. ","confidence":"High","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0010994","count":5},{"id":"GO:0010390","count":5},{"id":"GO:0038095","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0030509","count":5}]},{"hash":"1690108952204500264","title":"ERAD and UPR Protein Quality Control","description":"The cluster centers on unfolded protein response and ER-associated degradation, with terms like response to unfolded protein, ubiquitin-dependent glycoprotein ERAD pathway, and retrograde transport from ER to cytosol, plus related glycoprotein processing in the Golgi. These jointly point to ER quality control and protein degradation pathways handling misfolded glycoproteins. Some terms are peripheral or obsolete, but the core theme is coherent.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016576","count":2},{"id":"GO:0010288","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0043278","count":2},{"id":"GO:2000324","count":2}]},{"hash":"2034068441944832373","title":"DNA/RNA Repair and tRNA Modification in Cell Death","description":"This cluster centers on nucleic acid maintenance and RNA tRNA modifications, as shown by GO terms for DNA repair, RNA repair, mRNA processing, and tRNA wobble modification, plus translational regulation by tRNA modification. The presence of programmed cell death and mitochondrial permeability regulation terms suggests these proteins may link nucleic repair/modification to apoptosis or necroptosis pathways, making the theme cohesive though the set is small.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0035552","count":1},{"id":"GO:0035553","count":1},{"id":"GO:0012501","count":1}]},{"hash":"1690316008018485030","title":"Unknown","description":"There is no single coherent functional theme tying these GO terms together; terms span metal cluster assembly, methylation, multiple catabolic processes, cell wall assembly, and organismal behaviors, suggesting a heterogeneous cluster with no clear shared function.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016226","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0035641","count":1},{"id":"GO:0045493","count":1},{"id":"GO:0071769","count":1}]},{"hash":"1272194617977607890","title":"Bacterial LPS core synthesis and envelope metabolism","description":"The top GO terms cluster around lipopolysaccharide core biosynthesis, ADP-heptose and N-acetylglucosamine biosynthesis, and general carbohydrate metabolism, which together indicate processes involved in Gram-negative bacterial cell envelope construction. Additional terms for metal ion transport and calcium/homeostasis suggest supportive transporter and homeostatic roles that often accompany envelope maintenance. A few actin-related terms hint at bacterial cytoskeletal dynamics linked to envelope shaping. Overall, the cluster seems tied to bacterial envelope biogenesis with auxiliary transport processes.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009244","count":1},{"id":"GO:0070574","count":1},{"id":"GO:0097171","count":1},{"id":"GO:0006874","count":1},{"id":"GO:0006825","count":1}]},{"hash":"2050581039303810226","title":"Ion transport and membrane homeostasis","description":"The listed GO terms cluster around ion movement across membranes (sodium/potassium transport, proton translocation) and vacuolar acidification, which together support cell volume regulation and membrane homeostasis. Anomalous single term for BDNF signaling appears incidental and does not alter the core transport-related theme.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031547","count":1},{"id":"GO:0051595","count":1},{"id":"GO:1903281","count":1},{"id":"GO:0007035","count":1},{"id":"GO:1902600","count":1}]},{"hash":"801955051887518640","title":"Adipose signaling and angiogenesis under stress","description":"These proteins are annotated with terms centered on adipose tissue development and leptin signaling, suggesting a role in adipose tissue regulation, combined with endothelial proliferation/angiogenesis. The inclusion of ROS regulation and stress-induced senescence points to a stress-responsive component that could link adipose remodeling to vascular growth. Although some terms are obsolete, the dominant theme is adipose signaling with stress- and angiogenesis-related functions.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904179","count":2},{"id":"GO:0033210","count":2},{"id":"GO:0060303","count":2},{"id":"GO:0090400","count":2},{"id":"GO:2000378","count":2}]},{"hash":"1535497397897176739","title":"Excitatory cholinergic synapse assembly","description":"The most represented terms cluster around neuronal synapse development and cholinergic signaling\u2014excitatory synapse assembly, synaptic vesicle clustering, acetylcholine metabolism and postsynaptic potential regulation, along with neuron adhesion\u2014supporting a label related to excitatory cholinergic synapse formation and function. A few terms (liver development, xenobiotic response) may reflect broader or unrelated annotations, but the dominant signal is synaptic organization.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0001889","count":2},{"id":"GO:0042136","count":1},{"id":"GO:0002076","count":1},{"id":"GO:1904861","count":1}]},{"hash":"700030526006116431","title":"Unknown","description":"The GO terms are scattered across diverse processes (collagen catabolic process, chromatin organization, kidney development, various metabolic and development terms) and include obsolete annotations, giving no single cohesive function to the four proteins. Therefore, a meaningful, specific label cannot be confidently assigned.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030574","count":1},{"id":"GO:0035551","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0006212","count":1}]},{"hash":"1437566324731185002","title":"Sulfur amino acid and cofactor biosynthesis","description":"The top GO terms point to biosynthesis of sulfur-containing molecules (methionine, cysteine, glutathione) and cofactors (FAD), along with sulfate assimilation and related processes. This indicates the cluster centers on sulfur metabolism and amino acid/cofactor biosynthesis, with a few unrelated terms (e.g., heart development) likely noise. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009086","count":2},{"id":"GO:0070814","count":1},{"id":"GO:0006747","count":1},{"id":"GO:0006750","count":1},{"id":"GO:0019379","count":1}]},{"hash":"2068013740842157054","title":"Metabolism and Xenobiotic Stress Response","description":"These proteins show a mix of metabolism-related GO terms (UDP-glucose and UDP-glucuronate biosynthesis, UDP-alpha-D-glucose metabolic process, glycerol-3-phosphate catabolism, TCA cycle) and stress/detoxification terms (response to xenobiotic stimulus, cellular envelope stress, redox homeostasis). The common thread appears to be metabolic activity coupled with detoxification and stress response, rather than a single cohesive pathway, suggesting a general metabolic-stress-response theme for the cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0006813","count":1},{"id":"GO:0001702","count":1},{"id":"GO:0046676","count":1},{"id":"GO:0045454","count":1}]},{"hash":"1363268697305350472","title":"Unknown","description":"The GO terms are highly diverse, spanning neuron differentiation, hormone signaling, metabolism, proteostasis, and even plant-specific processes, with no single shared function tying the four proteins together, so there isn't a cohesive label beyond Unknown.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030182","count":2},{"id":"GO:1902325","count":2},{"id":"GO:0050689","count":2},{"id":"GO:0090526","count":2},{"id":"GO:0006463","count":2}]},{"hash":"423756080770720877","title":"Metal ion transport and nitrogen metabolism","description":"The GO terms are dominated by metal ion transport (copper, iron, arsenate) and nitrogen-related processes (nitrate assimilation, denitrification, reductive iron assimilation), suggesting a core theme around ion handling and nitrogen metabolism. A few outlier terms (cellulose catabolic process, FtsZ-dependent cytokinesis, platelet activation) may reflect broader cross-species annotations, but the strongest signal centers on metal transport and nitrogen metabolism. Confidence: Medium.","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006825","count":2},{"id":"GO:0043093","count":2},{"id":"GO:0033215","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0034755","count":2}]},{"hash":"2127555318597145792","title":"Intestinal lipid absorption and cholesterol transport regulation","description":"The cluster is dominated by GO terms related to lipid transport and regulation of intestinal lipid uptake, including lipoprotein transport, fatty acid catabolism, and negative regulation of intestinal cholesterol/phytosterol absorption. This points to proteins involved in lipid handling and modulation of intestinal lipid absorption, with some noise from a few unrelated terms. Overall, a coherent theme around intestinal lipid transport and cholesterol regulation is evident.","confidence":"High","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042953","count":3},{"id":"GO:0042760","count":3},{"id":"GO:0045796","count":3},{"id":"GO:0010949","count":3},{"id":"GO:1902943","count":3}]},{"hash":"440987511444963761","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0016584","count":3},{"id":"GO:0008306","count":3},{"id":"GO:0071049","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0045944","count":3}]},{"hash":"1503043676667774940","title":"Galactose Metabolism and Isoprenoid Biosynthesis","description":"The top GO terms cluster around galactose- and sugar-related metabolism (galactose, galacturonate, galactitol, carbohydrate phosphorylation) and major isoprenoid pathways (IPP biosynthesis via MEP/mevalonate) plus cholesterol biosynthesis, suggesting a metabolic module connecting sugar utilization with lipid/isoprenoid production. A single term on cell cycle regulation is present but does not dominate the theme; overall the cluster reflects coordinated metabolic processes linking carbohydrate catabolism to isoprenoid biosynthesis.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":2},{"id":"GO:0061623","count":1},{"id":"GO:0046396","count":1},{"id":"GO:0019402","count":1},{"id":"GO:0019288","count":1}]},{"hash":"352749055600239841","title":"Unknown","description":"The GO terms are highly diverse, spanning tRNA processing, nucleus organization, spindle regulation, vesicle trafficking, filamentous growth, viral life cycle, and development, with no single overarching function linking all proteins. Because no dominant theme emerges, a precise functional label cannot be confidently assigned.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":2},{"id":"GO:0006997","count":1},{"id":"GO:1901673","count":1},{"id":"GO:0043328","count":1},{"id":"GO:0030447","count":1}]},{"hash":"22930910652739183","title":"Lipid Transport and Sterol Metabolism","description":"Most GO terms point to transport of lipids, sterols, and related molecules (lipoprotein transport, very long-chain fatty acid catabolic process, regulation of intestinal cholesterol and phytosterol absorption, glycerophosphodiester transport). A few terms (ribosome biogenesis/disassembly, mercury response, bacteriocin transport) are less coherent with this theme and may reflect annotation noise or broader cellular roles. Overall, a lipid transport/metabolic theme dominates the cluster.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042953","count":1},{"id":"GO:0042760","count":1},{"id":"GO:0045796","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0032790","count":1}]},{"hash":"680884349233486189","title":"Unknown","description":"The GO terms are a disparate mix (virion assembly, translocation into host cytoplasm, cell division, B cell cytokine production, and various protein folding/refolding terms with obsolete annotations), with no shared, specific function linking all proteins and no observed edges. This lack of a common theme makes a reliable, concise label unlikely.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:1904871","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0051973","count":2},{"id":"GO:0051085","count":2}]},{"hash":"2233262177121811821","title":"Ribosome biogenesis and translation","description":"This cluster centers on core ribosome-related processes: translation, tyrosyl-tRNA aminoacylation, rRNA pseudouridine synthesis, and ribosome biogenesis, together with maintenance of translational fidelity. Although there are some transcription and stress-response terms present, the dominant signal points to ribosome assembly and function.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990145","count":2},{"id":"GO:0006353","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006437","count":2},{"id":"GO:0034605","count":2}]},{"hash":"1399142326611071160","title":"ER-Golgi and Endocytic Vesicle Trafficking","description":"The proteins are enriched for GO terms spanning ER-to-Golgi vesicle transport, retrograde transport between Golgi and ER, endocytosis, endosome-to-Golgi transport, and Golgi localization, indicating a cohesive role in intracellular vesicle trafficking within the secretory and endocytic pathways. Some outlier terms (pigmentation, neuronal maturation) are low in frequency and do not override the main vesicular trafficking theme.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0006897","count":3},{"id":"GO:0006623","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0042147","count":2}]},{"hash":"478791158782920781","title":"Cytoskeleton regulation and membrane trafficking","description":"This cluster shows enrichment for GTPase activity regulation and Rac signaling (GO:0043547, GO:0035021), and terms related to cell migration, implying actin cytoskeleton remodeling. Additional terms on membrane tubulation, vesicle transport, and lysosomal membrane organization suggest coordinated membrane dynamics. The combination points to proteins involved in cytoskeleton-driven remodeling and trafficking rather than a single narrow pathway.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055108","count":1},{"id":"GO:1902647","count":1},{"id":"GO:0016477","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0035021","count":1}]},{"hash":"1362127903945413267","title":"Embryonic Development and Organogenesis","description":"Based on the GO terms, the proteins cluster around embryonic development, tissue differentiation, and organ patterning (pancreatic development, placenta/trophoblast and endocrine system development, left-right patterning, cartilage morphogenesis, and heart-related EMT). Although one term is metabolic (acyl-CoA), the dominant theme is developmental processes during embryogenesis, suggesting the cluster represents embryonic development and organogenesis.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003323","count":1},{"id":"GO:0060806","count":1},{"id":"GO:0060707","count":1},{"id":"GO:0035270","count":1},{"id":"GO:0060536","count":1}]},{"hash":"922548876823663149","title":"Membrane dynamics and cytoskeleton remodeling","description":"The terms point to membrane-associated organization and cytoskeletal remodeling, including regulation of microvillus assembly, lamellipodium morphogenesis, and protein localization to cilium, plus lipid biosynthesis and secretory/vesicle maturation processes; despite a few broader developmental terms, the common thread is membrane shaping and trafficking in conjunction with actin-structured protrusions.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032534","count":2},{"id":"GO:0006654","count":2},{"id":"GO:0051044","count":1},{"id":"GO:0042063","count":1},{"id":"GO:1904179","count":1}]},{"hash":"692466174732599204","title":"Neural development and cell-cycle regulation","description":"The cluster shows strong enrichment for neural development processes (forebrain development, neural tube closure, neuron apoptotic process) alongside core cell-cycle and transcription functions (DNA-templated transcription, mitotic cell cycle, proliferation). The presence of ubiquitin-proteasome\u2013mediated protein turnover and TORC1 signaling suggests coordinated growth and protein regulation during neural development. While some terms (histone methylation, GTPase regulation) support broader chromatin and signaling roles, the dominant theme is neurodevelopment coupled with cell-cycle progression.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0030900","count":2}]},{"hash":"1034897369546137606","title":"Unknown","description":"The top GO terms are highly diverse (glycosylation, various metabolic and signaling processes across different organisms) and the four proteins have no reported interactions (no edges/triangles). This lack of a cohesive functional theme makes it impossible to assign a specific, representative label beyond Unknown, with no confidence in a shared function.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006487","count":2},{"id":"GO:0042136","count":1},{"id":"GO:0009939","count":1},{"id":"GO:0002076","count":1},{"id":"GO:0051791","count":1}]},{"hash":"1064564705173838114","title":"Histone modification and chromatin regulation","description":"Top terms point to histone post-translational modifications (H4-K16 acetylation, H4-K20 methylation), histone ubiquitination, histone catabolic process, and dosage compensation, indicating a chromatin-regulation theme. A few terms related to NF-kappaB signaling and ubiquitination are present but less central. Overall, the cluster appears to reflect histone modification and chromatin state regulation involved in transcriptional control.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903762","count":2},{"id":"GO:0042981","count":2},{"id":"GO:0051865","count":2},{"id":"GO:2000620","count":2},{"id":"GO:0036205","count":2}]},{"hash":"2192400376050296860","title":"Pentose and Hexose Sugar Catabolism","description":"The Top Terms are dominated by sugar catabolic processes across several substrates (xylulose, D-xylose, L-arabinose, rhamnose, D-gluconate, D-glucuronate), plus carbohydrate phosphorylation, indicating a unifying theme of sugar degradation/metabolism. A couple of outliers like quorum sensing and IL-13 response appear incidental rather than core to the cluster\u2019s function.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005998","count":1},{"id":"GO:0019521","count":1},{"id":"GO:0019640","count":1},{"id":"GO:0046167","count":1},{"id":"GO:0019569","count":1}]},{"hash":"1765860596725278498","title":"Muscle gene regulation and chromatin remodeling","description":"This cluster appears enriched for transcriptional and chromatin-related functions with muscle context: DNA-templated transcription and chromatin/nucleosome dynamics (including subtelomeric heterochromatin formation and nucleosome regulation) alongside muscle-specific regulation signals such as skeletal muscle fiber development and denervation-related muscle adaptation. The mix suggests a cohesive theme of muscle gene expression being modulated by chromatin state.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901300","count":4},{"id":"GO:0006348","count":4},{"id":"GO:0060303","count":4},{"id":"GO:0048742","count":4},{"id":"GO:0006351","count":4}]},{"hash":"201279269448616434","title":"Virus-host interaction and immune modulation","description":"Top terms include virion assembly, translocation into host cell cytoplasm, B cell cytokine production, and isotype switching, suggesting a theme of virus-host interactions and adaptive immune responses. Some terms are obsolete, which may reflect annotation noise, but the core signal points to viral processes coupled with immune signaling.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904871","count":3},{"id":"GO:0019068","count":3},{"id":"GO:0051973","count":3},{"id":"GO:0051085","count":3},{"id":"GO:0051086","count":3}]},{"hash":"458744650061901489","title":"Immune signaling and stress responses","description":"This cluster centers on immune-related GO terms, including T cell receptor signaling and neutrophil chemotaxis, with additional hints of stress/hormonal signaling (epinephrine response, cAMP regulation, dopamine metabolism). The combination suggests a module of immune signal transduction that also engages hormonal/stress pathways rather than a single, cohesive immune pathway.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050852","count":2},{"id":"GO:0033159","count":1},{"id":"GO:0050995","count":1},{"id":"GO:0006198","count":1},{"id":"GO:0042053","count":1}]},{"hash":"328904527190414921","title":"Neural development and transcriptional regulation","description":"The top GO terms point to neural development (forebrain development, neural tube closure, neuron apoptotic process), indicating a neural-development\u2013focused cluster. Additional terms related to transcriptional control and signaling regulation suggest coordinated gene expression and cellular processing during neural development, supporting a cohesive neurodevelopmental regulatory theme.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0030900","count":3},{"id":"GO:1904263","count":3},{"id":"GO:0051402","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0043547","count":3}]},{"hash":"1477550815366017638","title":"Protein Ubiquitination and Degradation","description":"The dominant GO terms describe various ubiquitin linkages (K48, K63, K6), autoubiquitination, ubiquitin-dependent proteolysis, and related regulatory roles (NF-kappaB signaling, histone catabolism, antiviral host defenses). This suggests a cluster of proteins involved in tagging substrates for degradation and modulating signaling through ubiquitination.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070936","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0051865","count":2},{"id":"GO:0097039","count":2},{"id":"GO:0036205","count":2}]},{"hash":"1233209071217927366","title":"Rab- and COPII-mediated vesicle trafficking","description":"The GO terms show strong enrichment for intracellular transport within the secretory/endocytic pathway: COPII vesicle cargo loading, Rab-regulated signaling, and multiple transport steps between plasma membrane, endosomes, and Golgi, including retrograde and recycling routes. This cohesive pattern supports labeling as Rab/COPII vesicle trafficking.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051534","count":2},{"id":"GO:0032486","count":1},{"id":"GO:0090110","count":1},{"id":"GO:0090630","count":1},{"id":"GO:0032483","count":1}]},{"hash":"2061481584647629434","title":"Thiamine biosynthesis and salvage","description":"The top GO terms are dominated by thiamine salvage and thiamine biosynthetic processes, indicating these proteins likely participate in thiamine (vitamin B1) metabolism. While other, more general or unrelated terms appear, the strongest and most coherent signal is thiamine biosynthesis/metabolism, supporting this label. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0036172","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0009228","count":1},{"id":"GO:0009229","count":1},{"id":"GO:0006450","count":1}]},{"hash":"1120002940181324166","title":"Thiamine-TPP dependent energy metabolism","description":"The GO terms show strong enrichment for thiamine biosynthesis and thiamine diphosphate biosynthesis, along with glucose metabolic processes and regulation of pyruvate decarboxylation to acetyl-CoA, all key components of thiamine/TPP-dependent energy metabolism. While there are some transport-related terms and a few unrelated entries, the dominant signal points to a cluster centered on thiamine/cofactor-driven central carbon metabolism and its regulation. ","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":2},{"id":"GO:0006006","count":2},{"id":"GO:0010510","count":2},{"id":"GO:0046239","count":1},{"id":"GO:0009229","count":1}]},{"hash":"1810054221858731833","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034247","count":1},{"id":"GO:0006198","count":1},{"id":"GO:0098789","count":1},{"id":"GO:0070292","count":1},{"id":"GO:1903999","count":1}]},{"hash":"1909257975417977920","title":"Golgi N-glycan trimming","description":"The top terms point to Golgi-localized processing of N-glycans, especially trimming of mannose residues (GO:1904381, GO:0036512, GO:0036509). This clear theme suggests the proteins in this cluster participate in Golgi-based glycan maturation, with other annotations being more peripheral. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0036512","count":1},{"id":"GO:0010103","count":1},{"id":"GO:0006879","count":1},{"id":"GO:1904154","count":1},{"id":"GO:0007039","count":1}]},{"hash":"1843781179723066479","title":"Meiotic recombination and DNA repair","description":"Many of the top terms point to meiotic recombination and genome maintenance (DNA replication; telomere maintenance via recombination; reciprocal meiotic recombination; DNA damage checkpoint signaling). Taken together, they indicate a functional cluster centered on meiotic DNA repair and genome stability.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0000722","count":2},{"id":"GO:0007131","count":2},{"id":"GO:0000710","count":1},{"id":"GO:0000077","count":1}]},{"hash":"105850682976392532","title":"Fungal Transcription-Regulated Metabolism","description":"The top GO terms point to transcription from RNA polymerase II promoter being positively regulated in various contexts (e.g., nitrogen catabolite activation, oleic acid response, general DNA-templated transcription) alongside diverse metabolic processes (lysine biosynthesis, ergosterol and aflatoxin biosynthesis, glyoxylate/glycolytic regulation, gluconeogenesis, cellular respiration). This suggests a cluster of proteins involved in coordinating transcriptional control with fungal metabolism and secondary metabolite production rather than a single specific pathway. Confidence: Medium","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001196","count":2},{"id":"GO:0035961","count":2},{"id":"GO:1901714","count":2},{"id":"GO:0061429","count":2},{"id":"GO:0035948","count":2}]},{"hash":"36710761234031735","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning mitochondrial translation and tRNA charging, plus various catabolic and developmental processes (including plant-specific terms) and obsolete terms. There is no clear, single shared function tying all proteins together, so a cohesive label cannot be confidently assigned.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":1},{"id":"GO:0070681","count":1},{"id":"GO:0006425","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0019260","count":1}]},{"hash":"1866428563865375903","title":"Cofactor biosynthesis and RNA methylation","description":"The top GO terms are dominated by biosynthetic processes for cofactors (thiamine, biotin, lipoate, molybdopterin) and RNA base/tRNA methylation, indicating a cluster of proteins involved in cofactor assembly and RNA modification pathways.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0006777","count":1},{"id":"GO:0009102","count":1},{"id":"GO:0070475","count":1}]},{"hash":"76844562179746457","title":"Ubiquitin-Mediated Signaling","description":"The top GO terms are dominated by ubiquitination processes (free ubiquitin chain polymerization, histone monoubiquitination, autoubiquitination) and NF-kappaB-related signaling, suggesting the cluster centers on ubiquitin-dependent regulation of signaling pathways, despite some diverse ancillary terms.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0010994","count":3},{"id":"GO:0010390","count":3},{"id":"GO:0038095","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0030509","count":3}]},{"hash":"1213316366289284344","title":"Nuclear ribosome import and export","description":"These terms cluster around import of ribosomal proteins into the nucleus and export of ribosomal subunits, plus nuclear pore complex assembly, which together reflect ribosome biogenesis inside the nucleus and transport through the nuclear envelope. Some ancillary terms appear, but the core signal is nuclear ribosome handling.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006610","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0051292","count":3},{"id":"GO:0060188","count":3},{"id":"GO:0000060","count":3}]},{"hash":"435682878764431830","title":"Mitochondrial Transport and Metabolism","description":"These proteins show GO annotations centered on mitochondria, energy production, and membrane transport, such as assembly of the ATP synthase complex and transmembrane transport of ions and cofactors (NAD, Mn, phosphate, deoxynucleotides, pyridoxal phosphate), with links to adaptive thermogenesis and oxidative stress. The common theme is mitochondrial transport and metabolic function driving energy homeostasis.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033615","count":1},{"id":"GO:0006828","count":1},{"id":"GO:0035352","count":1},{"id":"GO:0090152","count":1},{"id":"GO:0031921","count":1}]},{"hash":"787923589875616994","title":"Neuronal cytoskeleton and spine morphogenesis","description":"Based on the GO terms, the cluster centers on neuronal development and cytoskeletal organization: tubulin complex assembly, dendritic spine morphogenesis, interneuron migration, and related processes like apical protein localization and regulated exocytosis. These collectively point to cytoskeletal remodeling and synaptic/spine formation in neurons. A few terms (e.g., IL-23 regulation) appear peripheral and may reflect multifunctional proteins rather than a core theme of this cluster.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006998","count":3},{"id":"GO:0061001","count":3},{"id":"GO:0032707","count":3},{"id":"GO:0051893","count":3},{"id":"GO:0007021","count":3}]},{"hash":"1000953923372433553","title":"Neural Development","description":"This cluster\u2019s terms are dominated by nervous system development and neuron-associated processes (forebrain development, neural tube closure, neuron apoptotic process), supported by transcriptional regulation and signaling terms that commonly participate in developmental pathways. While there are also general cellular processes (GTPase regulation, ER-Golgi trafficking), the presence of multiple neural development terms suggests the proteins cluster around neural development and its regulation.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":1},{"id":"GO:1904263","count":1},{"id":"GO:0051402","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0043547","count":1}]},{"hash":"726894074002804962","title":"Ribosome biogenesis and translation","description":"The top GO terms concentrate on translation (GO:0006412) and ribosome biogenesis (GO:0090070; GO:1902626), indicating the proteins are tied to ribosome assembly and protein synthesis. Additional terms related to stress responses (cycloheximide, antibiotic, dexamethasone) and DNA repair appear as minor associations, but the core theme is translation machinery and preribosome assembly. Confidence reflects this strong, central link to ribosome/translation biology.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0090070","count":1},{"id":"GO:1902626","count":1},{"id":"GO:0046898","count":1},{"id":"GO:0046677","count":1}]},{"hash":"566003425150012240","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070935","count":2},{"id":"GO:0033129","count":2},{"id":"GO:0006895","count":1},{"id":"GO:0035542","count":1},{"id":"GO:0097352","count":1}]},{"hash":"1230310435735121263","title":"Meiotic spindle assembly and microtubule nucleation","description":"The cluster\u2019s GO terms cluster around cytoskeleton dynamics, with emphasis on microtubule nucleation, spindle assembly in female meiosis II, and cortical microtubule organization, suggesting a shared role in meiotic spindle formation and cytoskeleton organization. Some terms related to amino acid biosynthesis and antibiotic biosynthesis appear, but they are less coherent with the dominant microtubule/meiosis signal, indicating a mixed signal cluster.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033050","count":2},{"id":"GO:0043617","count":1},{"id":"GO:0070981","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0006541","count":1}]},{"hash":"1408289753928014213","title":"Unknown","description":"The top GO terms span phytochelatin biosynthesis (metal detoxification), autophagy regulation, enzyme activity regulation, and proteolysis, which do not converge on a single clear function for the cluster. A cohesive, specific label isn\u2019t justifiable from these terms alone.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046938","count":3},{"id":"GO:1904715","count":3},{"id":"GO:0043085","count":3},{"id":"GO:0006508","count":3}]},{"hash":"496316945607626646","title":"Membrane trafficking and lipid biosynthesis","description":"The strongest signals in the cluster are Golgi to plasma membrane protein transport and regulation of phosphatidylcholine biosynthesis (positive and negative), pointing to membrane trafficking and lipid metabolism. Other terms point to general stress or development (e.g., placenta-related terms are outliers), suggesting a small, possibly heterogeneous set of proteins with a membrane-centric theme. Confidence: Medium","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":1},{"id":"GO:0001890","count":1},{"id":"GO:0046909","count":1},{"id":"GO:2001247","count":1},{"id":"GO:0043001","count":1}]},{"hash":"1619577049131378749","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":2},{"id":"GO:0072321","count":2},{"id":"GO:0045039","count":2},{"id":"GO:0006046","count":1},{"id":"GO:0019557","count":1}]}]