[{"hash":"952910903443254731","title":"Spindle assembly and microtubule organization","description":"The top GO terms cluster around mitosis and cytoskeletal processes, including microtubule nucleation, spindle pole body duplication, and spindle midzone assembly, all tied to cell division. These points indicate a cohesive role in organizing microtubules and ensuring proper chromosome segregation. A few terms (neuron differentiation, adenosine biosynthetic process) are broader or ancillary, but do not override the main mitotic/cytoskeletal theme. Overall, the cluster likely represents proteins involved in spindle formation and microtubule-based cellular architecture during cell division.","confidence":"High","size":29,"edges":122,"triangles":256,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030182","count":10},{"id":"GO:0051301","count":7},{"id":"GO:0046086","count":7},{"id":"GO:0035690","count":7},{"id":"GO:0007020","count":6}]},{"hash":"1247641593375127503","title":"Cell Cycle and DNA Replication","description":"The cluster is dominated by GO terms related to the cell cycle and DNA replication (cell cycle, DNA replication, mitotic DNA replication, mitotic centrosome separation) and includes a DNA repair term, with supporting terms on ER\u2013Golgi transport and some differentiation notes. The core shared function appears to be cell cycle progression and DNA synthesis/maintenance, making this an appropriate, specific label.","confidence":"High","size":29,"edges":216,"triangles":831,"max_degree":25,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0060487","count":4},{"id":"GO:0007100","count":4},{"id":"GO:0007049","count":4},{"id":"GO:1902969","count":4},{"id":"GO:0006260","count":3}]},{"hash":"1519073306534020624","title":"Membrane trafficking and mitochondrial import","description":"The GO terms show a shared theme of cargo movement across membranes, including mitochondrial protein import (GO:0030150), regulation of mitochondrial membrane permeability, intracellular protein transport, clathrin-dependent endocytosis, and synaptic vesicle coating. While a couple of terms are obsolete, the recurring pattern centers on membrane trafficking and mitochondrial protein handling, supporting a cohesive cluster of proteins involved in membrane-associated transport.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010867","count":1},{"id":"GO:0070940","count":1},{"id":"GO:1903740","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0046902","count":1}]},{"hash":"2145951153218463142","title":"Receptor Signaling and Immune Response Network","description":"Proteins here map to multiple signaling pathways (dopamine response, T cell receptor signaling, Wnt pathway, ephrin receptor signaling) and innate immunity, plus RNA decay and metabolic signaling terms (CAMKK-AMPK). The common theme is receptor-mediated signal transduction linked to immune and developmental processes, suggesting a broad signaling network rather than a single pathway.","confidence":"Medium","size":29,"edges":22,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:1903351","count":4},{"id":"GO:0050852","count":3},{"id":"GO:0043552","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0048013","count":3}]},{"hash":"1302873472908605454","title":"Development and cell proliferation","description":"The cluster shows a strong signal for developmental processes and cell division: brain development, blastocyst development, mitotic cell cycle, and cell division. While there are metabolic terms (regulation of gluconeogenesis, triglyceride homeostasis) and RNA processing (box C/D snoRNP assembly) that are present, they appear ancillary to the dominant developmental/proliferation theme. Therefore, the label reflects the core pattern of growth and division activity in this set.","confidence":"Medium","size":29,"edges":56,"triangles":6,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0035070","count":2},{"id":"GO:0090526","count":2},{"id":"GO:0070328","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1060436620969334889","title":"Genome maintenance and RNA quality control","description":"This cluster centers on genome stability processes (DNA replication, DNA repair, and telomere maintenance) and RNA maturation/quality control (rRNA processing and mRNA decay), with additional involvement in protein quality control pathways. The combination suggests a cohesive theme around maintaining genome integrity and ensuring proper RNA/protein quality, rather than a single specialized pathway.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0070914","count":2},{"id":"GO:0031848","count":2},{"id":"GO:0010833","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1816678852107812366","title":"Fungal Cell Wall Biosynthesis and Secretory Targeting","description":"The cluster shows GO terms centered on fungal-type beta-glucan biosynthesis and protein targeting to membranes (SRP-dependent cotranslational and post-translational), pointing to secretory pathway activities needed for assembling the fungal cell wall. While some terms like DNA replication or oxidative stress response appear, the strongest signals align with cell wall biogenesis and membrane targeting, suggesting proteins involved in secretory trafficking to the cell surface. ","confidence":"Medium","size":29,"edges":49,"triangles":32,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0000902","count":4},{"id":"GO:0006616","count":4},{"id":"GO:0070389","count":4},{"id":"GO:0090084","count":4}]},{"hash":"1867564890066220222","title":"Chloroplast RNA processing and plastid-nucleus signaling","description":"The terms are dominated by chloroplast/plastid RNA metabolism (transcription, processing, RNA modification/editing) and chloroplast\u2013nucleus signaling, with specific mentions of plastid RNA modification and RNA editing. Although mitochondrial mRNA modification appears, the strongest, most consistent theme centers on plastid RNA processing and cross-talk to the nucleus, suggesting a functional cluster tied to chloroplast RNA maturation and signaling pathways.","confidence":"High","size":29,"edges":92,"triangles":67,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0000961","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0042793","count":3},{"id":"GO:0010019","count":3},{"id":"GO:0016554","count":2}]},{"hash":"1241673185528669413","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":19,"triangles":8,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0006281","count":1},{"id":"GO:0006367","count":1},{"id":"GO:0000288","count":1},{"id":"GO:0045948","count":1}]},{"hash":"733456633516473137","title":"Cardiac ion transport and excitation-contraction coupling","description":"Proteins here map to heart muscle function: ion transport across membranes (Na+, K+), maintenance of transmembrane electrochemical gradients, and intracellular Na+ homeostasis, all essential for cardiac excitability. The presence of T-tubule organization and Ca2+-dependent exocytosis of neurotransmitter aligns with excitation-contraction coupling in cardiomyocytes, while ATP biosynthesis signals the energy supply needed for contraction. Collectively, these terms suggest a cohesive module governing cardiac ion handling, membrane potential, and contraction regulation.","confidence":"High","size":29,"edges":99,"triangles":157,"max_degree":17,"top_function":"DNA repair","top_go_terms":[{"id":"GO:1903416","count":8},{"id":"GO:0036376","count":8},{"id":"GO:0098736","count":8},{"id":"GO:1903233","count":8},{"id":"GO:0006754","count":8}]},{"hash":"921864168552373065","title":"Multitissue Development and Differentiation","description":"Interpreting the top GO terms, the cluster centers on developmental processes across diverse tissues (hippocampus, cochlea, cartilage, somitogenesis, pigmentation) and regulatory differentiation events (e.g., T cell differentiation in thymus). There isn\u2019t a single dominant function or pathway; instead, the terms point to broad developmental differentiation programs affecting multiple tissues. Therefore, this cluster is best described as a general developmental/differentiation cluster.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051150","count":1},{"id":"GO:0021766","count":1},{"id":"GO:0090243","count":1},{"id":"GO:0090103","count":1},{"id":"GO:0032436","count":1}]},{"hash":"1624096739197859297","title":"GABAergic Neural Signaling and Brain Development","description":"The top terms show strong enrichment for GABAergic signaling and brain development (GO:0007214, GO:0032228, GO:0007420), pointing to neural signaling as the core theme. Related receptors and pathways (IGF receptor signaling, sensory perception) support a broader neural signaling context, while mRNA capping reflects general transcriptional processing in these genes. Thus, a label focusing on GABAergic neural signaling and brain development captures the dominant function of this cluster.","confidence":"Medium","size":29,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:0032228","count":1},{"id":"GO:0001402","count":1},{"id":"GO:2000560","count":1},{"id":"GO:0007214","count":1}]},{"hash":"771215721819816082","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006382","count":1},{"id":"GO:0009240","count":1},{"id":"GO:1901909","count":1},{"id":"GO:0034656","count":1},{"id":"GO:0006281","count":1}]},{"hash":"2233981909954600577","title":"Glycerophospholipid and sphingolipid biosynthesis","description":"This cluster shows strong and diverse enrichment for lipid biosynthesis, including phosphatidylglycerol and phosphatidylethanolamine (glycerophospholipids) as well as ceramide, sphingomyelin, and ceramide-related pathways, indicating coordinated lipid metabolism. A few terms like protein transport and cellular oxidant detoxification are present but not central, so the lipid biosynthesis focus best explains the set.","confidence":"High","size":29,"edges":82,"triangles":77,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":2},{"id":"GO:0046839","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0006655","count":2},{"id":"GO:0006646","count":2}]},{"hash":"2194003716611347350","title":"Ubiquitination-driven stress response and development","description":"The cluster shows strong enrichment for ubiquitination and autoubiquitination, with oxidative stress regulation and DNA damage\u2013related apoptotic signaling, plus developmental processes like vitellogenesis and heart morphogenesis, suggesting a theme of ubiquitin-dependent control of stress and developmental signaling.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0010310","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0007296","count":1}]},{"hash":"1719128573827767897","title":"Unknown","description":"This cluster has no GO terms or connectivity (no edges, no triangles, and an empty Top Terms list), so there is no clear shared functional theme to justify a specific label. Without a detectable common function, the appropriate label is Unknown.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"786389725960250666","title":"Unknown","description":"This cluster has no edges, no shared GO terms, and no functional signal to tie the 29 proteins together. ReCIPE added 20 proteins but there is no connectivity or common terms to define a specific biological role, so the cluster cannot be named beyond Unknown.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1345936845805976262","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":144,"triangles":431,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051591","count":9},{"id":"GO:0042853","count":8},{"id":"GO:0007219","count":8},{"id":"GO:0097053","count":8},{"id":"GO:0042866","count":6}]},{"hash":"1900779946833437245","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":38,"triangles":0,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0000453","count":1},{"id":"GO:0002938","count":1},{"id":"GO:0046338","count":1},{"id":"GO:0010898","count":1},{"id":"GO:2000480","count":1}]},{"hash":"1573876646510111298","title":"Unknown","description":"There are no GO terms or interaction edges to guide labeling, leaving no shared function to unite the 29 proteins; they appear unconnected and potentially uncharacterized, so a single interpretable label cannot be assigned.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1368467498374225094","title":"Nutrient and Xenobiotic Membrane Transport","description":"These proteins cluster around transport and trafficking across membranes, with GO terms for nitrate, glucose, trehalose, sialic acid, L-ascorbic acid, and xenobiotics transport, plus endosome-to-melanosome trafficking. The common thread is membrane-mediated uptake and export of nutrients and small molecules, with some intracellular transport related to organelle movement. ","confidence":"High","size":28,"edges":49,"triangles":26,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":4},{"id":"GO:0035646","count":3},{"id":"GO:0060731","count":3},{"id":"GO:0015739","count":3},{"id":"GO:0042908","count":3}]},{"hash":"2117202876435002381","title":"Redox-Driven Transcription Regulation","description":"The cluster shows strong representation of redox-related processes (cell redox homeostasis, cellular oxidant detoxification, oxidation-reduction process) alongside transcriptional regulation terms (DNA-templated transcription, positive regulation of DNA binding, negative regulation of RNA polymerase II regulatory region DNA binding) and other nuclear transport/modification terms, suggesting proteins involved in maintaining redox balance while modulating gene expression in the nucleus. Some terms (e.g., viral process) may reflect broader regulatory connections rather than a core function. Confidence: Medium","confidence":"","size":28,"edges":270,"triangles":1427,"max_degree":27,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":21},{"id":"GO:0098869","count":20},{"id":"GO:0055114","count":19},{"id":"GO:0043388","count":16},{"id":"GO:0006351","count":16}]},{"hash":"88765009553438912","title":"Immune signaling and cell cycle","description":"This cluster centers on B and T cell receptor signaling and innate immune response, with additional terms related to mitotic cell cycle and centrosome/centriole duplication, suggesting a link between immune activation and cell proliferation. Some terms (pollen recognition, embryonic morphogenesis) are less coherent with the main theme, but the dominant themes are immune signaling and cell division.","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050853","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0051298","count":2},{"id":"GO:0007099","count":2}]},{"hash":"1644325895716093164","title":"TLR/MyD88 Innate Immune Signaling","description":"The cluster is dominated by GO terms for MyD88-dependent toll-like receptor signaling, TLR1 signaling, and innate immune response, plus a response to dsRNA, indicating a cohesive theme around TLR-mediated pathogen recognition and signaling. Some terms (actin remodeling, Wnt signaling, dopamine response) appear less central and may reflect broader roles or secondary associations. Overall, the dominant theme is innate immune signaling via TLR pathways.","confidence":"High","size":28,"edges":14,"triangles":0,"max_degree":5,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002755","count":12},{"id":"GO:0034130","count":9},{"id":"GO:1903351","count":9},{"id":"GO:0051014","count":9},{"id":"GO:0045087","count":9}]},{"hash":"1112136385515445398","title":"Unknown","description":"This cluster's Top Terms are diverse and few, involving apoptosis in liver and myeloid cells, cell migration, epithelial polarity, chromatin organization, collagen degradation, translation, and dexamethasone response. With zero internal edges and no dominant shared function, there is no coherent GO-driven theme tying these proteins together, so a meaningful label cannot be assigned beyond Unknown.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097284","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0033028","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0034396","count":1}]},{"hash":"658064875665209280","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:0008315","count":2},{"id":"GO:0031047","count":2},{"id":"GO:1905612","count":2},{"id":"GO:0048820","count":2}]},{"hash":"872923835418068572","title":"Unknown","description":"There are no GO terms or network connections to define a shared function among the 28 proteins, so no coherent theme can be identified. Without enrichment or interactions, a specific label cannot be justified.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"711525781084541173","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":88,"triangles":170,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0032147","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0000453","count":2},{"id":"GO:0000462","count":2}]},{"hash":"1466708429060608185","title":"Zinc Homeostasis and Transport","description":"This cluster is dominated by GO terms for zinc ion import, intracellular zinc ion homeostasis, and detoxification, pointing to proteins involved in maintaining zinc levels and handling zinc flux across membranes. The presence of cadmium ion transport and cellular response to zinc ion starvation further support a zinc-centric theme, with limb development and IGF-related terms appearing only peripherally.","confidence":"High","size":28,"edges":9,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006882","count":6},{"id":"GO:0070574","count":6},{"id":"GO:0010312","count":6},{"id":"GO:1903615","count":4},{"id":"GO:0060173","count":4}]},{"hash":"1448109659220773149","title":"Mitotic spindle and kinetochore assembly","description":"This cluster is dominated by mitosis-related processes: regulation of spindle assembly, protein localization to kinetochore, centriole replication, and mitotic cell cycle arrest, indicating a cohesive role in cell division machinery. Some metabolic or signaling terms (e.g., TORC1 signaling, VEGF response) may reflect broader regulatory context but do not override the core mitotic theme.","confidence":"High","size":28,"edges":23,"triangles":9,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010800","count":28},{"id":"GO:0035924","count":28},{"id":"GO:0070509","count":28},{"id":"GO:0090169","count":28},{"id":"GO:1904262","count":28}]},{"hash":"1995182161986857942","title":"SRP-Mediated Membrane Targeting","description":"The two most frequent terms are SRP-dependent cotranslational targeting to membrane and post-translational targeting to membrane, indicating a membrane translocation pathway via the SRP system. The other terms (DNA repair, SOS response, transcription) appear only once and likely reflect incidental annotations, so the core theme is SRP-mediated protein targeting to membranes.","confidence":"High","size":28,"edges":200,"triangles":717,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0006616","count":2},{"id":"GO:0031204","count":2},{"id":"GO:0000746","count":1},{"id":"GO:0006465","count":1},{"id":"GO:0006281","count":1}]},{"hash":"78679552021489487","title":"Unknown","description":"There are no GO terms or connections to indicate a shared function for the 28 proteins (no edges, no triangles, and an empty top-terms list). Without a functional signal, the appropriate label is Unknown.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"329788185127927722","title":"Unknown","description":"This cluster has no interactions or shared GO terms (Edges 0, Triangles 0, Top Terms empty), so there is no evident common function to name. Without functional signals, it is not possible to assign a coherent label beyond Unknown.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2084519905232161473","title":"Unknown","description":"There is no shared GO annotation or network connectivity among the 28 proteins, and the only note is that 20 were re-added by ReCIPE. Without functional terms or interactions to tie the proteins together, a meaningful, specific label cannot be assigned, so the cluster is Unknown.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1301296498790236515","title":"Diverse Substrate Transmembrane Transporters","description":"This cluster is dominated by GO terms for transmembrane transport of many substrates (ions like K+ and Na+, sugars such as arabinose and galactose, nitrate, sialic acid, xenobiotics), plus a response to glucose starvation, indicating a set of membrane transport proteins with broad substrate specificity.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":8},{"id":"GO:0015706","count":8},{"id":"GO:0015739","count":7},{"id":"GO:0006855","count":7},{"id":"GO:0015751","count":6}]},{"hash":"1089785498034397704","title":"Chromatin organization and transcription regulation","description":"These terms cluster around chromatin dynamics: histone modification and exchange, chromatin assembly during DNA replication, heterochromatin formation, and transcription elongation regulation. Although a few terms are obsolete, the unifying theme is chromatin organization controlling gene expression and cell-cycle\u2013related transcription processes.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016573","count":1},{"id":"GO:0006348","count":1},{"id":"GO:0006337","count":1},{"id":"GO:0031567","count":1},{"id":"GO:0043486","count":1}]},{"hash":"710458910524460095","title":"Cardiogenesis with transcriptional control and apoptosis regulation","description":"Top terms point to heart development, DNA-templated transcription, apoptosis, and signaling pathways (insulin, Wnt), together with cell cycle/checkpoint activity, suggesting a cardiogenesis module that coordinates transcriptional programs with growth, survival, and developmental signaling.","confidence":"High","size":27,"edges":35,"triangles":12,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0007095","count":4},{"id":"GO:0008286","count":4},{"id":"GO:0043065","count":4}]},{"hash":"1958156753855333070","title":"Vesicle trafficking and proteostasis","description":"The cluster is dominated by GO terms for intracellular transport (ER-to-Golgi, endosome-to-Golgi, general protein transport) and vesicle targeting, along with proteostasis (SCF-dependent ubiquitin-proteasome\u2013mediated degradation and regulation of protein targeting to vacuolar membranes). A couple of terms link to synaptic development, but the strongest signal is coordinated trafficking and protein turnover, suggesting proteins involved in vesicle trafficking and degradation pathways. Confidence: High","confidence":"","size":27,"edges":32,"triangles":7,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0051965","count":2}]},{"hash":"1808529145166384816","title":"Flagellar Axoneme Assembly and Ciliary Motility","description":"Most terms point to cilium/flagellum biology: axoneme assembly, ciliary movement, flagellated sperm motility, and related microtubule dynamics. Tubulin PTMs (polyglycylation, polyglutamylation) support axonemal function, consistent with microtubule severing and axoneme integrity. A couple of terms relate to broader transcription or cell migration but do not outweigh the clear ciliary/flagellar theme. Overall, the cluster likely represents proteins involved in ciliary/flagellar structure and motility.","confidence":"High","size":27,"edges":7,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030516","count":3},{"id":"GO:0018094","count":3},{"id":"GO:0051013","count":3},{"id":"GO:0007288","count":3},{"id":"GO:0018095","count":3}]},{"hash":"621447160067358790","title":"Mitosis and chromosome segregation","description":"Top GO terms point to DNA replication, spindle assembly regulation, and kinetochore localization, with supporting signals in proteasomal degradation and growth pathway modulation, suggesting a cohesive role in cell cycle control and mitotic machinery.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000902","count":3},{"id":"GO:0032436","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1902416","count":2},{"id":"GO:0010800","count":2}]},{"hash":"1898416269303206399","title":"Nucleocytoplasmic transport & translation initiation","description":"The top GO terms point to nuclear pore\u2013related processes: nuclear pore complex assembly, mRNA and tRNA export, and nuclear localization, indicating nucleocytoplasmic transport. In addition, terms for translation reinitiation and preinitiation complex formation suggest a link to translation initiation. Some mitosis-related terms appear but are secondary to transport/translation themes. This combination supports a cluster centered on RNA trafficking and initiation of protein synthesis.","confidence":"Medium","size":27,"edges":224,"triangles":1134,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0051292","count":2},{"id":"GO:0051028","count":2}]},{"hash":"1445277984773765655","title":"Ribosome Biogenesis and Transcription Regulation","description":"The cluster is dominated by GO terms for translation, ribosome assembly, and transcription (DNA-templated transcription and positive regulation of transcription by RNA polymerase II), pointing to core gene expression machinery. Some peripheral terms (heart development, immune and steroid responses) are present but less central to the main theme.","confidence":"High","size":27,"edges":318,"triangles":2228,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:2000616","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0045944","count":2}]},{"hash":"145278821105272441","title":"Innate Immune Response to Pathogens and Xenophagy","description":"The terms cluster around innate immunity against viruses and bacteria, including dsRNA sensing, interferon-beta production, LPS signaling, and broader defense responses. The presence of NF-kappaB regulatory processes and protein ubiquitination supports a theme of immune signaling control, while xenophagy points to intracellular pathogen containment. Altogether, the proteins appear to function as a cohesive unit in sensing pathogens and coordinating defensive signaling, including autophagic pathways.","confidence":"High","size":27,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":4},{"id":"GO:0043124","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0043330","count":3},{"id":"GO:0031663","count":3}]},{"hash":"857520916755493077","title":"Developmental transcriptional regulation","description":"The GO terms point to development across multiple organs (heart, hippocampus, cerebellum) and to transcription-related processes (DNA-templated transcription, chromatin localization), suggesting the proteins act mainly in regulating gene expression during development. A ribosome biogenesis term appears but is less central to the cluster\u2019s theme.","confidence":"Medium","size":27,"edges":59,"triangles":38,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0033138","count":2},{"id":"GO:2000727","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0021695","count":2}]},{"hash":"165931901166015728","title":"Golgi-to-endosome and melanosome transport","description":"The cluster is enriched for vesicle trafficking terms, especially Golgi-to-endosome transport and endosome-to-melanosome transport, with supporting hints of redox and DNA repair processes, indicating a cohesive endosomal/vesicular transport module with related stress-response components.","confidence":"Medium","size":27,"edges":218,"triangles":959,"max_degree":24,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006915","count":5},{"id":"GO:0006895","count":4},{"id":"GO:0071375","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0035646","count":3}]},{"hash":"1488773775225925835","title":"Vertebrate Development and Signaling Pathways","description":"The top GO terms span broad developmental processes across multiple tissues (heart, skeletal muscle, nervous system) and several signaling routes (hippo signaling, B cell receptor signaling, neurotrophin TRK signaling). The inclusion of DNA replication and apoptosis terms suggests cellular decisions during growth and fate specification. Together, these indicate a cluster centered on vertebrate development with associated signaling and cell-cycle events rather than a single, focused pathway.","confidence":"Medium","size":27,"edges":21,"triangles":1,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0035329","count":10},{"id":"GO:0050853","count":10},{"id":"GO:0097194","count":10},{"id":"GO:0007507","count":10}]},{"hash":"973343948877608988","title":"Ribosome biogenesis and translation","description":"The cluster is strongly enriched for translation-related GO terms, including cytoplasmic translation, mitochondrial translation, ribosome biogenesis, and ribosomal large subunit assembly, pointing to proteins involved in the protein synthesis machinery. A few other terms (immune response, globoside biosynthesis) are present but represent a minority, suggesting incidental associations rather than core functions. Therefore, the cluster most likely reflects ribosome assembly and function.","confidence":"High","size":27,"edges":72,"triangles":91,"max_degree":19,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0002181","count":3},{"id":"GO:0019731","count":1},{"id":"GO:0002227","count":1},{"id":"GO:0000027","count":1}]},{"hash":"1842306107148189404","title":"Stress-Induced Transcription Regulation","description":"The cluster shows enrichment for stress-related responses (hydrogen peroxide, antibiotic response) alongside transcriptional regulation (DNA-templated transcription, NF-kappaB activity) and general mRNA processing, suggesting a theme of stress signaling coupled with transcription control. Some terms (like cobalamin biosynthesis and antibiotic biosynthesis) are less tightly connected, indicating broader or multi-function annotations, but the core signal points to stress-responsive transcriptional regulation.","confidence":"Medium","size":27,"edges":16,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0035970","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0042542","count":2},{"id":"GO:0051384","count":2}]},{"hash":"991275060816866236","title":"Amino acid catabolism and central metabolism","description":"The cluster centers on breakdown pathways for branched-chain amino acids (leucine and valine) and links to core energy metabolism (glycolysis, pyruvate decarboxylation to acetyl-CoA, and the TCA cycle) plus proteolysis and starvation response, suggesting a cohesive theme of nutrient recycling and energy production from amino acids under stress.","confidence":"High","size":27,"edges":101,"triangles":215,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006552","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0006096","count":4},{"id":"GO:0006086","count":4}]},{"hash":"2033647337931324168","title":"Unknown","description":"The terms show broad processes including transcription, embryonic development, myoblast fusion and satellite cell activation, stress responses, digestion, and apoptosis, with no single dominant theme. As a result, there is no clear, cohesive function to label the cluster.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007520","count":1},{"id":"GO:0001824","count":1},{"id":"GO:0071472","count":1},{"id":"GO:0014718","count":1}]},{"hash":"602713265448111119","title":"Diverse Substrate Catabolism","description":"The terms show catabolic processes on various substrates (nitrogen, uracil, nicotine, cellulose, phosphatidylserine), implying a cluster of proteins involved in diverse molecule breakdown. A few terms relate to broader processes like endothelial migration or toxin response, which are less specific to catabolism. Overall, the unifying theme is multifaceted catabolic activity rather than a single pathway, justifying a \u201cDiverse Substrate Catabolism\u201d label.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019740","count":1},{"id":"GO:0010710","count":1},{"id":"GO:0006660","count":1},{"id":"GO:0006212","count":1},{"id":"GO:0009086","count":1}]},{"hash":"1269639472172421064","title":"Unknown","description":"There are no GO terms or functional signals to tie the 27 proteins together, and the network shows no edges or shared terms, so a cohesive function cannot be inferred from the data provided. The ReCIPE re-added proteins do not establish a common theme here. ","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"769088415020893717","title":"Embryonic Patterning and Morphogenesis","description":"Most terms point to embryonic development, tissue morphogenesis, and organ formation (left/right patterning; digit and cartilage morphogenesis; EMT in heart cushions; placenta, pancreatic cell development; trophoblast differentiation; ciliary transition zone localization). A single term about mitochondrial complex IV assembly appears unrelated, suggesting a possible outlier; overall the cluster aligns with developmental processes and morphogenesis.","confidence":"Medium","size":27,"edges":26,"triangles":1,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0060972","count":1},{"id":"GO:0003198","count":1},{"id":"GO:0060806","count":1},{"id":"GO:0035270","count":1},{"id":"GO:0003323","count":1}]},{"hash":"1195824975662243024","title":"Unknown","description":"No GO terms are provided and there are no edges or triangles, so there is no shared function to define this cluster. The lack of connectivity and signals makes a meaningful label impossible.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1366675462856533545","title":"Unknown","description":"There are no GO terms or connections to reveal a common function; with zero edges/triangles and no top terms, no coherent theme is identifiable, despite ReCIPE additions.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1297827075556915763","title":"Plant defense signaling and phloem development","description":"Most GO terms point to plants: sieve element differentiation (phloem development), aerenchyma formation (hypoxia adaptation), and salicylic acid\u2013mediated signaling (defense). Lipid and carbohydrate catabolism may reflect metabolic remodeling during stress. The combination suggests a cluster related to plant defense signaling concurrent with phloem development, hence the name. A couple of terms (acetylcholine biosynthesis/secretion) look out of place and may be annotation noise.","confidence":"Medium","size":27,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006660","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0052651","count":2},{"id":"GO:0019433","count":2},{"id":"GO:2000124","count":2}]},{"hash":"1002189359793902077","title":"RNA processing, splicing, and surveillance","description":"The top GO terms cluster around rRNA maturation (LSU/5.8S), mRNA splicing via spliceosome (and its positive regulation), nonsense-mediated decay, and post-transcriptional gene silencing, all indicating RNA biogenesis and quality control, plus localization aspects such as protein targeting to stress granules. This points to a coherent theme of RNA processing and surveillance rather than a single enzymatic pathway, though some DNA repair terms may reflect multifunctional factors. Overall, labeling this cluster as RNA processing and quality control best captures the shared functions.","confidence":"High","size":26,"edges":128,"triangles":462,"max_degree":17,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0000463","count":12},{"id":"GO:0000466","count":12},{"id":"GO:0000184","count":12},{"id":"GO:0006283","count":12},{"id":"GO:0006301","count":11}]},{"hash":"908514964938427470","title":"Vertebrate embryonic and neural development","description":"The top terms emphasize developmental processes such as forebrain development, neural tube closure, multicellular organism development, and skeletal system development, all pointing to vertebrate embryogenesis and neurodevelopment. Other terms reflect general cellular stress responses and cell cycle activity, which are ancillary to the core developmental theme. Thus, the label captures the main function of the cluster with moderate confidence.","confidence":"Medium","size":26,"edges":43,"triangles":14,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":5},{"id":"GO:0051260","count":4},{"id":"GO:0006349","count":4},{"id":"GO:0030900","count":4},{"id":"GO:0007275","count":4}]},{"hash":"740379238046354090","title":"Large subunit ribosome biogenesis and export","description":"The cluster is dominated by ribosome biogenesis terms: preribosome assembly, maturation of 5.8S and LSU rRNA, and export of the large ribosomal subunit from the nucleus, indicating a cohesive role in assembling and exporting the large subunit. While a few endocytosis/lysosome-related terms appear, they are much less represented and likely secondary. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006897","count":2},{"id":"GO:1902626","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0000055","count":1}]},{"hash":"398795882202059057","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":34,"triangles":7,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1900865","count":3},{"id":"GO:1905639","count":3},{"id":"GO:0080156","count":3}]},{"hash":"732024867216226978","title":"TLR signaling components (MyD88-dependent)","description":"The cluster shows a clear enrichment for innate immune signaling terms, especially detection of bacterial lipopeptide and MyD88-dependent Toll-like receptor signaling (with a specific hint from TLR1 signaling). This points to a core theme of Toll-like receptor\u2013mediated immune responses, despite the presence of some broader signaling terms (e.g., Wnt signalosome, CAMKK-AMPK, mitotic regulation) that may reflect cross-pathway roles. Overall, the strongest common function across these proteins appears to be TLR-mediated signaling components.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070340","count":2},{"id":"GO:0034130","count":2},{"id":"GO:0071287","count":2},{"id":"GO:1905289","count":2},{"id":"GO:0035564","count":2}]},{"hash":"333032377828393086","title":"Protein trafficking and quality control","description":"The cluster centers on intracellular protein handling, with terms for ER to Golgi transport, ubiquitin-dependent ERAD, and peroxisomal matrix protein import, plus microtubule involvement and protein turnover. Although a few terms touch on chromatin assembly and cell division, the strongest signal is endomembrane trafficking and protein quality control, making this label representative overall.","confidence":"Medium","size":26,"edges":171,"triangles":462,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0070914","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0051013","count":3}]},{"hash":"686591123817569985","title":"TGF-beta/BMP signaling and development regulation","description":"This cluster is dominated by GO terms tied to TGF-beta signaling, SMAD/BMP pathway regulation, and developmental processes such as meristem identity, indicating a module of growth factor signaling that modulates development. Some terms are peripheral or organism-specific (e.g., photosystem stoichiometry, germ-line masculinization), but the central pattern points to regulation of TGF-beta/BMP-related signaling pathways in development.","confidence":"Medium","size":26,"edges":158,"triangles":534,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":9},{"id":"GO:0000173","count":7},{"id":"GO:0046827","count":7},{"id":"GO:0035970","count":7},{"id":"GO:0080005","count":7}]},{"hash":"1082385590706242410","title":"Developmental chromatin and transcription regulation","description":"The cluster is enriched for chromatin-related processes (CENP-A containing chromatin assembly; establishment of protein localization to chromatin) and transcription control (negative regulation of transcription by RNA polymerase II and by RNA polymerase I), alongside broad developmental terms (brain development, osteoblast differentiation, male gonad development, fertilization, multicellular growth). This points to a cohesive theme of chromatin-mediated gene regulation governing development across tissues. The Gram-positive defense term is peripheral, but does not outweigh the dominant chromatin-development signal.","confidence":"High","size":26,"edges":105,"triangles":198,"max_degree":18,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0050830","count":9},{"id":"GO:0000122","count":8},{"id":"GO:0007338","count":8},{"id":"GO:0001649","count":8},{"id":"GO:0007420","count":8}]},{"hash":"144790445932898954","title":"Nuclear transcription and DNA repair with stress response","description":"These proteins cluster around nuclear processes: DNA-templated transcription, mRNA processing, DNA repair, and chromatin-related histone modification and protein export from the nucleus, indicating coordinated regulation of gene expression within the nucleus. The presence of cadmium ion response and innate immune response terms suggests stress-related transcriptional changes, while mitotic cell cycle involvement points to cell-cycle coupled transcription and DNA maintenance. Hence a label summarizing nuclear transcription and DNA repair with stress response is appropriate.","confidence":"Medium","size":26,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0071276","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0000278","count":2},{"id":"GO:1903070","count":2}]},{"hash":"1565593971095933061","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":36,"triangles":4,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0033119","count":1},{"id":"GO:0006417","count":1},{"id":"GO:0006412","count":1}]},{"hash":"287386238428176690","title":"Unknown","description":"The GO terms are highly diverse, spanning cell cycle, transcription regulation, ubiquitination, Golgi organization, lipid droplets, mitochondrial depolarization, arsenic response, and even hippocampus development. There is no clear, shared functional theme or dominant pathway linking these terms, and the lack of edges reinforces that this cluster does not map to a single coherent function.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0051900","count":2},{"id":"GO:0046685","count":2}]},{"hash":"638809400572647299","title":"RNA splicing and gene silencing regulation","description":"Top GO terms strongly link spliceosome-related processes (splicing regulation, splice-site recognition, processome assembly) with RNA silencing pathways (regulatory ncRNA- and miRNA-mediated silencing) and translational control (translation reinitiation, mRNA stability in stress). This suggests a unifying theme of post-transcriptional RNA processing and gene expression regulation.","confidence":"High","size":26,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":5},{"id":"GO:0075525","count":5},{"id":"GO:1905663","count":5},{"id":"GO:0000381","count":5},{"id":"GO:0035278","count":5}]},{"hash":"1020439630206081273","title":"Multi-tissue development and glucocorticoid response","description":"The top GO terms point to heart and brain development (heart development, hippocampus development, gliogenesis) and to stress/hormone responses (cardiac hypertrophy in response to stress, cellular response to dexamethasone). A few terms touch on hepatocyte homeostasis and epigenetic regulation, suggesting a broad developmental program modulated by glucocorticoid signaling rather than a single pathway.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014898","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0071549","count":1},{"id":"GO:1990654","count":1},{"id":"GO:0021766","count":1}]},{"hash":"624514782851757877","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":48,"triangles":30,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:2000637","count":2},{"id":"GO:0034063","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000288","count":2},{"id":"GO:0000447","count":2}]},{"hash":"1387824043363307435","title":"Unknown","description":"The GO terms are highly diverse, spanning chromatin-related processes (subtelomeric heterochromatin formation, histone methylation), nucleotide biosynthesis (GTP, CTP, UTP synthesis), development (ventricular system development, spermatid differentiation), cilium movement, and apoptosis regulation. There is no clear shared function or pathway linking these terms, and the cluster has no edges, suggesting the proteins do not represent a single cohesive biological theme. Therefore, there is no confident, representative label beyond Unknown.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":1},{"id":"GO:0051568","count":1},{"id":"GO:0006183","count":1},{"id":"GO:0021591","count":1},{"id":"GO:1902176","count":1}]},{"hash":"1232792076273438571","title":"Mitotic chromosome alignment and CPC localization","description":"The top GO terms cluster around mitosis: chromatid biorientation, kinetochore localization, spindle midzone localization of the chromosome passenger complex (CPC), and mitotic checkpoint signaling, all indicative of proteins governing chromosome segregation and mitotic progression. Dephosphorylation terms suggest regulatory phosphatase activity during mitosis, while a couple of peripheral terms (mRNA capping, PI3K/AKT signaling) are likely less central to the core function of this cluster.","confidence":"High","size":26,"edges":217,"triangles":944,"max_degree":23,"top_function":"autophagy","top_go_terms":[{"id":"GO:0035335","count":14},{"id":"GO:1902310","count":10},{"id":"GO:0006370","count":10},{"id":"GO:0046959","count":10},{"id":"GO:1990598","count":10}]},{"hash":"2016901425973774093","title":"Ubiquitin-Dependent Proteolysis and DNA Maintenance","description":"Based on the GO terms, the cluster centers on ubiquitin-mediated protein degradation (autoubiquitination, ubiquitin-dependent catabolic processes, MVB sorting) paired with genome maintenance activities (DNA replication and DNA repair), along with growth-control processes (apoptosis, Hippo signaling, regulation of cell proliferation). This suggests a cohesive theme around proteostasis linked to DNA maintenance and cell growth control.","confidence":"Medium","size":26,"edges":21,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0043162","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0035329","count":2}]},{"hash":"1612816776448742728","title":"Unknown","description":"There are no GO terms or network connections to indicate a shared function among the 26 proteins, so a meaningful label cannot be inferred; Unknown is appropriate.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1642240099555059786","title":"Nuclear Transcription and RNA Processing Regulators","description":"These proteins show GO terms centered on transcription elongation by RNA polymerases I/II, mRNA capping and splicing, RNA localization, and rRNA processing, suggesting a shared role in nuclear transcription and RNA maturation processes.","confidence":"Medium","size":26,"edges":17,"triangles":1,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:2001209","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0034244","count":1},{"id":"GO:0008298","count":1},{"id":"GO:2001208","count":1}]},{"hash":"1841794489469749093","title":"Unknown","description":"There are no shared GO terms or network connections in this cluster (edges=0, triangles=0, Top Terms empty), so there is no clear biological theme to group these proteins. The ReCIPE re-additions do not reveal a common function.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1494683215693751752","title":"Unknown","description":"There are no GO terms or network connections defining a shared function (no edges, no terms), so a coherent label cannot be assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"582220911971282726","title":"Unknown","description":"There are no GO terms provided for this cluster, so no coherent shared function can be inferred. The network shows moderate connectivity (26 proteins, 61 edges, 9 triangles), but without functional enrichment the label cannot be determined.","confidence":"","size":26,"edges":61,"triangles":9,"max_degree":15,"top_function":null,"top_go_terms":[]},{"hash":"1028561697300026309","title":"Unknown","description":"There are 26 proteins with 0 edges and no GO terms listed, so there is no evident shared function or process linking them. The ReCIPE note indicates re-added proteins but does not imply interactions or functional coherence. Without GO terms or network structure to anchor a theme, the cluster cannot be confidently named.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1033964195840393497","title":"Fatty acid and sphingolipid biosynthesis","description":"The cluster\u2019s top GO terms predominantly point to lipid metabolism, especially fatty acid biosynthesis/elongation (long-, very long-, saturated, and polyunsaturated chains) and sphingolipid biosynthesis, indicating a cohesive lipid biosynthetic function. A few outliers (swim bladder development, pheromone metabolism, endosome-to-vacuole transport) are present but do not undermine the central lipid-focused theme.","confidence":"High","size":26,"edges":161,"triangles":351,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0042759","count":2},{"id":"GO:0006636","count":2},{"id":"GO:0048794","count":2},{"id":"GO:0042810","count":2},{"id":"GO:0042761","count":2}]},{"hash":"1287740223068172975","title":"Bacterial Biosynthesis and Stress Response","description":"The top GO terms point to multiple biosynthetic pathways (lipopolysaccharide, cobalamin, biotin), along with tRNA methylation, metal transport, and responses to antibiotics and xenobiotics. This combination suggests a prokaryotic metabolism-focused cluster with adaptation to chemical stress, rather than a single precise function.","confidence":"Medium","size":25,"edges":84,"triangles":149,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0046677","count":4},{"id":"GO:0009103","count":4},{"id":"GO:0009236","count":3},{"id":"GO:0042493","count":3}]},{"hash":"2267731271310405606","title":"ER-Golgi trafficking and protein ubiquitination","description":"This cluster centers on intracellular vesicle transport between ER, Golgi, and endosomes, plus ubiquitination and protein interaction dynamics, indicating a core function in vesicular trafficking and protein turnover. Some terms touch on neuronal dendrite development and angiogenic regulation, but the strongest signal is trafficking.","confidence":"High","size":25,"edges":76,"triangles":79,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":8},{"id":"GO:0016567","count":8},{"id":"GO:0016358","count":7},{"id":"GO:0034498","count":7},{"id":"GO:0045859","count":7}]},{"hash":"587206917112239992","title":"Regulated signaling and transcription control","description":"This cluster centers on regulatory processes: negative regulation of kinase activity, positive regulation of transcription by RNA Pol II, and other regulatory roles (cell polarity, barrier establishment), with additional hints from trafficking and environmental response terms. The common thread is modulation and control of signaling and transcription rather than a single specific function, suggesting proteins involved in regulatory pathways.","confidence":"Medium","size":25,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0001892","count":1},{"id":"GO:2000114","count":1},{"id":"GO:0043001","count":1}]},{"hash":"926699900612522334","title":"Organelle Protein Import and Genome Maintenance","description":"These terms cluster around protein trafficking into organelles (peroxisomes and mitochondria) and genome maintenance activities (nuclear and mitochondrial DNA replication, with viral genome replication as a related replication process). The inclusion of proteostasis elements like aggresome assembly and oxidation-dependent protein catabolic processes supports a broader cellular maintenance theme. ","confidence":"Medium","size":25,"edges":154,"triangles":571,"max_degree":21,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0070842","count":4},{"id":"GO:0006406","count":4},{"id":"GO:0019079","count":4},{"id":"GO:0090296","count":3}]},{"hash":"465951555508974151","title":"DNA Replication and Repair with Translesion Synthesis","description":"The cluster is dominated by GO terms for DNA synthesis, repair, and damage tolerance, including DNA-templated replication, nucleotide-excision repair, UV-C response, and both error-free and error-prone translesion synthesis, suggesting a cohesive module of DNA maintenance and damage tolerance.","confidence":"High","size":25,"edges":118,"triangles":298,"max_degree":19,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006261","count":7},{"id":"GO:0070987","count":7},{"id":"GO:0071494","count":7},{"id":"GO:0042276","count":7},{"id":"GO:0006281","count":7}]},{"hash":"683425553192552872","title":"Unknown","description":"There isn\u2019t a clear shared function among the top GO terms, spanning plant development and hormone metabolism, animal development, microbial biosynthesis, and basic cell-cycle processes, so a cohesive label cannot be justified.","confidence":"","size":25,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010800","count":2},{"id":"GO:0007118","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0031145","count":2},{"id":"GO:0001890","count":2}]},{"hash":"2004866909099844048","title":"RNA Modification and Redox Metabolism","description":"This cluster shows enrichment for tRNA wobble uridine modification and tRNA seleno-modification, alongside redox-related terms (redox homeostasis, oxidation-reduction process) and central metabolism (TCA cycle), suggesting a link between RNA-modifying enzymes and redox/metabolic regulation. Some outliers (pseudohyphal growth, spinal cord development) are less represented and may reflect broader GO annotations; overall, a coherent RNA modification and redox/metabolic module fits the data.","confidence":"Medium","size":25,"edges":50,"triangles":29,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:0002098","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0045648","count":3}]},{"hash":"2291133331644398399","title":"DNA replication and repair with phosphorylation response","description":"This cluster centers on nuclear maintenance processes: DNA repair and DNA replication, with an additional signal-regulatory aspect via phosphorylation, indicating coordinated DNA maintenance and stress signaling. Some terms (pollen germination, neural tube formation) seem unrelated and may reflect cross-species annotations rather than a core function. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0032957","count":1}]},{"hash":"1814105901440841871","title":"Ribosome Biogenesis and rRNA Processing","description":"The cluster shows strong enrichment for ribosome-related processes: ribosome biogenesis (GO:0042254), ribosomal large subunit biogenesis (GO:0042273), ribosomal large subunit export from nucleus (GO:0000055), and rRNA processing steps (GO:0000447), indicating a cohesive group of proteins involved in ribosome assembly, maturation, and export. Some unrelated terms appear among the list, but the dominant signal is ribosome production and processing.","confidence":"High","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002244","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0007080","count":1}]},{"hash":"1779434188638517292","title":"Unknown","description":"The GO terms are highly diverse, including immune evasion, insect development (dorsal appendage formation), lipid catabolism, ER targeting, signaling pathways, blue light signaling, and hypoxia detection. With edges = 0 and no clear shared function or pathway linking these proteins, there is no coherent theme to define a meaningful, specific cluster label beyond Unknown.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0020012","count":2},{"id":"GO:0046843","count":1},{"id":"GO:0046338","count":1},{"id":"GO:0031161","count":1},{"id":"GO:0045047","count":1}]},{"hash":"400221697586219858","title":"Calcium-Driven Signaling and Cytoskeletal Regulation","description":"This cluster is dominated by terms tying calcium signaling to cytoskeletal dynamics and post-translational regulation: cellular response to calcium, regulation of actomyosin filament sliding and contractile ring assembly, and increased kinase activity and methylation-related processes. The convergence on calcium response, actin-myosin organization, and phosphorylation/kinase regulation suggests a cohesive module coordinating calcium signals with cytoskeletal remodeling and signaling cascades, with some broader transcriptional/post-translational regulation signals. Overall, the theme is calcium-linked signaling coupled to cytoskeletal regulation.","confidence":"Medium","size":25,"edges":82,"triangles":130,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043123","count":12},{"id":"GO:0033234","count":11},{"id":"GO:0071277","count":11},{"id":"GO:0032972","count":11},{"id":"GO:0010800","count":11}]},{"hash":"1042904060459597824","title":"Developmental Growth and Metabolism","description":"Most represented functions center on protein synthesis (translation), with accompanying development-related processes (gastrulation, vasculogenesis, cell proliferation) and metabolism (glycolysis, redox). This suggests a cluster of proteins that support growth and development through translation and energy metabolism. ","confidence":"Medium","size":25,"edges":50,"triangles":82,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0007568","count":4},{"id":"GO:0016575","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0007369","count":3}]},{"hash":"637884404768167089","title":"Unknown","description":"There are no GO terms or interactions linking these 25 proteins, and the network has no edges or top terms to define a shared function, so a meaningful label cannot be assigned. The fact that 20 proteins were re-added by ReCIPE does not establish a common role.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"970518505389780730","title":"Unknown","description":"The GO terms are highly diverse, spanning keratinocyte apoptosis regulation, cellular responses to growth factors and steroids, two mRNA decay pathways, PMA response, T cell homeostasis, and developmental processes, with no single unifying function evident across all proteins. This functional heterogeneity makes it hard to assign a coherent label.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902172","count":1},{"id":"GO:0044344","count":1},{"id":"GO:0071385","count":1},{"id":"GO:0000288","count":1},{"id":"GO:1904628","count":1}]},{"hash":"1735552388579012786","title":"Unknown","description":"There are no GO terms to define a shared function; the cluster has no edges or top terms, so there is no detectable common process, despite ReCIPE re-adding some members. Without functional signals, a reliable label cannot be assigned.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1170293308692633172","title":"Unknown","description":"The GO terms are highly diverse, spanning immune evasion, development of lung and brain regions, meiotic recombination, kinetochore localization, metabolism, and neural remodeling. There is no single coherent biological theme tying these proteins together, making a specific functional label inappropriate. Therefore, the cluster is best described as Unknown.","confidence":"","size":25,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0020012","count":2},{"id":"GO:0030324","count":1},{"id":"GO:0021762","count":1},{"id":"GO:0010780","count":1},{"id":"GO:0034501","count":1}]},{"hash":"813518772255401127","title":"Unknown","description":"No enriched GO terms or connections are reported (Top Terms is empty; Edges, Triangles, and Max Degree are zero). With no shared functional annotation or interaction structure, there is no clear theme to assign a precise label.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"862914159047846172","title":"ER-Golgi Trafficking and Golgi Retention","description":"This cluster is dominated by GO terms tied to the secretory pathway, especially ER-to-Golgi vesicle transport and protein retention in the Golgi, with additional hints of Golgi-associated processing like glycosylation. Together these terms point to a cohesive role in trafficking and maturation of proteins through the ER-Golgi network, rather than a single isolated process. Some broader or obsolete terms appear, but the central theme remains ER-Golgi trafficking and Golgi-based maturation.","confidence":"Medium","size":25,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0045730","count":2},{"id":"GO:0060576","count":2},{"id":"GO:0045053","count":1}]},{"hash":"1423344405191312261","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006547","count":1},{"id":"GO:0010224","count":1},{"id":"GO:0031291","count":1},{"id":"GO:1905869","count":1},{"id":"GO:0000278","count":1}]},{"hash":"965887740760021791","title":"Unknown","description":"The listed GO terms span several distinct processes\u2014innate immune signaling (NOD2 pathway, NF-kappaB regulation), adipogenesis (fat cell differentiation), post-translational modification (ADP-ribosylation), cell cycle/spindle assembly, and stress/ligand responses (temperature sensing, salicylic acid, capsazepine). There is no single predominant function linking these proteins, so a coherent, specific label isn\u2019t apparent.","confidence":"","size":24,"edges":24,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0071446","count":1},{"id":"GO:0070213","count":1}]},{"hash":"1453068485798603398","title":"Developmental gene regulation","description":"This cluster centers on terms related to transcriptional control and developmental processes, including DNA-templated transcription and multiple facets of multicellular development (nervous system, skeletal muscle). Added signals such as B cell receptor signaling, VEGF response, and calcium import suggest regulatory pathways that influence cell fate and tissue development. The overall theme is regulatory functions guiding development, despite the lack of direct interactions in this dataset.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0071732","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0050853","count":2}]},{"hash":"2133132203826811393","title":"Vesicle trafficking and cell polarity","description":"The top GO terms cluster around intracellular transport and membrane remodeling (multivesicular body assembly; Golgi-to-transport vesicle transport; pre-miRNA export) and cell shape/polarity (cell spreading, establishment/maintenance of cell polarity, regulation of cell shape). This points to a core theme of membrane trafficking coupled with polarity regulation, with a few developmental terms (balance, kidney size, cuticle pattern) likely reflecting broader tissue patterning roles. Thus a label focused on vesicle trafficking and polarity best captures the shared function.","confidence":"Medium","size":24,"edges":208,"triangles":1169,"max_degree":23,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1900026","count":5},{"id":"GO:0071963","count":4},{"id":"GO:0036258","count":4},{"id":"GO:0050885","count":4},{"id":"GO:0035281","count":4}]},{"hash":"766692875381512444","title":"Mitosis: spindle assembly and centriole replication","description":"Most terms cluster around cell division and mitosis: centriole replication, protein localization to kinetochore, regulation of spindle assembly, and mitotic cell cycle arrest. While some additional terms touch on growth signaling and calcium flux, the core signal is mitotic spindle/centrosome\u2013related processes, supporting this label as representative. ","confidence":"Medium","size":24,"edges":118,"triangles":360,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0010800","count":1},{"id":"GO:0035924","count":1},{"id":"GO:0070509","count":1},{"id":"GO:0090169","count":1},{"id":"GO:1904262","count":1}]},{"hash":"196938013259800792","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":55,"triangles":94,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0000902","count":5},{"id":"GO:0071038","count":4},{"id":"GO:0045006","count":4},{"id":"GO:0034475","count":4},{"id":"GO:2000627","count":4}]},{"hash":"391886578098080100","title":"Epigenetic DNA methylation and chromatin regulation","description":"The terms cluster around DNA methylation and chromatin-related processes\u2014epigenetic programming, histone methylation, and heterochromatin formation\u2014suggesting proteins involved in establishing or maintaining methylation marks that regulate gene expression and chromatin state. Although some GO entries are obsolete, the dominant theme remains methylation-driven epigenetic regulation.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043045","count":1},{"id":"GO:0043046","count":1},{"id":"GO:0010425","count":1},{"id":"GO:0009307","count":1},{"id":"GO:0051571","count":1}]},{"hash":"511518708007930642","title":"Chromatin Regulation and Signaling","description":"This cluster centers on chromatin-related regulation, including covalent chromatin modification and histone exchange, and extends to regulatory signaling processes such as NF-kappaB signaling, maintenance of RNA localization, and regulation of integrin activation, implying a shared theme of gene expression control and cellular signaling across members. Some terms are obsolete or plant-specific, suggesting annotation breadth and multifunctionality rather than a single cohesive pathway. ","confidence":"Medium","size":24,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016569","count":1},{"id":"GO:2000270","count":1},{"id":"GO:0043486","count":1},{"id":"GO:0009688","count":1},{"id":"GO:0045190","count":1}]},{"hash":"678598711125004747","title":"Translation machinery and mRNA turnover","description":"The terms cluster around core translation steps (initiation, elongation, termination), general translation, and regulation of translational fidelity, plus deadenylation-dependent mRNA decay and selenocysteine incorporation, pointing to a cohesive group of proteins involved in protein synthesis and post-transcriptional regulation. Glial proliferation and response to antibiotic appear as less central, likely context-specific.","confidence":"High","size":24,"edges":251,"triangles":1592,"max_degree":23,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0046677","count":11},{"id":"GO:0000288","count":10},{"id":"GO:0001514","count":10},{"id":"GO:0014009","count":10}]},{"hash":"560780139949766988","title":"DNA Replication and Cell Cycle Core","description":"The cluster is dominated by GO terms for DNA-templated transcription and multiple DNA replication steps (premeiotic replication, pre-replicative complex assembly, unwinding, strand elongation) along with cell cycle processes, indicating a module of nuclear replication machinery and transcription regulation. Chromatin-related activity (histone H3-K9 methylation) supports a chromatin-regulation theme that accompanies replication. A couple of terms like hippocampus development and root meristem growth appear as broader or cross-species annotations but are secondary to the replication/cell cycle signal.","confidence":"High","size":24,"edges":10,"triangles":1,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007049","count":3},{"id":"GO:0021766","count":3},{"id":"GO:0051567","count":3},{"id":"GO:0006279","count":2}]},{"hash":"897818107738795337","title":"Unknown","description":"The GO terms are diverse and sparse, with only one term each for centromeric chromatin assembly (CENP-A), senescence regulation, ion transport regulation, and DNA methylation, plus a few obsolete terms, giving no clear cohesive function for the 24 proteins.","confidence":"","size":24,"edges":26,"triangles":9,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:2000774","count":1},{"id":"GO:0032463","count":1},{"id":"GO:0034080","count":1},{"id":"GO:0034766","count":1},{"id":"GO:0044030","count":1}]},{"hash":"215622945122136382","title":"Unknown","description":"The top terms are diverse and include cell cycle (mitotic centrosome separation), adhesion, plant-type cell wall organization, and lipid/inositol phosphate related pathways, plus several obsolete or questionable symbiont-host terms. There is no single coherent function tying all proteins together, suggesting either mixed roles or noisy annotations. Confidence: None","confidence":"","size":24,"edges":77,"triangles":106,"max_degree":19,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:1902769","count":4},{"id":"GO:0007100","count":4},{"id":"GO:0036523","count":4},{"id":"GO:0052014","count":4},{"id":"GO:0007155","count":4}]},{"hash":"191986711909211317","title":"Unknown","description":"There are no shared GO terms or functional connections among these proteins (no edges, no triangles, max degree 0, and no Top Terms). Without evidence of a common function, I cannot infer a meaningful theme, so the label is Unknown.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1274627568522517900","title":"Unknown","description":"There are 24 proteins but no edges, no triangles, and no GO terms to guide a shared function, so there is no detectable functional coherence to label the cluster. ReCIPE-added members show zero connectivity, reinforcing the lack of identifiable common function.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"781453792997023954","title":"Golgi-ER trafficking and protein maturation","description":"Top GO terms cluster around secretory pathway processes: COPI-coated vesicle budding, Golgi ribbon formation, and regulation of protein exit from the ER, along with protein maturation and Wnt secretion. While iron metabolism terms and placenta development appear as outliers, the strongest and most recurrent theme is ER-to-Golgi trafficking and Golgi organization, indicating the cluster largely represents secretory pathway maturation rather than iron metabolism. ","confidence":"Medium","size":24,"edges":9,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0016226","count":1},{"id":"GO:0009399","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0051604","count":1},{"id":"GO:0070863","count":1}]},{"hash":"2247160738021509009","title":"Tubulin PTMs and axoneme assembly","description":"This cluster is dominated by GO terms related to tubulin post-translational modifications (polyglycylation, polyglutamylation), microtubule severing, and sperm axoneme assembly, pointing to microtubule remodeling and flagellum/cilia-related functions. Obsolete mitochondrial transport terms appear less informative, so the core signal is tubulin modification and axoneme assembly.","confidence":"High","size":24,"edges":13,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0072321","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0045039","count":2},{"id":"GO:0006796","count":1},{"id":"GO:0035987","count":1}]},{"hash":"1513587753920801101","title":"Plant lipid metabolism and strigolactone biosynthesis","description":"The cluster shows strong signals for lipid turnover (triglyceride catabolic process, phospholipid dephosphorylation) and strigolactone biosynthesis, a plant hormone linked to shoot development (secondary shoot formation). While other metabolic processes (redox, aromatic compound degradation) are present, the co-enrichment of lipid catabolism with strigolactone synthesis suggests a module centered on plant lipid metabolism integrated with hormone-driven growth regulation. ","confidence":"High","size":24,"edges":69,"triangles":71,"max_degree":13,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0019433","count":14},{"id":"GO:2000124","count":13},{"id":"GO:0098869","count":12},{"id":"GO:0006212","count":11},{"id":"GO:0055114","count":11}]},{"hash":"612015250295721322","title":"Developmental Growth and Trafficking","description":"This cluster mixes terms tied to morphogenesis and growth (pseudohyphal growth, invasive growth, multicellular development, cartilage condensation) with cellular trafficking and secretion (endocytic recycling, ER exit, protein localization to the cell surface, secretion of lysosomal enzymes). The common theme appears to be coordination of growth/ development processes with protein trafficking and secretion pathways, suggesting proteins involved in developmental signaling coupled to intracellular transport. ","confidence":"Medium","size":24,"edges":84,"triangles":166,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007124","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0032456","count":2},{"id":"GO:0001502","count":2},{"id":"GO:0007275","count":2}]},{"hash":"741446727547703383","title":"Plant Stress Signaling and Defense","description":"The top GO terms point to plant-specific stress responses and defense pathways (salicylic acid signaling, camalexin biosynthesis, aerenchyma formation) plus ion transport and signaling processes (sodium transport, guanylate cyclase activity). There are also shifts in cellular remodeling and turnover (cellulose catabolism, vacuolar processing, autophagy of the nucleus, phosphatidylserine catabolism) that commonly accompany stress adaptation. Taken together, these terms suggest a cohesive module involved in plant responses to abiotic/biotic stress and defense, rather than a single narrow process.","confidence":"Medium","size":24,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0006814","count":2},{"id":"GO:0031284","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0080151","count":1}]},{"hash":"1046730375958062649","title":"Neural development and signaling regulation","description":"These proteins cluster around neural development and signaling pathways. The top GO terms emphasize neural morphogenesis (regulation of branching morphogenesis of a nerve), neuronal activity modulation (negative regulation of excitatory postsynaptic potential), and signaling cascades (Wnt signalosome assembly, CAMKK-AMPK signaling). A mechanical stimulus response also ties into neuronal mechanotransduction. Additional terms on metal ion homeostasis and intracellular trafficking may reflect supporting neuronal metabolism and protein handling, but the central theme appears to be neural development and signaling. ","confidence":"Medium","size":23,"edges":44,"triangles":12,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000055","count":5},{"id":"GO:0032258","count":5},{"id":"GO:0006878","count":5},{"id":"GO:1905289","count":5},{"id":"GO:0035564","count":5}]},{"hash":"934082932173612865","title":"ESCRT-driven vesicle formation and cytokinesis abscission","description":"These proteins are enriched for ESCRT-mediated vesicle formation and multivesicular body trafficking, including viral budding via ESCRT and cytokinesis abscission, suggesting a cohesive vesicle-trafficking module.","confidence":"High","size":23,"edges":187,"triangles":1030,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:1902188","count":2},{"id":"GO:0071454","count":2},{"id":"GO:0009838","count":2},{"id":"GO:0070676","count":2},{"id":"GO:0010458","count":2}]},{"hash":"298351872539307732","title":"Mitosis and Spindle Assembly Regulation","description":"The top GO terms cluster around mitosis-related processes: protein localization to kinetochore, centriole replication, regulation of spindle assembly, and cell cycle arrest in response to pheromone. Additional terms on phosphorylation and TORC1 signaling relate to growth-control coupled cell-cycle regulation, reinforcing the core theme of cell division machinery and its control. Some terms like pollen recognition or cardiac development are broader annotations and don\u2019t override the central mitotic signal.","confidence":"High","size":23,"edges":47,"triangles":23,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010800","count":19},{"id":"GO:0035924","count":19},{"id":"GO:0070509","count":19},{"id":"GO:0090169","count":19},{"id":"GO:1904262","count":19}]},{"hash":"559337452759574054","title":"Mitosis and Chromatin Organization","description":"The top GO terms cluster around mitosis and chromatin dynamics\u2014cell division, mitotic chromosome condensation, mitotic cell cycle, chromatin organization, and CENP-A\u2013containing assembly\u2014indicating a cohesive theme of chromosome regulation during cell division. A couple of terms about ER-to-Golgi transport and ERAD are present but less representative of the main signal.","confidence":"High","size":23,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006888","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051013","count":2}]},{"hash":"2028752996897027024","title":"Regulation of Translational Initiation","description":"This cluster is dominated by translational initiation terms (formation of translation preinitiation complex, IRES-dependent viral translational initiation, and regulation of translational initiation), indicating a core role in controlling protein synthesis initiation; a few other processes like DNA repair and cell morphogenesis appear as minor associations but do not define a single cohesive function.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006446","count":2}]},{"hash":"930504442558266171","title":"Cytoskeleton Remodeling and Cell Migration in Development","description":"Dominant GO terms center on actin cytoskeleton reorganization, Rho signaling, and general cell migration, with developmental context from hippocampus and heart development and modulation by Wnt signaling, plus links to proteasomal degradation and apoptosis. This suggests a cohesive module of cytoskeletal dynamics driving cell movement during development and tissue remodeling. ","confidence":"High","size":23,"edges":11,"triangles":1,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021766","count":4},{"id":"GO:0007266","count":4},{"id":"GO:0031532","count":4},{"id":"GO:0090090","count":4},{"id":"GO:0016477","count":4}]},{"hash":"990446673195475277","title":"ESCRT-Mediated Viral Budding and Vesicle Formation","description":"This cluster is enriched for terms involving viral budding via the host ESCRT complex, defense against viruses, and ESCRT-driven vesicle formation (intralumenal vesicles, abscission, mitotic exit), as well as tubulin-associated trafficking. These collectively point to ESCRT-mediated membrane remodeling used in viral budding and host antiviral responses.","confidence":"High","size":23,"edges":22,"triangles":22,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1902187","count":3},{"id":"GO:0007021","count":3},{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:1902188","count":2}]},{"hash":"1029077791146083671","title":"Mitotic and secretory pathway regulators","description":"Represents a mix of mitotic processes (spindle assembly, cleavage furrow ingression, general cell division) and secretory/ER-related trafficking (Golgi transport, COPII coating, ER stress response), with growth signaling and development terms (EGFR signaling, brain development, kidney size). This pattern suggests proteins that coordinate cell division with vesicle trafficking and growth signaling during development, rather than a single, narrow function.","confidence":"Medium","size":23,"edges":81,"triangles":158,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":10},{"id":"GO:0090307","count":9},{"id":"GO:1990386","count":9},{"id":"GO:1905289","count":9},{"id":"GO:0055108","count":9}]},{"hash":"2281012406069910813","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0071374","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0006626","count":2}]},{"hash":"1531841970884531244","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":12,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010606","count":3},{"id":"GO:0000289","count":3},{"id":"GO:0006824","count":2},{"id":"GO:1903830","count":2},{"id":"GO:0045016","count":2}]},{"hash":"1381207901736131714","title":"Mitotic actomyosin contractile ring assembly","description":"The cluster centers on mitotic contractile ring localization and actin filament bundle assembly, with additional terms on centrosome maintenance and regulation of GTPase activity, indicating a cohesive theme around actomyosin-driven cytokinesis during mitosis. This supports labeling the cluster as mitotic actomyosin contractile ring assembly. ","confidence":"High","size":23,"edges":94,"triangles":205,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:1902405","count":2},{"id":"GO:1903477","count":2},{"id":"GO:0051661","count":2},{"id":"GO:1903478","count":2},{"id":"GO:0045769","count":2}]},{"hash":"596220850271173406","title":"Central Carbon Metabolism","description":"The top GO terms cluster around core energy-producing pathways: glycolysis (glycolytic process), the TCA cycle, and glucose metabolism, plus related steps in acetyl-CoA formation and pyruvate flux (pyruvate decarboxylation to acetyl-CoA) and thiamine biosynthesis. An outlier term related to olfactory development is present but does not overpower the metabolic signal, so the cluster most representatively reflects central carbon metabolism, especially glycolysis and TCA activities.","confidence":"High","size":23,"edges":80,"triangles":114,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0006096","count":7},{"id":"GO:0006099","count":7},{"id":"GO:0061034","count":6},{"id":"GO:0009228","count":6}]},{"hash":"914187250311658133","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":9,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031440","count":2},{"id":"GO:0046726","count":2},{"id":"GO:0035526","count":2},{"id":"GO:0031338","count":2},{"id":"GO:0031030","count":2}]},{"hash":"1542454558581228550","title":"DNA Damage Response and Neddylation Regulation","description":"The cluster\u2019s top GO terms include DNA damage response signals (response to UV-C, response to gamma radiation) and repair via homologous recombination, indicating a core theme of DNA damage response. Supporting terms involve protein post-translational modification and turnover (neddylation and ubiquitin-protein transferase activity, protein catabolic processes), suggesting coordinated proteostasis during damage responses. A couple of terms related to ribosomal RNA processing and septum digestion appear as related cellular processes but do not define the main theme; overall, the dominant signal ties DNA damage response with regulation of protein modification/degradation pathways.","confidence":"Medium","size":23,"edges":77,"triangles":98,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0000920","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0000724","count":2},{"id":"GO:0010225","count":1},{"id":"GO:0045116","count":1}]},{"hash":"1976255438655472846","title":"Vacuolar Transport and Ion Homeostasis","description":"This cluster centers on membrane transport and organelle maintenance, especially vacuolar functions (vacuole organization, vacuolar acidification, protein targeting to vacuole) and transmembrane movement of ions and metabolites (sodium, copper, uridine, thymine, protons). The common theme is transport across membranes coupled with vacuolar ion balance and pH regulation.","confidence":"Medium","size":23,"edges":20,"triangles":0,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0015862","count":2},{"id":"GO:0035364","count":2},{"id":"GO:0007033","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0006814","count":1}]},{"hash":"215449249985002625","title":"ER Stress Proteostasis and Trafficking","description":"Top GO terms point to heat response regulation, ER stress\u2013driven translation initiation, chaperone-assisted refolding, and post-translational targeting to membranes, all suggesting a focus on maintaining proteome integrity and directing proteins through secretory/ER pathways under stress. While a DNA replication term appears unrelated, the dominant theme across the cluster is proteostasis and protein trafficking in stressed conditions.","confidence":"High","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1900035","count":23},{"id":"GO:0006260","count":23},{"id":"GO:0070389","count":23},{"id":"GO:0090084","count":23},{"id":"GO:0031204","count":23}]},{"hash":"1786471014593667365","title":"Viral life cycle and virion assembly","description":"The top GO terms cluster around core viral processes: viral life cycle, virion assembly, uncoating, fusion of viral membranes with host membranes, and viral release, indicating the proteins are largely linked to viral replication and assembly steps. Some protein folding terms and a leukocyte migration term appear as ancillary annotations, likely reflecting host\u2013virus interaction context, but the dominant theme is viral lifecycle events.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019076","count":1},{"id":"GO:2000276","count":1},{"id":"GO:0010849","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0000413","count":1}]},{"hash":"2302736171013590304","title":"Mitosis and DNA replication machinery","description":"Dominated by DNA replication, spindle assembly, kinetochore localization, and mitotic arrest terms, the cluster centers on mitosis and DNA replication machinery. Growth signaling (TORC1) and calcium import may modulate mitosis, while development terms likely reflect broader roles of these proteins. Overall: mitosis/DNA replication core.","confidence":"High","size":23,"edges":65,"triangles":68,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0001893","count":7},{"id":"GO:0010800","count":6},{"id":"GO:0035924","count":6},{"id":"GO:0070509","count":6}]},{"hash":"1308127574909249364","title":"Stem Cell Maintenance Regulation","description":"The only prominent GO term is negative regulation of stem cell population maintenance, suggesting a potential link to stem cell regulation. However, with no edges or multiple related terms, this label is tentative and may not fully represent all proteins in the cluster.","confidence":"Low","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902455","count":1}]},{"hash":"2021008707684141606","title":"Interferon-driven antiviral response and dsRNA sensing","description":"Most terms cluster around innate immune defense and responses to viral components, especially cellular response to Type I interferon, response to exogenous dsRNA, and innate immune response, with additional related ubiquitination. A weaker signal for cell division appears but does not override the antiviral/innate signaling theme, so the label emphasizes interferon and dsRNA\u2013mediated antiviral activity.","confidence":"Medium","size":23,"edges":56,"triangles":58,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":12},{"id":"GO:0071357","count":12},{"id":"GO:0006463","count":11},{"id":"GO:0046661","count":11},{"id":"GO:0030850","count":11}]},{"hash":"1929540502093723584","title":"Unknown","description":"The top GO terms are highly diverse, spanning chromatin modification and transcription regulation, membrane trafficking (receptor recycling, endosome size), signaling (Rho pathway), synaptic transmission, calcium-release channel activity, viral RNA replication, antigen processing, and heart contraction. With only a couple of edges and low connectivity, there is no clear shared function tying these proteins together, so a single cohesive label is not justifiable.","confidence":"","size":23,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0051036","count":1}]},{"hash":"1174025571953906005","title":"Unknown","description":"No common GO terms or network connections are evident; 0 edges/triangles and 0 degree, so a shared function cannot be inferred.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1240355012199745204","title":"Arabinogalactan protein and seed mucilage biosynthesis","description":"This cluster\u2019s prominent GO terms center on plant cell wall components and glycosylation: arabinogalactan protein metabolism, seed coat mucilage biosynthesis, root hair development, and related glycan biosynthetic processes. A few terms (insect follicle epithelium/polarity) seem extraneous or cross-species noise, but the dominant signal ties to plant glycoprotein biosynthesis and cell wall\u2013related development.","confidence":"Medium","size":23,"edges":112,"triangles":353,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0010493","count":7},{"id":"GO:0048354","count":7},{"id":"GO:0075015","count":7},{"id":"GO:0018258","count":7},{"id":"GO:0001744","count":7}]},{"hash":"567034214501947878","title":"Unknown","description":"The cluster has only two weakly enriched terms (ER to Golgi vesicle transport and positive regulation of phagocytosis), each appearing once, with no clear shared function across most proteins, and no internal interactions. This makes it impossible to assign a specific, representative label.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:0050766","count":1}]},{"hash":"111507976930245999","title":"Nuclear mRNA processing and decay factors","description":"The cluster shows strong enrichment for mRNA processing terms, especially mRNA splicing via the spliceosome and both deadenylation-dependent and -independent mRNA decay, indicating a core RNA metabolism function. While there are some developmental and signaling-related terms, they are less represented, making RNA maturation and turnover the central theme for this cluster.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:1902172","count":1},{"id":"GO:0044344","count":1},{"id":"GO:0071385","count":1},{"id":"GO:0000288","count":1}]},{"hash":"1136149779928017906","title":"Insulin Secretion and Mitochondrial Metabolism","description":"The cluster combines GO terms related to glucose-stimulated insulin secretion and mitochondrial metabolism (positive regulation of insulin secretion, pyruvate import into mitochondria, mitochondrial acetyl-CoA biosynthesis from pyruvate, and mitochondrial calcium regulation), along with ER-to-Golgi vesicle transport and calcium handling, suggesting a cohesive theme of secretory pathway function coupled to mitochondrial energy and calcium signaling in insulin release. Some terms appear less related (e.g., plant-specific brassinosteroid biosynthesis), but the dominant signal points to insulin secretion linked with mitochondrial metabolism.","confidence":"Medium","size":23,"edges":215,"triangles":1142,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0016132","count":2},{"id":"GO:0035774","count":2},{"id":"GO:1902361","count":2}]},{"hash":"1516937919202354924","title":"Unknown","description":"The term set is fragmented: translation and translational elongation point to protein synthesis, while DNA transposition and mitochondrial respiratory chain complex assembly do not share a unifying function, making a cohesive label unreliable.","confidence":"","size":22,"edges":88,"triangles":128,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0006414","count":1},{"id":"GO:0006313","count":1},{"id":"GO:0033108","count":1}]},{"hash":"1991974029596828958","title":"Meiosis: chromatid cohesion and spindle dynamics","description":"The cluster\u2019s top GO terms are dominated by meiotic processes\u2014sister chromatid cohesion, cohesion centromeric, meiotic spindle elongation, and female meiotic nuclear division\u2014along with meiotic cell cycle regulation in oocyte maturation. Other terms related to nuclear import and protein regulation appear ancillary but do not override the clear meiosis-centric signal. This suggests the proteins function together in meiosis-specific chromosomal events and spindle dynamics rather than general cellular processes.","confidence":"High","size":22,"edges":176,"triangles":881,"max_degree":21,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0051754","count":8},{"id":"GO:0006610","count":8},{"id":"GO:0006607","count":8},{"id":"GO:0051306","count":7},{"id":"GO:0007143","count":7}]},{"hash":"439834462215145588","title":"Unknown","description":"Top GO terms cover insect neural development, transcription regulation, stress responses, hormone receptor assembly, and plant-specific processes, with no clear unifying function across all proteins.","confidence":"","size":22,"edges":25,"triangles":4,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0016319","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0090394","count":2}]},{"hash":"1877477803731135796","title":"Nuclear transcription, replication, and chromatin assembly","description":"The top GO terms point to core nuclear processes: DNA-templated transcription, DNA replication, centromeric (CENP-A) chromatin assembly, mRNA export, ribosomal subunit assembly, and RNA decay/quality control. Together these reflect a coordinated program of genome maintenance, transcriptional activity, and chromatin organization within the nucleus, rather than a single isolated pathway. Hence, a concise label that emphasizes transcription, replication, and chromatin assembly captures the cluster\u2019s shared function.","confidence":"High","size":22,"edges":165,"triangles":739,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0070370","count":4},{"id":"GO:0061641","count":4},{"id":"GO:0006406","count":4}]},{"hash":"1099010743586353291","title":"Neuronal signaling and protein trafficking","description":"The strongest signals are excitatory synaptic activity and regulation of glutamate release and synaptic plasticity, pointing to neuronal signaling. Supporting signals involve intracellular trafficking and processing: protein localization to ER, nuclear import, lipidation, and lipid droplet organization. The combination suggests proteins that participate in neuron communication while also handling cellular protein localization and modification, yielding a cohesive label of neuronal signaling with protein trafficking.","confidence":"Medium","size":22,"edges":12,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060079","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0097051","count":1},{"id":"GO:1903061","count":1}]},{"hash":"498873829068941705","title":"Unknown","description":"GO annotations among the proteins are varied and include developmental processes (pituitary gland development, mesoderm morphogenesis), stress responses (response to oxidative stress, apoptotic processes), and general cellular activities (rRNA processing regulation, protein isomerization), with no clear single function tying the cluster together. This lack of a cohesive theme makes a specific, representative label untenable.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021983","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006979","count":2},{"id":"GO:0010124","count":2},{"id":"GO:0043525","count":1}]},{"hash":"1810354242383993485","title":"Symbiont-Mediated Immune Suppression and Ubiquitination","description":"The cluster is dominated by GO terms pointing to host immune modulation by symbionts, including suppression of adaptive immune responses and altered antigen processing/presentation via MHC II, along with ubiquitin-related pathways (ubiquitin-like modifications and polyubiquitination). A few terms about barrier biosynthesis (cutin/suberin) appear but are secondary to the main theme of immune modulation through ubiquitin-related processes. Confidence in this naming is High because the immune modulation and ubiquitination signals strongly align across multiple terms.","confidence":"High","size":22,"edges":107,"triangles":300,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0010143","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0002495","count":2},{"id":"GO:0010345","count":2},{"id":"GO:0039648","count":2}]},{"hash":"1328463558959259116","title":"Unknown","description":"The GO terms are very diverse with no single dominant function, including histone modification, steroid receptor assembly, chlorophyll biosynthesis regulation, ER-stress\u2013linked translation, adipose development, stress responses, metabolism, immune response, and sex differentiation; no cohesive theme emerges.","confidence":"","size":22,"edges":17,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016570","count":1},{"id":"GO:0006463","count":1},{"id":"GO:1902325","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0060613","count":1}]},{"hash":"88443137477937325","title":"DNA replication and repair with organelle protein import","description":"The cluster shows a clear enrichment for DNA replication and DNA damage response (DNA replication, UV-damage excision repair, mitotic DNA replication checkpoint signaling), indicating genome maintenance functions. In addition, there are several terms related to protein import into peroxisomes and mitochondrial membrane insertion, suggesting involvement in organelle protein trafficking/assembly. Together, these points hint at a module combining nuclear genome maintenance with organelle protein import processes, though the latter may be secondary to the replication/repair core.","confidence":"Medium","size":22,"edges":12,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001824","count":2},{"id":"GO:0070914","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0033314","count":2},{"id":"GO:0090296","count":1}]},{"hash":"1225792477496594451","title":"RNA Methylation & Modification","description":"It seems dominated by methylation-related processes: 7-methylguanosine capping, guanine-N7 methylation, tRNA methylation including wobble uridine modification, and protein arginine methylation. This points to a common function in methylation-based modification of both RNA and proteins, rather than a single pathway. Some GO terms like nodulation and chlorophyll biosynthesis, and antibiotic biosynthesis, may reflect plant/bacterial context or annotation spillover rather than core cluster identity.","confidence":"High","size":22,"edges":192,"triangles":939,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":13},{"id":"GO:0036265","count":13},{"id":"GO:0017000","count":12},{"id":"GO:0030488","count":11},{"id":"GO:0009877","count":11}]},{"hash":"378882121374351463","title":"Unknown","description":"Top terms are empty and there are no interactions among the proteins, so no shared functional signal can be inferred. Without GO-term enrichment or connectivity, the cluster cannot be assigned a specific biological role.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"337948865947659110","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by translation-related terms (GO:0006412) and multiple ribosome biogenesis and rRNA maturation terms, indicating members of the protein synthesis machinery and ribosome assembly pathways. While there are ancillary terms like transcription elongation and stress responses, the core signal ties to ribosomes and translation. Confidence: High","confidence":"","size":22,"edges":122,"triangles":374,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":19},{"id":"GO:0042254","count":6},{"id":"GO:0046677","count":4},{"id":"GO:0000463","count":3},{"id":"GO:0042274","count":3}]},{"hash":"2157740973690200507","title":"Pancreatic development and glucose-stimulated insulin secretion","description":"Top terms point to pancreas development and glucose-stimulated insulin secretion, suggesting a cluster of proteins involved in pancreatic function and insulin release in response to glucose. With only two low-count terms and no interactions shown, this label is a best-fit representation rather than a strong, comprehensive annotation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031016","count":1},{"id":"GO:0035773","count":1}]},{"hash":"1086129869428265126","title":"Cell Cycle and DNA Repair Proteins","description":"This cluster is enriched for mitotic cell cycle, cell division, DNA-templated transcription, and DNA repair terms, suggesting a core role in cell cycle progression and genome maintenance. Additional terms like protein homooligomerization point to protein complex formation, while some terms (ERAD-related, nonfunctional rRNA decay) imply broader quality-control or RNA-processing connections. The presence of obsolete GO terms introduces some annotation noise, but the dominant signals support a cohesive theme around cell division and genome integrity. Confidence: Medium","confidence":"","size":22,"edges":12,"triangles":2,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0051301","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0070651","count":3}]},{"hash":"1027723449738310594","title":"Unknown","description":"There are no edges, no triangles, and no GO terms to define a shared function, so there\u2019s no clear theme connecting these proteins. The lack of functional signals means a precise, representative label cannot be determined; the set appears unannotated or heterogeneous.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1511136175208463637","title":"Unknown","description":"There are no GO terms or top terms to guide naming, and the graph has no edges or triangles (Max Degree 0). With no functional signal tying the proteins together, no coherent theme can be inferred; the cluster may be arbitrary or an artifact of the ReCIPE process.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1957658930289261396","title":"Unknown","description":"There are no shared GO terms or network connections to define a common function, and the lack of top terms makes it impossible to infer a theme; the cluster appears uncharacterized.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2302772738055338516","title":"Unknown","description":"There are no top GO terms provided and the cluster has no edges or triangles, so there is no detectable shared function among the 22 proteins. Without functional annotations to tie them together, a meaningful label cannot be assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"934322105369753826","title":"Unknown","description":"There are no GO terms listed and no network connections (Edges 0, Triangles 0) to indicate a shared function among the 22 proteins. Although ReCIPE re-added 20 proteins, without identifiable terms or interactions, a coherent functional label cannot be inferred.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"839844812305705841","title":"Unknown","description":"No shared GO terms or interactions are reported for this cluster (edges and triangles are zero), and 20 proteins were re-added by ReCIPE without clarifying functional themes. Without a unifying function, the safest label is Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2294898376529126472","title":"Methylation-Related Enzymes","description":"These proteins show a strong enrichment for methylation-related GO terms, including arginine methylation (asymmetrical-dimethyl), glutamine methylation, rRNA methylation, and histone methylation, suggesting a cluster of methyltransferases and methylation-regulating proteins. Additional terms relating to transcription regulation and cellular growth/senescence appear to be downstream effects or broader context. Some outlier annotations (cobalamin biosynthesis, tellurium ion response) exist, but the dominant theme is methylation biology. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046690","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0090398","count":1},{"id":"GO:0016049","count":1}]},{"hash":"1351821830762551241","title":"Unknown","description":"The cluster has 22 proteins but no edges or triangles and no GO terms listed, so there is no shared functional signature to anchor a label. Although 20 proteins were re-added by ReCIPE with a degree of 0.75, there are still zero edges among the proteins, and no enrichment signals to tie them to a specific process. Consequently, a generic Unknown label is most appropriate.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"329396529865706626","title":"Motile cilium assembly and ciliary signaling","description":"This cluster centers on ciliogenesis and ciliary function, highlighted by terms like motile cilium assembly, axoneme assembly, cilium movement, and ciliary transition zone assembly, with additional links to ciliary signaling (Smoothened pathway) and opsin transport, plus left-right symmetry determination and embryonic brain development. The shared theme across these terms strongly suggests a cohesive role in ciliogenesis and ciliary signaling.","confidence":"High","size":22,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0044458","count":2},{"id":"GO:0032516","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0035082","count":1},{"id":"GO:0060294","count":1}]},{"hash":"2026331021913143513","title":"Unknown","description":"The cluster has no edges and no GO terms to indicate a shared function, so there is no clear functional theme to name it. Without enrichment or interaction signals, a confident label cannot be assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"441730834891978838","title":"Unknown","description":"There are no GO terms or network connections to cluster by a shared function, so no common theme is detectable among the 22 proteins. Without features tying them together, the safest label is Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2290962637003538602","title":"Unknown","description":"This cluster has 22 proteins but no edges and no GO terms to bind them to a common function, so there is no clear functional theme to name. The absence of shared terms makes an accurate label impossible; thus Unknown is the safest designation.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"221872690057314882","title":"Mitochondrial lipid remodeling and synthesis","description":"This cluster is dominated by lipid biosynthesis and remodeling terms (triglyceride biosynthesis, phosphatidylcholine and cardiolipin remodeling) and by mitochondrial energy production (mitochondrial ATP synthesis). These collectively point to a cohesive theme around lipid metabolism in mitochondrial membranes, with a few outlier terms that are broader or organism-specific, but the core signal is lipid-related mitochondrial function.","confidence":"High","size":22,"edges":62,"triangles":84,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0019432","count":5},{"id":"GO:0009405","count":4},{"id":"GO:0042775","count":4},{"id":"GO:0010143","count":4},{"id":"GO:2001246","count":4}]},{"hash":"1117932725148312741","title":"Unknown","description":"The GO terms are highly diverse, spanning vacuole fusion, sebaceous gland development, lipid modification, plant hormone signaling, xenobiotic response, cellulose catabolism, and neuronal signaling. There is no single unifying function or pathway that ties these proteins together, making it unclear how to label the cluster with a coherent biological theme.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":3},{"id":"GO:0048733","count":3},{"id":"GO:0018230","count":3},{"id":"GO:0009740","count":1},{"id":"GO:0050783","count":1}]},{"hash":"1617004967163194425","title":"Ubiquitin-mediated NF-kappaB signaling and apoptosis","description":"The cluster shows a strong emphasis on protein ubiquitination (including K6-linked ubiquitination) and pathways that activate NF-kappaB signaling, along with regulation of apoptotic processes. This suggests a coherent theme where ubiquitination modulates signaling cascades that control cell survival and inflammatory responses. Some terms listed are obsolete or peripheral (e.g., histone methylation regulation, X chromosome dosage effects), but the dominant tied functions are ubiquitin-dependent signaling and apoptosis regulation.","confidence":"Medium","size":21,"edges":26,"triangles":7,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":7},{"id":"GO:1903762","count":5},{"id":"GO:0007250","count":5},{"id":"GO:0070512","count":5},{"id":"GO:1900095","count":5}]},{"hash":"2247068447956148893","title":"Organellar RNA processing and translation regulation","description":"The cluster\u2019s GO annotations concentrate on organellar RNA metabolism\u2014mitochondrial and chloroplast/plastid RNA processing, transcription, and RNA modification\u2014with also a term for regulation of mitochondrial translation. A nuclear spliceosomal splicing term appears but the dominant signal ties to organellar RNA processing and expression control, suggesting a cohesive role in organelle gene expression.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0009451","count":1},{"id":"GO:0042793","count":1},{"id":"GO:0000961","count":1}]},{"hash":"559862390120037838","title":"Immune signaling and lymphocyte differentiation","description":"The cluster is strongly enriched for immune-related GO terms, including innate immune response, T cell receptor signaling, Fc receptor\u2013mediated signaling, and B cell differentiation. While some terms touch on general signaling or development, the dominant theme is immune cell signaling and lymphocyte maturation, justifying the label. ","confidence":"High","size":21,"edges":57,"triangles":73,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0006915","count":3},{"id":"GO:0048666","count":3}]},{"hash":"1226545959797209441","title":"Spliceosome Assembly and RNA Processing","description":"This cluster is dominated by GO terms tied to RNA splicing and processing (spliceosomal complex assembly, mRNA splicing via spliceosome, snRNP assembly) and RNA maturation steps (SSU-rRNA maturation) as well as related nuclear transport and transcription termination processes, suggesting a cohesive set of proteins involved in RNA processing and gene expression regulation within the nucleus. The ABA and water deprivation signals appear as secondary contextual associations, possibly reflecting stress-related transcriptional regulation. Overall, the core theme is spliceosome-mediated RNA processing and maturation. ","confidence":"High","size":21,"edges":134,"triangles":458,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009737","count":17},{"id":"GO:0042633","count":13},{"id":"GO:0009414","count":13},{"id":"GO:0000245","count":13},{"id":"GO:0045292","count":13}]},{"hash":"1273964074238528912","title":"Membrane lipid biosynthesis and trafficking","description":"The GO terms cluster around phosphatidylinositol biosynthesis, endomembrane system organization, and protein localization to the plasma membrane, plus autophagosome assembly, all pointing to membrane biogenesis and vesicle trafficking; a few unrelated/obsolete terms are present but do not alter the core theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031321","count":1},{"id":"GO:0014066","count":1},{"id":"GO:0032288","count":1},{"id":"GO:1902635","count":1},{"id":"GO:0035855","count":1}]},{"hash":"1243282585621746178","title":"Ribosome biogenesis and rRNA maturation","description":"The cluster is strongly enriched for ribosome-related processes: maturation of SSU/LSU/5.8S rRNA, ribosomal large subunit biogenesis, and formation of the translation preinitiation complex, indicating a coherent theme of ribosome assembly and translation initiation. Additional terms like mRNA splicing, cell division, vesicle transport, and DNA repair appear but are less central to the main ribosome-focused functions. ","confidence":"High","size":21,"edges":107,"triangles":265,"max_degree":20,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0000462","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0000466","count":4}]},{"hash":"413395247497924309","title":"Ribosome Biogenesis and Large Subunit Assembly","description":"This cluster is dominated by GO terms related to ribosome assembly/biogenesis, maturation/export of the large ribosomal subunit, and translation, indicating proteins involved in ribosome production and protein synthesis. The convergence on rRNA maturation and large subunit processes with translation supports a cohesive ribosome-focused group.","confidence":"High","size":21,"edges":187,"triangles":1006,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0000055","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0042255","count":2}]},{"hash":"1523352238951122038","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":9,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0000398","count":6},{"id":"GO:0042273","count":6},{"id":"GO:0000462","count":6},{"id":"GO:0000463","count":6}]},{"hash":"388147046911932504","title":"Actin Cytoskeleton and Cell Division","description":"The top GO terms point to actin-related processes (cortical localization, thin filament assembly) and cell division activities (vacuole inheritance, mitotic cytokinesis, chromosome movement), with additional notes on cell polarity and development. This suggests a cohesive theme centered on cytoskeleton-driven organization during division and related developmental processes.","confidence":"High","size":21,"edges":68,"triangles":106,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0000011","count":6},{"id":"GO:0000281","count":6},{"id":"GO:0010628","count":5},{"id":"GO:0043983","count":5},{"id":"GO:1904623","count":5}]},{"hash":"1509585916881199930","title":"Chromatin modification and protein acetylation","description":"This cluster is dominated by GO terms tied to chromatin and histone modification (histone H4 acetylation, subtelomeric heterochromatin formation, centromeric cohesion) and a range of protein post-translational modifications (N-terminal propionylation, putrescine and spermidine acetylation). While other terms like angiogenesis or melatonin biosynthesis appear, the strongest signal centers on chromatin regulation and acetylation-related processes, supporting a label focused on chromatin modification and protein acetylation.","confidence":"Medium","size":21,"edges":67,"triangles":107,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":8},{"id":"GO:0030187","count":7},{"id":"GO:0043967","count":7},{"id":"GO:0006526","count":7},{"id":"GO:0032920","count":7}]},{"hash":"1255626859612282947","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":101,"triangles":219,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045454","count":15},{"id":"GO:0006626","count":14},{"id":"GO:1900035","count":14},{"id":"GO:0006458","count":14},{"id":"GO:0030433","count":14}]},{"hash":"826623169313978601","title":"Ciliogenesis and mitotic spindle dynamics","description":"The cluster is dominated by terms tied to ciliary biology (motile cilium assembly, intraciliary retrograde transport), microtubule-based movement, and mitosis (mitotic spindle orientation, mitotic cell cycle), plus vesicle transport along the ER-Golgi axis. This pattern suggests proteins that function in ciliogenesis and in microtubule-dependent cellular processes governing cell division and intracellular trafficking, with a few transcription-related terms as possible noise. ","confidence":"High","size":21,"edges":26,"triangles":19,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0071560","count":2},{"id":"GO:0044458","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0000132","count":2}]},{"hash":"267161346333586351","title":"GPI-anchor Biosynthesis and Membrane Lipids","description":"This cluster centers on membrane-associated lipid biosynthesis and modification: strong signals from GPI anchor biosynthetic process, phospholipid and sphingolipid metabolism, and phospholipid turnover, along with related transport and membrane-associated processes. While there are some signaling-related terms present (e.g., Wnt-related and germ cell repulsion), the core theme is synthesis and remodeling of membrane lipids and GPI-anchored proteins that decorate the cell surface, which justifies the label. ","confidence":"Medium","size":21,"edges":129,"triangles":396,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":5},{"id":"GO:0006655","count":4},{"id":"GO:0006668","count":3},{"id":"GO:0046839","count":3},{"id":"GO:0035233","count":3}]},{"hash":"730300601426315930","title":"Unknown","description":"The top GO terms span several unrelated biological areas: RNA metabolism (RNA catabolic process, ribosome assembly, mRNA splicing regulation), intracellular trafficking (ER-Golgi and endosome-Golgi transport), and immune/developmental processes (interferon signaling regulation, neutrophil chemotaxis, skeletal development). With no evident shared function or interaction scaffold among the proteins (edges are zero), there is no cohesive theme to name this cluster beyond Unknown.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006401","count":1},{"id":"GO:0001501","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0032689","count":1}]},{"hash":"883548376035421635","title":"Golgi and Synaptic Vesicle Transport","description":"The top GO terms cluster around vesicle trafficking through the Golgi and secretory pathway (ER-to-Golgi, intra-Golgi, Golgi ribbon formation, SNARE complex assembly) as well as synaptic vesicle dynamics (postsynaptic receptor insertion, presynaptic vesicle fusion, and long-term potentiation), indicating a cohesive function in Golgi-mediated transport and synaptic vesicle trafficking.","confidence":"High","size":21,"edges":56,"triangles":69,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":9},{"id":"GO:0006888","count":8},{"id":"GO:0090161","count":8},{"id":"GO:0006891","count":8},{"id":"GO:0035493","count":7}]},{"hash":"834807318069383288","title":"Heart development and cardiac muscle signaling","description":"Based on the top GO terms, the cluster is enriched for heart development and cardiac muscle contraction, suggesting a cardiovascular focus. Additional terms like VEGF response, insulin receptor signaling, and endosomal transport point to broader signaling and trafficking processes that can intersect cardiac pathways. Some terms (sensory perception of sound, microtubule-based movement) are less specific, but the dominant heart-related terms justify this label as a cohesive theme. Confidence: Medium","confidence":"","size":21,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046329","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0060048","count":2},{"id":"GO:0007018","count":1}]},{"hash":"1469471665483603159","title":"Fe-S cluster biogenesis","description":"This cluster's top GO terms center on [2Fe-2S] cluster assembly and maturation, indicating involvement in Fe-S biogenesis. Some terms reference iron-responsive transcription regulation, but the dominant theme is Fe-S cluster assembly and maturation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044571","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0097428","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0051220","count":1}]},{"hash":"1595484324747332090","title":"Unknown","description":"There are no GO terms or network connections to indicate a shared function among the 21 proteins (edges = 0, triangles = 0, max degree = 0). With most proteins re-added by ReCIPE but no interactions, a cohesive theme cannot be inferred.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1268061176271528867","title":"Unknown","description":"All 21 proteins show no interactions (edges) and no GO terms are provided, so there is no detectable functional theme linking them. Without shared annotations or network structure, a concise, representative label cannot be determined.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1333540586942538965","title":"Unknown","description":"There are no GO terms or network connections to define a shared function for these 21 proteins (edges/triangles = 0, max degree 0), so a specific functional label cannot be inferred.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2123897516572483466","title":"Unknown","description":"There are no GO terms or functional connections reported for this cluster (Edges 0, Triangles 0, Max Degree 0, no top terms), so there is no clear shared function to name it. Unknown is the safest label given the lack of interpretable signal.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2034583192746152499","title":"Zinc Ion Homeostasis and Transport","description":"The GO terms are dominated by zinc-related processes: zinc import across the plasma membrane, intracellular zinc ion homeostasis, detoxification of zinc, and response to zinc starvation, with related cadmium transport. This pattern strongly points to a cluster of zinc transporters and metal homeostasis proteins, rather than developmental roles (the limb development term appears incidental).","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090305","count":2},{"id":"GO:1903615","count":1},{"id":"GO:0006882","count":1},{"id":"GO:0060173","count":1},{"id":"GO:0006831","count":1}]},{"hash":"402138262251885090","title":"Unknown","description":"There are no edges and no enriched GO terms; the top terms list is empty, so there is no clear shared function among the proteins. The cluster thus cannot be confidently assigned a specific biological role.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1628007657416745276","title":"Unknown","description":"There are no GO terms or functional signals provided for this cluster (top terms are empty and the network has no edges), so a cohesive biological function cannot be inferred. The ReCIPE remark indicates some proteins were re-added, but without shared annotations a meaningful label cannot be assigned.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1809500943001328558","title":"Vacuolar amino acid transporters","description":"The top GO terms point to transmembrane import/export into the vacuole for multiple amino acids (serine, proline, glutamate, histidine, lysine, arginine, tyrosine) and related transport activity, indicating a cohesive set of proteins functioning as vacuolar amino acid transporters. This shared role in shuttling amino acids across the vacuolar membrane underpins the cluster\u2019s theme.","confidence":"High","size":21,"edges":46,"triangles":27,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0090516","count":13},{"id":"GO:0015824","count":13},{"id":"GO:0090515","count":13},{"id":"GO:0089708","count":13},{"id":"GO:1901481","count":13}]},{"hash":"2294005657389199076","title":"Sphingolipid and Fatty Acid Biosynthesis","description":"This cluster is enriched for GO terms related to sphingosine and sphinganine metabolism, as well as monounsaturated fatty acid biosynthesis and general fatty acid response, indicating a core association with lipid biosynthesis pathways (sphingolipids and fatty acids). Some outlier terms like photoinhibition and tarsal gland development are present but do not outweigh the predominant lipid metabolism signal, supporting a cohesive label around lipid synthesis.","confidence":"High","size":21,"edges":110,"triangles":318,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0034435","count":5},{"id":"GO:0046512","count":4},{"id":"GO:0010873","count":4},{"id":"GO:0010205","count":4},{"id":"GO:0044130","count":4}]},{"hash":"911079418614628531","title":"Developmental Regulation and Signaling","description":"This cluster combines terms tied to tissue development (heart, cerebellar cortex, hippocampus), immune differentiation, and signaling through transcriptional regulation and phosphorylation, plus VEGF response. The proteins likely participate in broad developmental signaling networks rather than a single tissue- or process-specific function.","confidence":"Medium","size":20,"edges":29,"triangles":3,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046638","count":4},{"id":"GO:0021695","count":4},{"id":"GO:0043433","count":4},{"id":"GO:0033138","count":4},{"id":"GO:0007507","count":4}]},{"hash":"469541411559113042","title":"Mitotic Cell Cycle Regulation and Ubiquitination","description":"The terms cluster around mitosis and ubiquitin signaling (mitotic cell cycle; G1/S and G2/M transitions; K11-linked ubiquitination; histone H2A monoubiquitination), suggesting a cohesive module of cell cycle control and chromatin regulation, with some related developmental processes appearing as secondary context.","confidence":"Medium","size":20,"edges":154,"triangles":699,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0070979","count":5},{"id":"GO:0000082","count":5},{"id":"GO:0000086","count":5},{"id":"GO:0045773","count":4}]},{"hash":"1581206895823550339","title":"Immune cell differentiation and cytoskeletal remodeling","description":"The top GO terms point to hematopoietic/immune lineage differentiation (T cell differentiation in thymus, alpha-beta T cell differentiation, granulocyte differentiation, hematopoietic stem cell proliferation), suggesting a cluster centered on immune cell development. Additional terms like filopodium assembly and endosomal transport imply cytoskeletal dynamics and intracellular trafficking, consistent with immune cell migration and signaling regulated by Rho pathways. Some entries are obsolete, but the overall pattern supports a theme of immune differentiation intertwined with cytoskeletal remodeling.","confidence":"Medium","size":20,"edges":33,"triangles":17,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0033077","count":1},{"id":"GO:1903955","count":1},{"id":"GO:0046638","count":1},{"id":"GO:0071425","count":1}]},{"hash":"1415326151543563993","title":"Spindle Assembly and Microtubule Dynamics","description":"The major GO terms describe microtubule-based processes critical for chromosome segregation and spindle organization (centrosome separation, meiotic spindle orientation, spindle midzone assembly, mitotic metaphase chromosome recapture, microtubule depolymerization) and related nuclear migration and development contexts (root development, neuron projection maintenance). These collectively point to a cluster of proteins involved in organizing the microtubule cytoskeleton during mitosis/ meiosis and associated cellular movements. A few terms reflect broader cytoskeletal roles or stress-related remodeling, but the unifying theme is spindle/spindle-associated microtubule dynamics.","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:1990535","count":20},{"id":"GO:0010938","count":20},{"id":"GO:0007100","count":20},{"id":"GO:0051296","count":20},{"id":"GO:0033624","count":20}]},{"hash":"599705731112447847","title":"Ribosome biogenesis and translation initiation","description":"This cluster is enriched for GO terms tied to ribosome assembly and translation: 90S preribosome and large-subunit biogenesis, formation of the translation preinitiation complex, translation reinitiation, and general ribosome biogenesis. The presence of cell-cycle terms likely reflects coupling of ribosome production with proliferation, but the dominant pattern is ribosome assembly and initiation of translation.","confidence":"High","size":20,"edges":184,"triangles":1036,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0070262","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0000278","count":4}]},{"hash":"1514327739761796948","title":"Proton Motive Force and Ion Transport","description":"This cluster is driven by GO terms indicating membrane-associated transport and energy generation, especially sodium ion transport, proton transmembrane transport, vacuolar acidification, and proton motive force\u2013driven ATP synthesis, suggesting a shared theme of using proton gradients to power transport and energy production. Some terms like osteoblast differentiation, protein secretion by the Type III secretion system, and proteasome storage granule assembly appear as noise or cross-annotation and do not fit the core theme.","confidence":"Medium","size":20,"edges":54,"triangles":46,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":3},{"id":"GO:0006814","count":3},{"id":"GO:0007035","count":3},{"id":"GO:0042777","count":3},{"id":"GO:0015991","count":3}]},{"hash":"692522922032933018","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":188,"triangles":1105,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":7},{"id":"GO:0000472","count":6},{"id":"GO:0000480","count":6},{"id":"GO:0042273","count":5},{"id":"GO:0000447","count":5}]},{"hash":"1519723130413097896","title":"Chloroplast Translation and Plastid Biogenesis","description":"These proteins are tied to plastid/chloroplast gene expression and protein handling: plastid transcription, chloroplast organization, translation, protein import into organelles, membrane targeting/insertion, and protein folding. A high-light response term also fits chloroplast function. The bitter-taste detection term appears unrelated noise. ","confidence":"Medium","size":20,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0050790","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0009644","count":1}]},{"hash":"497195080187367621","title":"Mitosis exit and DNA repair with ubiquitination","description":"The cluster includes terms tied to mitotic progression and exit (exit from mitosis, sister chromatid biorientation) and DNA damage response (regulation of DSB repair via HR, UV-damage excision repair, HR regulation), with a strong emphasis on protein modification via ubiquitination (and methylation). While there are some vesicle trafficking and lipid metabolism terms present, the strongest shared theme is cell-cycle control and DNA repair coordinated with protein modification pathways.","confidence":"Medium","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0006479","count":3},{"id":"GO:0031134","count":3},{"id":"GO:0010569","count":3},{"id":"GO:0010458","count":3}]},{"hash":"1330635861022055933","title":"Cell Cycle and Mitochondrial Regulation","description":"Top terms indicate a core theme around mitosis and cell-cycle control (mitotic cytokinesis; negative regulation of G1/S transition) together with mitochondrial functions (regulation of mitochondrial membrane permeability; protein import into mitochondrial matrix). This points to a link between mitochondrial state and cell division. Some developmental GO terms appear, which may reflect broad annotations rather than a cohesive signal, so the label emphasizes the mitochondrial\u2013cell-cycle axis.","confidence":"Medium","size":20,"edges":101,"triangles":308,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0000281","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0048364","count":2},{"id":"GO:1904888","count":2},{"id":"GO:0010867","count":1}]},{"hash":"274203835752902470","title":"Antiviral Innate Immunity and Xenophagy","description":"These terms collectively indicate an antiviral innate immune program\u2014responses to dsRNA, LPS signaling, and interferon-beta production\u2014with active xenophagy, suggesting autophagic targeting of intracellular pathogens; some metabolism-related terms hint at immune-metabolic regulation but do not change the overall theme.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:1904262","count":3},{"id":"GO:0034198","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0043330","count":2}]},{"hash":"2171328874656361399","title":"Unknown","description":"There are no GO terms or interactions provided to reveal a shared function among the 20 proteins, so no coherent theme can be inferred. Without annotations or connections, the appropriate label is Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"47510905493451562","title":"Redox Homeostasis and Oxidative Stress Response","description":"The cluster is dominated by redox-related terms: cellular oxidant detoxification, cell redox homeostasis, and cellular response to oxidative stress, plus protein deglutathionylation. While a few terms are tangential, the shared theme is redox regulation and oxidative stress response.","confidence":"High","size":20,"edges":75,"triangles":165,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":12},{"id":"GO:0045454","count":8},{"id":"GO:0071473","count":6},{"id":"GO:0030416","count":6},{"id":"GO:0080058","count":6}]},{"hash":"877618928978702657","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":101,"triangles":228,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0006337","count":2},{"id":"GO:0043085","count":2},{"id":"GO:0000350","count":1},{"id":"GO:0000387","count":1}]},{"hash":"337197915272238973","title":"Metabolic redox homeostasis and nitrosative stress","description":"The top GO terms cluster around diverse metabolic pathways (retinol, fructose, prostaglandin, furaldehyde metabolism; pyruvate fermentation) and redox-related processes (oxidation-reduction, response to nitrosative stress, peptidyl-cysteine S-nitrosylation) with a secondary note of transcriptional activity. This pattern suggests a theme of metabolism intertwined with redox balance and nitrosative stress response, rather than a single isolated pathway.","confidence":"Medium","size":20,"edges":68,"triangles":156,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042572","count":7},{"id":"GO:0046370","count":7},{"id":"GO:0055114","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0006693","count":4}]},{"hash":"118927975855158216","title":"Vesicle trafficking and melanosome assembly","description":"The top GO terms cluster around COPII vesicle coating, ER-to-Golgi and intra-Golgi transport, plus melanosome assembly and pigmentation, with regulation of GTPase activity linking to vesicle dynamics and autophagy intersecting with vesicular processes. Together they point to a common function in secretory vesicle trafficking and pigment-related organelle biogenesis, despite some peripheral terms like cuticle development. This label captures the main shared function of the cluster.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048208","count":1},{"id":"GO:0042338","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0043473","count":1},{"id":"GO:1903232","count":1}]},{"hash":"800969009156756358","title":"RNA splicing regulation and miRNA silencing","description":"The cluster's terms are dominated by RNA processing and post-transcriptional regulation: spliceosome components, splicing regulation, splice-site recognition, and miRNA/ncRNA\u2013mediated gene silencing, indicating a coherent theme around RNA maturation and silencing rather than a single metabolic pathway. Minor terms about development or glycan processing appear incidental.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010977","count":1},{"id":"GO:0001889","count":1},{"id":"GO:0006491","count":1},{"id":"GO:0072001","count":1},{"id":"GO:0031047","count":1}]},{"hash":"1701995141269447578","title":"Immune Homeostasis and Developmental Signaling","description":"The prominent terms are T cell and B cell homeostasis, with additional signals tied to development (proepicardium/mesendoderm) and responses to growth factors and hormones, suggesting a theme of immune regulation intertwined with developmental signaling, hence the label.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0043029","count":4},{"id":"GO:0001782","count":4},{"id":"GO:1902172","count":3},{"id":"GO:0044344","count":3},{"id":"GO:0071385","count":3}]},{"hash":"1476236586969182247","title":"Unknown","description":"This cluster provides no GO term signal or interactions to unify the proteins; all proteins appear isolated with no enriched functions, so a coherent function name cannot be inferred.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1153756286855928330","title":"Unknown","description":"The cluster has 20 proteins but no GO terms or connections are reported (Edges: 0, Triangles: 0, Max Degree: 0), so a coherent functional label cannot be inferred.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"242370907746574818","title":"Unknown","description":"The GO terms span cardiac electrophysiology (ventricular depolarization, action potential), peroxisomal protein import, glycerol and lipid metabolism, gluconeogenesis, NADPH regeneration, and cAMP signaling, with no single coherent function linking them. Therefore no clear cluster label can be assigned beyond Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060373","count":1},{"id":"GO:0016558","count":1},{"id":"GO:0006650","count":1},{"id":"GO:2000010","count":1},{"id":"GO:0006094","count":1}]},{"hash":"831815305086066470","title":"Unknown","description":"Top Terms are empty and there are no edges, so there is no shared biological function to infer. Without GO enrichment or interaction data, the cluster cannot be given a specific label.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2092962393391216142","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning meiosis, glycogen metabolism, plant stomatal movement, early embryonic mitotic cycles, general transcription, ER stress, leptin signaling, mammary gland proliferation, viral transcription, and more. With only single-term associations and no clear, shared function linking the proteins, there isn\u2019t a cohesive theme to define a meaningful cluster name beyond Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007129","count":1},{"id":"GO:0005979","count":1},{"id":"GO:1990069","count":1},{"id":"GO:0035186","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1665687534134446907","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":25,"triangles":9,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3}]},{"hash":"992301299421187864","title":"Mitosis, Chromatin Regulation, and DNA Repair","description":"The proteins in this cluster are enriched for cell division and mitosis-related terms (cell division, exit from mitosis), chromatin regulation (histone ubiquitination regulation, heterochromatin formation), and genome maintenance (postreplication DNA repair) with a developmental context (embryonic development). This points to a cohesive role in coordinating cell cycle progression, chromatin state, and DNA damage response, rather than disparate functions.","confidence":"High","size":19,"edges":52,"triangles":68,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:0051026","count":8},{"id":"GO:0001701","count":8},{"id":"GO:0033182","count":7},{"id":"GO:0061186","count":7}]},{"hash":"1706651781994123181","title":"Genome maintenance and mitotic machinery","description":"This cluster shows strong enrichment for DNA-templated transcription, DNA replication, nucleotide-excision repair, and key mitotic processes (centrosome separation, spindle assembly, cell division). These terms point to a cohesive group of proteins involved in genome integrity and progression through mitosis. The presence of translation-related terms and stress granule disassembly suggests additional RNA metabolism and gene-expression coordination that often accompanies cell-cycle control, but the dominant theme remains genome maintenance and mitosis.","confidence":"Medium","size":19,"edges":58,"triangles":58,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006412","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0006260","count":3}]},{"hash":"1132248513190101716","title":"RNA processing and gene expression regulation","description":"The top terms are dominated by RNA processing and regulation: mRNA splicing via spliceosome and its positive regulation, post-transcriptional gene silencing, and maturation of SSU-rRNA, indicating a cluster centered on RNA metabolism and expression control, with supporting signals from DNA replication/damage tolerance and a developmental term that may reflect broad gene-expression roles. ","confidence":"High","size":19,"edges":135,"triangles":665,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006301","count":9},{"id":"GO:0000398","count":9},{"id":"GO:0048026","count":9},{"id":"GO:0006605","count":9},{"id":"GO:0016441","count":9}]},{"hash":"1345342652714655807","title":"Cardiac Morphogenesis and Glucose Regulation","description":"The terms point mainly to heart development and function (ventricular cardiac muscle morphogenesis, heart trabecula formation, regulation of cardiac conduction) with metabolic signaling roles (response to glucose, negative regulation of insulin secretion). A couple of terms are less directly related (amyloid fibril formation, steroid hormone receptor complex assembly), but the dominant pattern ties cardiac morphogenesis to metabolic regulation.","confidence":"Medium","size":19,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006463","count":1},{"id":"GO:1990000","count":1},{"id":"GO:0016925","count":1},{"id":"GO:1903779","count":1},{"id":"GO:0009749","count":1}]},{"hash":"943187227853845993","title":"Unknown","description":"The GO terms are highly diverse, including immune response (lipopolysaccharide), RNA modification, ROS regulation, neural signaling, ion transport, regeneration, epithelial differentiation, and learning. With no clear shared biological process or network pattern (edges are zero), there isn\u2019t a coherent theme to label the cluster beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":2},{"id":"GO:0002943","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0007270","count":1},{"id":"GO:0006820","count":1}]},{"hash":"1558631613955021170","title":"Male meiosis and germline development","description":"Based on the GO terms, the strongest recurring signal is around male meiosis and germline differentiation (male meiosis cytokinesis, chromosome segregation, and male germ-line cyst formation). There are also hints of post-transcriptional regulation (negative regulation of translation, deadenylation) that can accompany germline development. Some terms (dex dexamethasone response, lung development) appear as outliers, suggesting heterogeneity, but the core pattern centers on male germline meiosis processes. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071549","count":1},{"id":"GO:0019827","count":1},{"id":"GO:0030324","count":1},{"id":"GO:0000289","count":1},{"id":"GO:0007112","count":1}]},{"hash":"2215591878735950037","title":"Mitochondrial Import and Cell Cycle Regulation","description":"The cluster centers on mitochondrial functions (protein import into the mitochondrial matrix, regulation of mitochondrial membrane permeability) alongside cell-cycle control signals (negative regulation of G1/S transition, cell division), suggesting a cohesive theme where mitochondrial regulation intersects with cell-cycle progression and broader metabolic control. Other terms like GTPase regulation and ubiquitination may reflect regulatory layers connected to these core processes.","confidence":"High","size":19,"edges":14,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:2000134","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0010867","count":3},{"id":"GO:0070940","count":3},{"id":"GO:1903740","count":3}]},{"hash":"1141932423542715265","title":"Innate immune signaling suppression","description":"Based on the GO terms, the cluster is dominated by negative regulation of innate immune pathways, including type II interferon production and RIG-I/MDA-5 signaling, suggesting proteins that dampen antiviral responses. A few terms touch on mRNA splicing and other processes, but the strongest signal is suppression of innate immune signaling.","confidence":"High","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032689","count":1},{"id":"GO:0039534","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0090023","count":1},{"id":"GO:0051897","count":1}]},{"hash":"171194289628875129","title":"Unknown","description":"The GO terms are highly diverse with no dominant shared function: biosynthesis of NAD+ and CoA, DNA repair, various phosphorylation and nucleotide processes, microtubule movement, and responses to VEGF and sound. With no prevalent theme or enrichment, there isn't a clear functional cluster to name beyond Unknown.","confidence":"","size":19,"edges":17,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0009435","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0015937","count":1}]},{"hash":"2084774815803993659","title":"Unknown","description":"The top terms are scattered across RNA processing, metabolism, organelle organization, and translation, with only a couple of terms pointing to mitochondrial translation and tRNA biosynthesis. The lack of a cohesive, single function linking all proteins makes it unclear to assign a specific label, so an Unknown category is most appropriate.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":1},{"id":"GO:0009062","count":1},{"id":"GO:0007029","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0070681","count":1}]},{"hash":"486167804988912290","title":"Mitochondrial energy metabolism and insulin signaling","description":"The top terms point to mitochondrial functions (membrane fission, ATP transport, nucleotide import into mitochondrion, CoA transport) and energy regulation, with additional links to insulin/IGF signaling and thermogenesis, amino acid starvation response, and cellular energy homeostasis. This combination suggests a cluster centered on mitochondrial energy metabolism tightly coupled with insulin signaling pathways.","confidence":"High","size":19,"edges":154,"triangles":801,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0061179","count":17},{"id":"GO:1990314","count":16},{"id":"GO:0030302","count":16},{"id":"GO:0090149","count":16},{"id":"GO:1990519","count":16}]},{"hash":"1527578324501427816","title":"Developmental polarity and fate specification","description":"The terms cluster around establishing cell polarity and fate during development (planar polarity, asymmetric localization, axis specification, germarium/oocyte fate decisions, germ-band extension), with some neural differentiation references (myelination) that still fit the broader theme of developmental patterning.","confidence":"Medium","size":19,"edges":39,"triangles":34,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0021535","count":1},{"id":"GO:0090250","count":1},{"id":"GO:0007314","count":1},{"id":"GO:0045167","count":1},{"id":"GO:0007294","count":1}]},{"hash":"874508245671791668","title":"Unknown","description":"There are no shared GO terms to anchor a function, and with zero edges/triangles, plus a note of re-added proteins but no functional context, no coherent label can be assigned.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1859146666581559992","title":"Unknown","description":"ReCIPE added 20 proteins but there are no edges, triangles, or GO-term signals to tie their functions together, and no Top Terms are provided. Without a shared functional theme or enrichment, there\u2019s no basis for a specific label beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"681954942540504534","title":"Unknown","description":"The cluster shows no edges or GO term enrichment to tie the proteins to a common function, and thus no unifying theme can be inferred. Without a detectable shared function, the appropriate label is Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"944846634450230414","title":"Unknown","description":"No GO terms or interaction data are provided (edges 0, triangles 0, top terms empty), so there is no coherent functional theme linking these proteins. Without such signal, the appropriate label is Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1744370475851274725","title":"Peroxisome Biogenesis and Dynamics","description":"The cluster is dominated by GO terms related to peroxisomes: organization, fission, and size regulation, suggesting proteins that participate in peroxisome formation and maintenance. The brown fat differentiation term is less central but may reflect metabolic context rather than core function. Overall, peroxisome biogenesis/dynamics is the best unifying theme.","confidence":"High","size":19,"edges":23,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0050873","count":1},{"id":"GO:0007031","count":1},{"id":"GO:0044375","count":1},{"id":"GO:0016559","count":1}]},{"hash":"1579777204318383928","title":"Unknown","description":"Insufficient functional signal: there are no top GO terms and no connections among the 19 proteins, so there isn't a shared process, component, or function to name. Therefore the cluster is Unknown with None confidence.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2038488972479804582","title":"Unknown","description":"There are no GO terms or functional connections evident in the cluster (Top Terms is empty and there are no edges or triangles), so a shared function cannot be inferred; ReCIPE-readded proteins with degree 0 do not provide a functional signal.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1357320373669665307","title":"Endosome trafficking and synaptic signaling","description":"The cluster includes receptor recycling, regulation of endosome size, and glutamatergic synaptic transmission, along with Rho signaling and sphingosine biosynthesis, pointing to membrane trafficking and lipid-signaling processes at synapses. A few terms about transcription regulation appear peripheral, but the core theme is endosomal trafficking and synaptic signaling.","confidence":"Medium","size":19,"edges":35,"triangles":43,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0051036","count":1}]},{"hash":"2041853209226024523","title":"Ribosome Biogenesis and Vesicle Trafficking","description":"This cluster combines strong signals for translation and ribosome biogenesis with significant terms related to vesicle transport, lysosome targeting, and exosome assembly/secretion, suggesting a module involved in coordinating protein synthesis with intracellular trafficking and secretion (alongside a sporulation-related assembly term that may reflect a broader vesicle/secretory context). ","confidence":"Medium","size":18,"edges":10,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0048025","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006622","count":1},{"id":"GO:1903551","count":1}]},{"hash":"213803355735979449","title":"Mitosis and transcription during development","description":"These proteins appear enriched for mitotic processes (mitotic cell cycle, cell division, APC/C-dependent catabolic process) and transcription (DNA-templated transcription), with developmental context (multicellular development, skeletal system development). A minority of terms reflect stress or immune responses (cadmium response, defense to Gram-positive bacteria), but the dominant pattern is cell-cycle regulation coupled with transcription during development.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071276","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0051301","count":3},{"id":"GO:2001162","count":3}]},{"hash":"834206209463084041","title":"Sterol and fatty acid metabolism with hormone response","description":"This cluster centers on lipid metabolism (fatty acid oxidation; cholesterol and ergosterol biosynthesis; lipase regulation) and hormonal signaling (FSH and peptide hormones), with added xenobiotic/toxic stimulus responses and IL-8 production, suggesting a lipid-focused module that also links hormone signaling and environmental stress.","confidence":"Medium","size":18,"edges":23,"triangles":12,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0019395","count":6},{"id":"GO:0071372","count":6},{"id":"GO:0071375","count":6},{"id":"GO:0042493","count":6},{"id":"GO:0009636","count":5}]},{"hash":"693174690243428258","title":"RNA pseudouridylation enzymes","description":"The top GO terms point to widespread pseudouridine synthesis across rRNA, snRNA, tRNA, and mRNA, i.e., RNA modification by pseudouridylation, plus related transcription-associated processing terms. This cohesive signal suggests the cluster is enriched for enzymes that catalyze pseudouridylation of various RNAs, rather than a broader metabolic or signaling function. Confidence: High","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":1},{"id":"GO:0009301","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0031120","count":1},{"id":"GO:1990481","count":1}]},{"hash":"274843560833973441","title":"Cytoskeleton and mitosis-related cilia functions","description":"The top terms are largely centered on the cytoskeleton and cell division, including microtubule anchoring, preprophase band assembly, and mitotic DNA replication termination, together with epithelial cilium movement involved in left-right asymmetry. This points to a core theme of cytoskeletal dynamics guiding mitosis and ciliogenesis, with a few peripheral terms related to development and signaling.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071171","count":1},{"id":"GO:1902979","count":1},{"id":"GO:0009640","count":1},{"id":"GO:0050999","count":1},{"id":"GO:0040022","count":1}]},{"hash":"1044295829013777530","title":"Mixed neural development and immune signaling","description":"This cluster shows strong signals for neural development and synaptic processes (visual perception, corpus callosum development, positive regulation of synapse assembly, axonogenesis), suggesting a neural function theme. At the same time, immune-related terms (B cell receptor signaling, interferon-beta production, response to dsRNA) indicate immune signaling involvement. Because the terms span both neural development and immune pathways without a single dominant function, the label reflects a mixed neural-immune signaling cluster.","confidence":"Medium","size":18,"edges":14,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0022038","count":2},{"id":"GO:0051965","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0043330","count":2}]},{"hash":"386392202425161246","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms related to ribosome biogenesis, cytoplasmic translation, and nuclear export of the ribosomal large subunit, with additional signals of cell division/cell cycle processes. The core functions point to a module of ribosome assembly and protein synthesis, with possible coordination to cell cycle progression.","confidence":"High","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006400","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0042254","count":2}]},{"hash":"2238019869065636242","title":"Unknown","description":"The top GO terms are widely scattered across chromatin modification, nucleotide biosynthesis, development, cilium movement, and spermatid differentiation, with only single-term annotations and no interaction edges, making it unclear what cohesive function ties these proteins together.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":1},{"id":"GO:0051568","count":1},{"id":"GO:0006183","count":1},{"id":"GO:0021591","count":1},{"id":"GO:1902176","count":1}]},{"hash":"2023327503621762929","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":11,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0097309","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0032211","count":1},{"id":"GO:1904744","count":1},{"id":"GO:0000390","count":1}]},{"hash":"280958724497773438","title":"Purine Nucleotide Metabolism and Salvage","description":"The dominant GO terms point to nucleotide metabolism: ADP and CDP biosynthesis, AMP salvage, purine ribonucleotide interconversion, and ITP metabolism, plus broad phosphorylation activity. This suggests the cluster collectively functions in nucleotide biosynthesis and salvage rather than a tissue-specific process, though a few development terms may reflect multifunctional annotations. High","confidence":"","size":18,"edges":107,"triangles":344,"max_degree":17,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0046939","count":8},{"id":"GO:0046940","count":8},{"id":"GO:0006172","count":6},{"id":"GO:0044209","count":6},{"id":"GO:0046041","count":6}]},{"hash":"432902828261974074","title":"Chromosome maintenance and mitosis","description":"Based on the prominent GO terms for DNA replication, DNA-templated transcription, cell division, and CENP-A chromatin assembly (with supportive microtubule severing), the cluster appears centered on chromosome maintenance and mitotic progression, despite some additional terms related to ER transport and protein quality control; these latter terms may reflect housekeeping roles layered onto core cell-cycle functions.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0051013","count":4},{"id":"GO:0061641","count":4}]},{"hash":"1496085912697217639","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":149,"triangles":756,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":15},{"id":"GO:0042254","count":5},{"id":"GO:0000027","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0002181","count":2}]},{"hash":"862395372393938421","title":"Unknown","description":"The top terms are a mixed bag including mitochondrial-related hints (though marked obsolete), redox/homeostasis and sulfur transfer chemistry, some protein modification processes, and unrelated developmental terms. With no coherent functional theme linking these terms and no edges between proteins, there isn't a clear, unified function to label this cluster. Therefore the appropriate label is Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072321","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0045039","count":1},{"id":"GO:2000220","count":1},{"id":"GO:0018192","count":1}]},{"hash":"2262340368369850838","title":"TLR3-mediated antiviral response","description":"This cluster shows strong signals for Toll-like receptor 3 signaling, TRIF/MyD88-independent pathways, dsRNA response, and interferon/chemokine production, indicating an innate antiviral immune function. A couple of terms (spermatogenesis, axis specification) may be less related noise, but the core theme is dsRNA sensing and antiviral signaling.","confidence":"High","size":18,"edges":37,"triangles":30,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007283","count":2},{"id":"GO:0000132","count":2},{"id":"GO:0034138","count":2},{"id":"GO:0045078","count":2},{"id":"GO:0007352","count":2}]},{"hash":"453763005241679229","title":"Immune signaling and neurite outgrowth","description":"The top GO terms mix immune-related signaling (T cell receptor signaling, beta selection, mast cell degranulation) with neuronal morphogenesis and cytoskeletal remodeling (filopodium assembly, dendrite morphogenesis, axon extension), suggesting proteins that participate in immune signaling pathways and in neurite outgrowth/cytoskeletal dynamics. This dual theme is best captured by the label \u201cImmune signaling and neurite outgrowth.\u201d","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050852","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0048813","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0046330","count":2}]},{"hash":"30417816159593593","title":"Transcription and Translation with Growth Signals","description":"The most represented terms are translation and DNA-templated transcription, with additional links to mitotic cell cycle, development, and growth-related processes (e.g., budding growth and nervous system development). This points to a cluster centered on gene expression machinery (transcription/translation) that interfaces with growth and developmental signaling, rather than a single, narrow function. Confidence: Medium","confidence":"","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0043087","count":2},{"id":"GO:0007399","count":2}]},{"hash":"1290909472877912598","title":"Metabolic Regulation and Biosynthesis","description":"The cluster features GO terms spanning biosynthetic pathways (pyrimidine nucleotide biosynthesis, ergosterol biosynthetic process, sulfate assimilation) along with regulatory/signaling processes (negative regulation of lipase activity, NO production regulation, peptide hormone response). This pattern suggests proteins involved in coordinating metabolism with cellular signaling, rather than a single, cohesive pathway, warranting a label focused on metabolic regulation and biosynthesis.","confidence":"Medium","size":18,"edges":51,"triangles":127,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0060192","count":3},{"id":"GO:0071375","count":3},{"id":"GO:0032770","count":3},{"id":"GO:0006221","count":3},{"id":"GO:0006696","count":3}]},{"hash":"359932392549809403","title":"Symbiont-Mediated Immune Evasion","description":"The GO term indicates the proteins are involved in evading the host immune response via a symbiotic relationship, so this label captures the shared theme. With only one annotation, the label reflects the main function but may not encompass all protein roles, so confidence is Medium.","confidence":"Medium","size":18,"edges":12,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0020012","count":1}]},{"hash":"1316773856087685824","title":"ERAD and Retrograde Protein Transport","description":"The cluster is enriched for ubiquitin-dependent ERAD, misfolded protein transport, and retrograde Golgi-to-ER trafficking, plus post-translational targeting to membranes, indicating a group involved in ER quality control and secretory-pathway protein handling. Some outlier terms (lipoprotein remodeling, chlorophyll catabolic processes) likely reflect broad annotations, but the dominant signals point to ER proteostasis and trafficking functions.","confidence":"Medium","size":18,"edges":20,"triangles":10,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0031204","count":2},{"id":"GO:0070843","count":2},{"id":"GO:0006890","count":1},{"id":"GO:0034374","count":1}]},{"hash":"152077721711309381","title":"Unknown","description":"There are no GO terms listed and the network has zero edges, triangles, and no degree, providing no shared functional signal to define a cohesive label for the 18 proteins.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2096100315369861972","title":"Transmembrane Transporters","description":"This cluster appears to consist of membrane transport proteins, as indicated by multiple transmembrane transport GO terms across diverse substrates (nitrate/nitrite, xenobiotics, sugars like arabinose and sialic acid, potassium, and neurotransmitter loading), pointing to a cohesive transport-related function rather than a single substrate.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010197","count":4},{"id":"GO:0015706","count":3},{"id":"GO:0042128","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0015739","count":2}]},{"hash":"721329587666908216","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070651","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0071042","count":1},{"id":"GO:0016973","count":1},{"id":"GO:0071051","count":1}]},{"hash":"677262162791329903","title":"Nuclear gene expression and cell cycle","description":"Top GO terms point to nuclear processes of gene expression and cell division: transcription (DNA-templated), RNA processing (splicing and rRNA processing), and ribosome biogenesis, along with mitotic events such as spindle orientation. Some stress and ciliary-related terms are present but likely represent ancillary connections rather than defining the cluster.","confidence":"Medium","size":17,"edges":58,"triangles":108,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000398","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000278","count":2}]},{"hash":"139484692817196017","title":"Retroviral integration and latency","description":"The top GO terms center on retroviral processes: RNA-templated DNA synthesis (reverse transcription), DNA integration and recombination, establishment of proviral latency, and viral entry into the host nucleus, plus host cell entry and vesicle transport hijacked during infection. This cohesive set points to retroviral lifecycle stages and genome integration as the cluster\u2019s core function.","confidence":"High","size":17,"edges":47,"triangles":56,"max_degree":10,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006278","count":4},{"id":"GO:1903704","count":4},{"id":"GO:0075713","count":4},{"id":"GO:0075732","count":4},{"id":"GO:0046718","count":4}]},{"hash":"541920252653002603","title":"ER-to-Golgi Vesicle Transport","description":"The cluster shows enrichment for GO terms tied to movement of proteins between the endoplasmic reticulum and the Golgi (COPII vesicle coating, intracellular protein transport). This points to the secretory pathway as the unifying theme, with a few additional terms related to development that may reflect broader roles of secretion in morphogenesis. Overall, the dominant signal is ER-to-Golgi trafficking.","confidence":"High","size":17,"edges":33,"triangles":40,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0035149","count":2},{"id":"GO:0080119","count":2},{"id":"GO:0035909","count":2},{"id":"GO:0048081","count":2}]},{"hash":"1065065770787170943","title":"Intracellular trafficking and ribosome biogenesis","description":"The cluster is enriched for vesicle-mediated transport (ER to Golgi, endosome pathways), plus ribosome biogenesis and protein complex assembly, pointing to a set of proteins involved in intracellular cargo movement and ribosome production. Some terms like viral process or NK cell degranulation may reflect broader cellular contexts or incidental annotations, but the dominant pattern ties to trafficking and ribosome-related assembly.","confidence":"Medium","size":17,"edges":78,"triangles":156,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0000060","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0042254","count":2}]},{"hash":"503160885248284366","title":"Chromatin regulation and RNA processing","description":"The cluster is driven by histone methylation (H3-K4 and H3-K79), DNA-templated transcription, and mRNA splicing terms, suggesting a shared role in chromatin state controlling transcription and RNA processing; other signals (stress and cell division) appear secondary. ","confidence":"Medium","size":17,"edges":28,"triangles":27,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051568","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0007338","count":1},{"id":"GO:0007018","count":1}]},{"hash":"246048900333744003","title":"Unknown","description":"The top GO terms span DNA replication/repair, RNA silencing (RISC assembly, mRNA cleavage, rRNA processing), vesicle formation, and signaling, with no single cohesive function linking all terms. This suggests a mix of diverse roles rather than a well-defined cluster function.","confidence":"","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070914","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0033314","count":2},{"id":"GO:0070676","count":2}]},{"hash":"594540251002673793","title":"Fatty acid metabolism and transport","description":"The cluster is dominated by GO terms related to lipid metabolism, especially fatty acid beta-oxidation (including acyl-CoA oxidase), long-chain and medium-chain fatty acid metabolic processes, and fatty acid transport, suggesting a cohesive theme around lipid utilization and energy production. A few terms (antibiotic biosynthesis, acetylcholine biosynthesis, and ovarian follicle growth) appear as outliers or annotations that may reflect broader biosynthetic capabilities or dataset noise, but do not override the lipid-centric pattern. Overall, the set most strongly points to fatty acid metabolism and transport as the core function of the cluster.","confidence":"Medium","size":17,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0032000","count":1},{"id":"GO:0015909","count":1},{"id":"GO:0001547","count":1},{"id":"GO:0019254","count":1}]},{"hash":"1997813352513062870","title":"Unknown","description":"The terms are scattered across stress responses (lithium, dexamethasone), development (hippocampus, gliogenesis), metabolism (hepatocyte homeostasis), cardiac hypertrophy, splicing, and histone modifications, with no common biological process tying the cluster together. Because there is no clear shared function among the proteins suggested by the GO annotations, I cannot assign a precise, representative label.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010226","count":1},{"id":"GO:0000388","count":1},{"id":"GO:0071549","count":1},{"id":"GO:1990654","count":1},{"id":"GO:0014898","count":1}]},{"hash":"1407262622163871197","title":"Transcriptional Regulators and Signaling Modulators","description":"This cluster includes GO terms tied to nuclear processes (DNA-templated transcription, DNA replication, ribosomal gene transcription) and various signaling/regulatory pathways (apoptosis regulation, Ras signaling, cGMP signaling, receptor signaling, T cell receptor signaling). The proteins likely function as regulators coordinating transcription and signaling rather than a single, narrow function, making this broad yet cohesive label appropriate.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0010754","count":2}]},{"hash":"1652150715494715951","title":"Neural Development and Plasticity Regulators","description":"The top GO terms are dominated by neural-related processes (substantia nigra development, regulation of long-term neuronal synaptic plasticity, and neuron apoptotic regulation), suggesting a cluster geared toward brain development and activity-dependent plasticity. A few terms relate to general cell differentiation or other processes (cell cycle exit, cell polarity), and a couple may be annotation noise (e.g., cell wall biosynthesis, skeletal muscle satellite cell migration). Overall, the theme centers on neural development and plasticity functions.","confidence":"Medium","size":17,"edges":20,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043525","count":1},{"id":"GO:0090316","count":1},{"id":"GO:0071338","count":1},{"id":"GO:0048169","count":1},{"id":"GO:0090334","count":1}]},{"hash":"1914817776278637212","title":"RNA processing and translation initiation control","description":"These proteins cluster around post-transcriptional gene regulation: strong signals for translation initiation/reinitiation steps (preinitiation complex formation, reinitiation), coupled with RNA processing events (mRNA splicing and spliceosome regulation, splice site recognition) and RNA silencing pathways (miRNA- and ncRNA-mediated silencing), as well as mRNA stability under stress. This combination suggests a coordinated role in controlling gene expression at the RNA processing and translation levels.","confidence":"High","size":17,"edges":105,"triangles":393,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0002188","count":11},{"id":"GO:0001731","count":11},{"id":"GO:0031047","count":10},{"id":"GO:0075525","count":10},{"id":"GO:1905663","count":10}]},{"hash":"252023223260287354","title":"Neural development and synaptic signaling","description":"This cluster shows strong signals for neural-related functions: visual perception and long-term synaptic potentiation, plus Schwann cell development, which together point to neural development and synaptic activity. It also includes broader developmental processes (multicellular organism development, heart development) and phosphorylation-based signaling (protein phosphorylation, peptidyl-threonine phosphorylation), suggesting signaling pathways active in development and neural contexts. This combination makes Neural development and synaptic signaling the best single-theme label.","confidence":"Medium","size":17,"edges":5,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010800","count":4},{"id":"GO:0006468","count":4},{"id":"GO:0014044","count":4},{"id":"GO:0060291","count":4},{"id":"GO:0007601","count":4}]},{"hash":"210942205226845450","title":"Glycolysis and Pentose Phosphate Pathway","description":"The cluster is strongly enriched for glycolysis (glycolytic process, canonical glycolysis) and the pentose phosphate shunt (oxidative and non-oxidative branches), plus gluconeogenesis, pointing to central carbohydrate metabolism and energy/redox balance. The presence of a hypoxia response term aligns with glycolytic upregulation under low oxygen. Other terms (angiogenesis, plasminogen activation) appear tangential to core metabolism. Confidence reflects a coherent metabolic theme. ","confidence":"High","size":17,"edges":106,"triangles":455,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006098","count":4},{"id":"GO:0006096","count":3},{"id":"GO:0006094","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0009052","count":3}]},{"hash":"1624404137967099441","title":"Unknown","description":"No GO terms or interactions tie these 17 proteins together (edges and triangles are zero), so no common function is identifiable. Unknown is the most appropriate label.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1860578201991677420","title":"Unknown","description":"There are no edges or enriched GO terms linking these 17 proteins, and no top terms are provided, so a coherent functional label cannot be inferred.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"96342144981644996","title":"Cytoskeleton Regulation and Golgi Vesicle Trafficking","description":"The cluster is enriched for cytoskeleton organization, centrosome/Golgi maintenance, cell morphogenesis, and post-Golgi vesicle transport, plus positive regulation of GTPase activity. This points to a functional module coordinating cytoskeletal dynamics with Golgi- and vesicle trafficking. While a few terms (methylglyoxal response, galactose metabolism, potassium transport) appear, they are less central to the core theme.","confidence":"High","size":17,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0051595","count":1},{"id":"GO:0071805","count":1},{"id":"GO:0006012","count":1},{"id":"GO:0000902","count":1}]},{"hash":"1104833795724748407","title":"Unknown","description":"No GO terms are provided for this cluster (Top Terms is empty), so I can't identify a shared biological function to name it. The network metrics (3 edges, max degree 3, no triangles) and the note about proteins re-added by ReCIPE offer limited context but do not reveal a common GO-driven theme. As a result, I assign Unknown with None confidence.","confidence":"","size":17,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[]},{"hash":"193198622835437143","title":"Bacterial LPS and exopolysaccharide biosynthesis","description":"The cluster\u2019s top GO terms are dominated by lipopolysaccharide and related exopolysaccharide biosynthetic processes (O antigen, LPS core, colanic acid), with associated sugar biosynthesis (heptose, rhamnose, galactose). This points to a cohesive theme of surface polysaccharide production in Gram-negative bacteria, despite a couple outliers likely representing annotation noise. ","confidence":"High","size":17,"edges":83,"triangles":231,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0009242","count":8},{"id":"GO:0055114","count":8},{"id":"GO:0009243","count":8},{"id":"GO:0009699","count":8},{"id":"GO:0006012","count":8}]},{"hash":"836241084700463353","title":"Unknown","description":"This cluster has no edges and no GO terms linked to its proteins, so there is no clear shared function to label; it likely represents noise or unannotated proteins.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1814475481356166776","title":"Unknown","description":"This cluster has no shared GO terms or network connections (Top Terms is empty; Edges, Triangles, and Max Degree are all zero), so there is no coherent functional theme to name it after. Without evidence of common function, a reliable label cannot be assigned.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"253828825979664963","title":"ER-Golgi N-glycan trimming and ERAD","description":"The cluster is dominated by GO terms related to N-glycan trimming and glycoprotein quality control in the ER and Golgi (e.g., Golgi mannose trimming, trimming of mannose branches, and the ubiquitin-dependent ERAD pathway), indicating involvement in glycosylation processing and ER-associated degradation. A minor term about L-leucine transport is peripheral and does not define the cluster\u2019s main function.","confidence":"High","size":17,"edges":43,"triangles":71,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0036512","count":3},{"id":"GO:0036510","count":3},{"id":"GO:1904154","count":3},{"id":"GO:1904381","count":3},{"id":"GO:0006486","count":3}]},{"hash":"1264712546301929460","title":"Autophagy-related organelle turnover","description":"The set of GO terms centers on autophagy processes: autophagy of mitochondrion, reticulophagy, and protein localization to the phagophore assembly site, which collectively point to autophagy-driven turnover of organelles. Additional terms related to protein folding and complex oligomerization suggest assembly and function of autophagy-related protein complexes. Overall, the cluster appears to reflect autophagy- and organelle turnover functions.","confidence":"High","size":17,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051259","count":1},{"id":"GO:0032781","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0030218","count":1}]},{"hash":"364198341472545960","title":"TLR3 Antiviral Signaling and Cytokine Production","description":"The cluster is dominated by GO terms related to Toll-like receptor signaling (TLR3 pathway, MyD88-independent signaling), response to dsRNA, and regulation of interferon and chemokine production, fitting a cohesive innate antiviral immune response. A couple of terms such as lipid A biosynthesis and tRNA export appear as outliers but do not change the overall theme.","confidence":"High","size":17,"edges":41,"triangles":35,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0009245","count":2},{"id":"GO:0034138","count":1},{"id":"GO:0045078","count":1},{"id":"GO:0007352","count":1},{"id":"GO:0002756","count":1}]},{"hash":"655793262472550526","title":"ER-Golgi vesicle transport","description":"This cluster is dominated by GO terms tied to protein transport, especially vesicle movement from the ER to the Golgi and retrograde transport from endosomes to the Golgi, indicating a core role in the secretory pathway. Additional signals related to actin ubiquitination and TORC1 signaling suggest links to cytoskeletal regulation and nutrient-responsive control of trafficking, but the strongest, most consistent theme is ER-Golgi vesicle transport and related intracellular trafficking. High","confidence":"","size":17,"edges":133,"triangles":638,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":2},{"id":"GO:0006888","count":1},{"id":"GO:0042147","count":1},{"id":"GO:1904262","count":1},{"id":"GO:0006915","count":1}]},{"hash":"1773773935940750946","title":"Oxidative Stress Response and DNA Repair","description":"The cluster shows a strong enrichment for oxidative stress response (cellular response to hydrogen peroxide) and DNA repair processes (base-excision repair, DNA recombination), with accompanying apoptosis and xenobiotic response signals. While some terms indicate broader signaling (cAMP, phosphatidylinositol dephosphorylation), the dominant theme ties oxidative damage protection to genome maintenance.","confidence":"Medium","size":16,"edges":18,"triangles":1,"max_degree":6,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0070301","count":4},{"id":"GO:0046856","count":4},{"id":"GO:2000327","count":3},{"id":"GO:0071375","count":3},{"id":"GO:0006284","count":3}]},{"hash":"1600663128541916047","title":"ER-Golgi vesicle trafficking and ERAD","description":"This cluster primarily groups proteins involved in vesicle transport within the secretory pathway: ER-to-Golgi and Golgi-to-ER trafficking, plus ER-associated degradation (ERAD) and related sorting pathways such as the Cvt pathway. Microtubule-based movement supports these transport processes, and autophagy-related transport to the vacuole aligns with the Cvt term. A few terms related to cytokinesis and fertilization are also present but likely reflect broader cytoskeletal connections rather than distinct functions. Overall, the cluster seems centered on intracellular transport and protein quality control in the secretory pathway.","confidence":"Medium","size":16,"edges":51,"triangles":79,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0007112","count":2}]},{"hash":"786010682455435501","title":"Vertebrate Development and Growth","description":"The top GO terms center on vertebrate developmental processes\u2014spinal cord development, neural tube closure, skeletal system development, multicellular organism development, and growth\u2014indicating a cohesive theme around organismal development and growth. Some terms reflect stress or immune responses (cadmium response, defense to Gram-positive bacteria), but the dominant pattern points to developmental biology, so the label captures the core function of the cluster.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":3},{"id":"GO:0071276","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0007275","count":2}]},{"hash":"186443533758838060","title":"Exosome Biogenesis and Epithelial Polarity","description":"This cluster is enriched for terms related to exosome biology (positive regulation of exosomal secretion, exosome assembly, intralumenal vesicle formation) and epithelial cell junctions/polarity (adherens junction organization, maintenance of apical/basal polarity, regulation of cell migration). Together, they suggest a vesicle trafficking module linked to epithelial cell adhesion and polarity. A lone term like penicillin biosynthetic process appears unrelated noise.","confidence":"Medium","size":16,"edges":11,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1903543","count":1},{"id":"GO:1903553","count":1},{"id":"GO:0030334","count":1},{"id":"GO:0070676","count":1},{"id":"GO:0045199","count":1}]},{"hash":"1406051724310324526","title":"Stimulus-Responsive Signaling and RNA Regulation","description":"The top GO terms point to cellular responses to external stimuli such as growth factors (FGF), steroids (glucocorticoids), and PMA, as well as keratinocyte apoptosis regulation, T cell homeostasis, and development events (proepicardium, mesendoderm). In addition, there are RNA-level processes (deadenylation-dependent/independent decay and mRNA localization) indicating post-transcriptional control. Together, these suggest a cluster of proteins involved in signaling pathways activated by stimuli and coordinated regulation of gene expression, across development and immune contexts.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902172","count":2},{"id":"GO:0044344","count":2},{"id":"GO:0071385","count":2},{"id":"GO:0000288","count":2},{"id":"GO:1904628","count":2}]},{"hash":"987308692856200825","title":"Neural and cardiac development and signaling","description":"The top GO terms cluster around development of brain regions (hippocampus, cerebellar cortex) and heart, suggesting a role in neural and cardiac morphogenesis. Additional terms point to transcriptional activity (DNA-templated transcription) and signaling, including phosphorylation regulation and calcium signaling (VEGF response, calcium import), indicating these proteins participate in developmental transcriptional control and signaling in neural and cardiac contexts.","confidence":"High","size":16,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021766","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0021695","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0043433","count":3}]},{"hash":"1480514355263581426","title":"Unknown","description":"The GO terms span very diverse processes (ER/SRP-dependent protein targeting, immune signaling such as interleukin-2 and interferon production, neutrophil homeostasis, and cardiac/retinal development), with no single dominant function tying the proteins together. Therefore a generic Unknown label best fits.","confidence":"","size":16,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006614","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0032743","count":1},{"id":"GO:0019934","count":1},{"id":"GO:0001780","count":1}]},{"hash":"2073413193295412725","title":"Endosomal trafficking and receptor signaling regulation","description":"The GO terms point to endocytic processes and regulation of receptor activity: negative regulation of growth hormone receptor signaling, negative regulation of protein localization to the cell surface, and late endosome to vacuole transport via multivesicular body sorting. Together they suggest a coherent theme of endosomal trafficking, particularly ESCRT-mediated sorting to lysosome/vacuole, which modulates surface receptor signaling. Despite only one hit per term, this common mechanism best explains the cluster\u2019s functions.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060400","count":1},{"id":"GO:2000009","count":1},{"id":"GO:0032511","count":1}]},{"hash":"1244015439121597624","title":"Actin Cytoskeleton Dynamics and Myofibril Assembly","description":"The top GO terms point to actin-related processes: actin nucleation, actin filament network formation, and substrate-dependent cell migration, suggesting a shared role in remodeling of the actin cytoskeleton. Additional terms touch development and muscle-related assembly (brain development, female gamete generation, and cardiac myofibril assembly), indicating the cluster may include proteins involved in actin dynamics across developmental and muscle contexts. Although there are some outlier terms and no reported edges, the core theme centers on actin-based structural changes and assembly.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0061164","count":1},{"id":"GO:1904171","count":1},{"id":"GO:0045010","count":1},{"id":"GO:0010467","count":1}]},{"hash":"1896208313388019583","title":"Vacuolar acidification and metal ion homeostasis","description":"This cluster shows strong signals of vacuolar function (vacuole organization, protein targeting to vacuole, vacuolar acidification) and proton-driven transport, plus ion homeostasis (sodium and copper). The combination points to vacuolar proton-pump activity and metal ion storage/handling as the core theme.","confidence":"Medium","size":16,"edges":98,"triangles":340,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0007033","count":2},{"id":"GO:0042777","count":2},{"id":"GO:0006814","count":2},{"id":"GO:0006623","count":2},{"id":"GO:0006878","count":2}]},{"hash":"2279417777958553676","title":"Ribosome Biogenesis and Translation","description":"Based on GO terms, this cluster is dominated by ribosome-related processes: ribosome biogenesis, large/small subunit maturation, rRNA maturation, translation initiation and translation itself, and formation of preinitiation complexes. This points to proteins involved in assembling ribosomes and enabling protein synthesis.","confidence":"High","size":16,"edges":81,"triangles":192,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0051260","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0000463","count":3}]},{"hash":"330125601351385099","title":"Organelle Protein Targeting","description":"The top GO terms center on directing proteins to specific organelles and assembling membrane complexes (ER targeting, mitochondrial inner-membrane insertion, vacuolar V-type ATPase assembly), i.e., a common theme of protein trafficking and insertion into organelle membranes.","confidence":"Medium","size":16,"edges":45,"triangles":40,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":1},{"id":"GO:0032979","count":1},{"id":"GO:0070072","count":1},{"id":"GO:0045047","count":1},{"id":"GO:0006465","count":1}]},{"hash":"2023437879534980043","title":"Neural and cardiac development transcription regulators","description":"The top GO terms cluster around development in neural (hippocampus, cerebellar cortex) and heart tissues, coupled with DNA-templated transcription and regulation of transcription factor activity. Additional terms point to signaling modulation and broader regulatory processes (phosphorylation, autophagy, calcium signaling, dexamethasone response), suggesting these proteins function as transcriptional/regulatory regulators shaping neural and cardiac development. Confidence reflects a coherent but broad regulatory theme rather than a single well-defined pathway.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021766","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0021695","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0043433","count":2}]},{"hash":"1253700638302690929","title":"Mitochondrial-ER protein import and redox homeostasis","description":"This cluster centers on GO terms related to mitochondrial intermembrane space protein import, ER-to-cytosol retrograde transport, ER retention of proteins, and responses to oxidative stress and iron homeostasis. Together these suggest a theme of mitochondrial/ER protein handling and quality control under redox stress, with some autophagy regulation signals. Confidence is Medium.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045041","count":1},{"id":"GO:0006879","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0016242","count":1},{"id":"GO:0055114","count":1}]},{"hash":"2051157018445253374","title":"Golgi Trafficking and Secretion Regulators","description":"Most terms point to the secretory pathway and Golgi function (COPI-coated vesicle budding, positive regulation of protein exit from ER, and Golgi ribbon formation) and to Wnt secretion, suggesting the proteins mainly participate in ER\u2013Golgi trafficking and secretion; a few terms involve translation or developmental processes that are less central to the core theme.","confidence":"Medium","size":16,"edges":68,"triangles":190,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:1990090","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0070863","count":1},{"id":"GO:1902003","count":1}]},{"hash":"1915145247697904521","title":"Unknown","description":"Top terms are absent (no GO terms) and there are no edges or interactions, so a coherent shared function cannot be inferred for this cluster.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1713910117066255798","title":"Unknown","description":"There are no shared GO terms, no connections (edges/triangles), and no functional signals to pair the proteins; thus no coherent function can be inferred from the cluster.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"392768349522650483","title":"Unknown","description":"No GO terms or meaningful interactions are reported (Edges: 0, Max Degree: 0) and the only note is \"20 proteins re-added by ReCIPE,\" which does not specify a shared function. Without a detectable theme or enrichment, the cluster cannot be confidently named.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2207832906752850170","title":"Proteolysis","description":"Cluster appears centered on the proteolysis process (protein cleavage), but only one protein is annotated for this term and there are no reported interactions within the cluster, suggesting limited evidence for a tightly connected proteolytic module. It likely reflects a loose grouping of proteins with proteolysis-related function or potential involvement in proteolytic pathways.","confidence":"Low","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":1}]},{"hash":"2133511557348154245","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":53,"triangles":60,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006626","count":13},{"id":"GO:1900035","count":13},{"id":"GO:0006458","count":13},{"id":"GO:0030433","count":13},{"id":"GO:0035719","count":13}]},{"hash":"1225092670364791051","title":"Unknown","description":"There are no apparent interactions (Edges: 0, Triangles: 0) and no GO terms provided to define a shared function, so a coherent functional label cannot be inferred for this cluster.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1941532442431297065","title":"Unknown","description":"This cluster has no edges and no enriched GO terms to suggest a common function, and the proteins show no shared functional signal, so a descriptive label cannot be inferred.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"754735778560376345","title":"Unknown","description":"There are no shared GO terms or network connections among the proteins (no edges, no terms), so there is no coherent function to label the cluster. The absence of top terms and interactions means the cluster cannot be meaningfully named beyond Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"343906750796418917","title":"Symbiont-driven immune modulation","description":"Top GO terms point to host immune interaction, including antigen processing and presentation via MHC class II, regulation/suppression of MHC II biosynthesis, regulation of tolerance induction, and symbiont-mediated suppression of host adaptive immune response, as well as perturbation of ubiquitin-like protein modification. A couple of biosynthetic terms for cutin and suberin are present but less central. Overall, the cluster seems to reflect how symbionts modulate host immunity and tolerance.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010143","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0002495","count":2},{"id":"GO:0010345","count":2},{"id":"GO:0039648","count":2}]},{"hash":"1147776113235806482","title":"Fatty acid elongation and sphingolipid biosynthesis","description":"The cluster\u2019s top GO terms cluster tightly around fatty acid biosynthesis and elongation (long-, very long-, saturated, unsaturated, polyunsaturated, and long-chain acyl-CoA) and include sphingolipid biosynthesis, indicating a cohesive lipid metabolism module. A few terms like swim bladder development or pheromone metabolism are less central and may reflect species-specific biology, but overall the dominant signal is lipid biosynthesis. ","confidence":"High","size":16,"edges":82,"triangles":208,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0042759","count":2},{"id":"GO:0006636","count":2},{"id":"GO:0048794","count":2},{"id":"GO:0042810","count":2},{"id":"GO:0042761","count":2}]},{"hash":"2152872474817021445","title":"Gene expression control and proteostasis","description":"The cluster is dominated by terms related to gene expression regulation and protein handling: RNA splicing, transcription, chromatin remodeling, ribosome biogenesis, and translation initiation, along with ubiquitin-proteasome\u2013dependent degradation and ERAD pathways, plus TORC1 signaling. A couple of terms referencing immune signaling (defense to Gram-positive bacteria, TGF-beta response) suggest broader regulatory context, but the core theme centers on coordinating gene expression with protein synthesis and turnover.","confidence":"Medium","size":15,"edges":49,"triangles":69,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0071560","count":3},{"id":"GO:0001731","count":3}]},{"hash":"179605327680952423","title":"Calcium-regulated vesicle trafficking","description":"This cluster is dominated by intracellular trafficking functions: Golgi-to-plasma membrane transport, ER exit regulation, Golgi ribbon formation, and endosome-to-Golgi transport, plus lysosome targeting. The calcium-responsive GO term and the regulation of synaptic vesicle exocytosis point to Ca2+-dependent control of vesicle trafficking and secretion, while VEGF receptor-2 signaling suggests membrane receptor trafficking aspects. The ABA signaling term is less central but does not override the primary vesicle transport and calcium-regulated themes. Overall, the data align with a membrane-traffic and calcium-signaling cluster.","confidence":"High","size":15,"edges":15,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071277","count":2},{"id":"GO:0036324","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0006622","count":1}]},{"hash":"1832570903301446493","title":"Nuclear DNA replication and transcription machinery","description":"Top terms cluster around nuclear DNA replication, DNA-templated transcription, and cell division, suggesting a shared role in genome maintenance and cell cycle progression. Some terms point to broader cellular homeostasis, including protein turnover and organelle-associated processes, with heart development likely reflecting broader developmental regulatory roles rather than a primary function.","confidence":"Medium","size":15,"edges":14,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1903715","count":2}]},{"hash":"1996888443831069703","title":"Keratinocyte differentiation and epithelial junction regulation","description":"This cluster is enriched for keratinocyte differentiation, tight junction assembly regulation, and signaling pathways (Wnt, Hippo) that govern epithelial barrier integrity and tissue homeostasis; defense and xenophagy terms suggest skin innate responses but the dominant theme is epithelial maturation and junction maintenance.","confidence":"Medium","size":15,"edges":8,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":4},{"id":"GO:0006915","count":3},{"id":"GO:0090314","count":3},{"id":"GO:0090263","count":3},{"id":"GO:2000810","count":3}]},{"hash":"1386061908635734664","title":"Nucleolar ribosome biogenesis and transcription","description":"The top GO terms cluster around nucleolar processes and ribosome production, including ribosome biogenesis, nucleologenesis, and rRNA/tRNA transcription by RNA polymerases I\u2013III, plus regulatory ncRNA\u2013mediated heterochromatin formation, indicating a nucleolar/ribosome-focused function. A few terms related to CNS myelin maintenance and lipid metabolism may reflect annotation noise or multi-function proteins.","confidence":"Medium","size":15,"edges":26,"triangles":17,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0001172","count":2},{"id":"GO:0006366","count":2},{"id":"GO:0031048","count":2},{"id":"GO:0017126","count":2}]},{"hash":"485190048347665727","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":1},{"id":"GO:0036265","count":1},{"id":"GO:0006353","count":1},{"id":"GO:0098507","count":1},{"id":"GO:0034968","count":1}]},{"hash":"1688545053969721395","title":"Oocyte pole plasm assembly and oskar mRNA localization","description":"This cluster centers on pole plasm assembly and the organization/polarization of the oocyte microtubule cytoskeleton, plus regulation and maintenance of oskar mRNA localization, which define oocyte posterior polarity. The presence of EGFR/Ras signaling and development terms adds context to oogenesis and developmental signaling pathways, reinforcing the oocyte polarity and mRNA localization theme. Confidence: High","confidence":"","size":15,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007315","count":1},{"id":"GO:0008103","count":1},{"id":"GO:0046579","count":1},{"id":"GO:0016325","count":1},{"id":"GO:0007275","count":1}]},{"hash":"1372089079219746832","title":"Unknown","description":"The proteins have GO terms spread across diverse processes (osteoblast differentiation, proteasome storage granule assembly, type III secretion, amino acid/ion homeostasis, lipid metabolism, transport, and transcription regulation), with no clear unifying function or pathway, so a cohesive label cannot be assigned to this cluster. ","confidence":"","size":15,"edges":87,"triangles":296,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0001649","count":2},{"id":"GO:1902906","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0030254","count":2},{"id":"GO:0090463","count":2}]},{"hash":"80499093589234856","title":"Unknown","description":"There are no edges, no GO terms, and no identifiable shared function among the 15 proteins, so no coherent label can be assigned to this cluster.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1244484296639048252","title":"Unknown","description":"There are no GO terms or network connections to tie these 15 predicted proteins together, and Top Terms are empty with 0 edges/triangles. Without functional annotations or interactions, a meaningful, specific label cannot be assigned beyond Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"142374049996082154","title":"Chromatin remodeling and histone modification","description":"Top GO terms cluster around chromatin dynamics, including nucleosome disassembly, subtelomeric heterochromatin formation, and histone modification processes such as acetylation and ubiquitination, suggesting the proteins work together in chromatin regulation. A few metabolic or signaling terms appear as secondary signals, but the core theme is chromatin structure regulation.","confidence":"High","size":15,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006491","count":2},{"id":"GO:0035335","count":1},{"id":"GO:0030389","count":1},{"id":"GO:0016573","count":1},{"id":"GO:0006348","count":1}]},{"hash":"1193071628522039517","title":"Unknown","description":"There are no GO terms provided to define a common function for the proteins, and the network is very sparse (2 edges, max degree 1) with no triangles, so a cohesive biological theme cannot be inferred.","confidence":"","size":15,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"488496863047075074","title":"Unknown","description":"This cluster has no GO terms listed and minimal connectivity (one edge, max degree 1), providing no shared functional signal to define a common role. Without annotations to guide a theme, a meaningful label cannot be determined.","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"28285170155984246","title":"Unknown","description":"There are no GO terms or shared annotations listed, and the cluster has 0 edges/triangles, indicating no apparent functional connection among its proteins. Without enrichment or common terms, a specific label cannot be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2140061637573161202","title":"Mitochondrial energy metabolism and protein processing","description":"The top terms cluster around mitochondrial respiration, Complex IV assembly, and proton-motive-force\u2013driven ATP synthesis, suggesting a core theme of mitochondrial energy production. While there are a few outlier terms related to protein maturation and trafficking, the mitochondrial functions dominate, making this label representative of the cluster\u2019s main function.","confidence":"Medium","size":15,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000185","count":1},{"id":"GO:0006817","count":1},{"id":"GO:0051604","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0006506","count":1}]},{"hash":"2178023536344139955","title":"Unknown","description":"The GO terms are diverse (nucleotide transport, metabolism, and a mitotic spindle checkpoint signal) with no single shared function linking all members, and there are no interactions detected among them. This cluster does not reveal a coherent module, so a specific functional label cannot be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015862","count":2},{"id":"GO:0035364","count":2},{"id":"GO:0008216","count":1},{"id":"GO:0006749","count":1},{"id":"GO:0032516","count":1}]},{"hash":"1468196031010882196","title":"DNA replication and repair under stress","description":"Proteins here are enriched for core replication and repair activities (DNA replication, primer synthesis, DNA unwinding/topology, nucleotide-excision repair) along with stress responses (SOS response, hypoxia). This suggests a cohesive module coordinating genome maintenance under cellular stress.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006268","count":11},{"id":"GO:0009432","count":11},{"id":"GO:0006269","count":10},{"id":"GO:0006306","count":10},{"id":"GO:0006260","count":10}]},{"hash":"211449356156807776","title":"Golgi and Endocytic Vesicle Trafficking","description":"This cluster is dominated by GO terms describing vesicle transport centered on the Golgi, including Golgi localization, Golgi to vacuole transport, ER-to-Golgi transport, retrograde transport from endosomes to Golgi, and endocytosis. Together they point to a cohesive set of proteins involved in the Golgi\u2013endosome\u2013vacuole secretory and trafficking pathway, with a few unrelated terms likely incidental. ","confidence":"High","size":14,"edges":36,"triangles":37,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006896","count":1},{"id":"GO:0006623","count":1},{"id":"GO:0021691","count":1},{"id":"GO:0051645","count":1},{"id":"GO:0016185","count":1}]},{"hash":"1798474329303647644","title":"Cell growth, metabolism, and protein homeostasis","description":"This cluster centers on core cellular processes: glycolysis (energy metabolism), ribosome biogenesis (protein synthesis capacity), autophagy (protein quality control and turnover), ER-to-Golgi trafficking (protein processing/trafficking), and cell division, with additional stress response signals (cadmium) and regulation of GTPase activity. While a brain development term appears, the dominant themes point to general metabolism and proteome maintenance rather than a specific tissue function, making a label around cellular growth/metabolism/protein homeostasis appropriate.","confidence":"Medium","size":14,"edges":19,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0007420","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0006888","count":2}]},{"hash":"1803433713483250175","title":"DNA metabolism and RNA processing","description":"This cluster is enriched for core DNA metabolic processes (replication, unwinding, recombination, transcription termination, and damage tolerance) alongside multiple RNA processing terms (splicing via the spliceosome and its regulation), plus regulatory ncRNA silencing and stress-granule localization. Together these suggest a functional theme around nuclear DNA maintenance coupled with post-transcriptional RNA regulation, with a developmental context indicated by cranial skeleton morphogenesis. ","confidence":"Medium","size":14,"edges":70,"triangles":213,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0048701","count":6},{"id":"GO:0006268","count":5}]},{"hash":"90701433551262112","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":89,"triangles":340,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0000184","count":4}]},{"hash":"1876592226951886843","title":"DNA Replication and Pre-Replication Complex Assembly","description":"These proteins are strongly linked to DNA replication processes, including DNA replication itself, premeiotic DNA replication, and pre-replicative complex assembly, with support from DNA strand elongation and mitotic initiation terms. The dominant theme is replication machinery and initiation during the cell cycle, so the label precisely captures the cluster\u2019s core function; a minor unrelated term about meristem growth does not override the main signal.","confidence":"High","size":14,"edges":54,"triangles":156,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006268","count":7},{"id":"GO:0006260","count":7},{"id":"GO:0051260","count":4},{"id":"GO:0006279","count":4},{"id":"GO:0006267","count":4}]},{"hash":"293495513143874437","title":"Unknown","description":"The top GO terms span transcription, nervous system structure, muscle regulation, immune responses, and signaling with no clear single theme linking them, so a coherent functional label cannot be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0021629","count":2},{"id":"GO:0014809","count":2},{"id":"GO:0016203","count":2},{"id":"GO:0043330","count":2}]},{"hash":"1020269942923505565","title":"Vacuolar amino acid transporters","description":"GO terms show transmembrane movement of various amino acids into and out of the vacuole (serine, glutamate, histidine, tyrosine, lysine, arginine, proline) and even lithium transport, indicating a cohesive set of proteins involved in vacuolar amino acid and related ion transport across the vacuolar membrane.","confidence":"High","size":14,"edges":49,"triangles":75,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0090516","count":7},{"id":"GO:0015824","count":7},{"id":"GO:0090515","count":7},{"id":"GO:0089708","count":7},{"id":"GO:1901481","count":7}]},{"hash":"1868395411016728259","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":88,"triangles":329,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0000466","count":5},{"id":"GO:0000472","count":4},{"id":"GO:0000480","count":4}]},{"hash":"202049339256396733","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":59,"triangles":124,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0042254","count":4},{"id":"GO:0000470","count":3},{"id":"GO:0034965","count":2},{"id":"GO:0048235","count":2}]},{"hash":"1162520599121277186","title":"ROS-Linked Apoptosis Regulation","description":"The top GO terms point to apoptosis and, notably, hydrogen peroxide-mediated programmed cell death, including negative regulation of apoptotic processes. This indicates the cluster is mainly about how ROS influences apoptosis, with some peripheral terms that are less directly related. Overall, naming it around ROS-regulated apoptosis best captures the shared function.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901299","count":1},{"id":"GO:0030707","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0030097","count":1},{"id":"GO:0006915","count":1}]},{"hash":"1873427089256597287","title":"Mitotic Regulation and Protein Turnover","description":"The top GO terms cluster around mitosis and protein turnover: regulation of spindle assembly, protein localization to the kinetochore, mitotic cell cycle arrest in response to signals, and positive regulation of proteasomal ubiquitin-dependent protein catabolic process. Together these point to coordinated control of cell cycle progression and protein degradation, with some peripheral signaling terms (calcium import, VEGF response, cocaine response) that may reflect broader regulatory context. This makes \u201cMitotic Regulation and Protein Turnover\u201d a concise, representative label.","confidence":"Medium","size":14,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032436","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0010800","count":2},{"id":"GO:0035924","count":2},{"id":"GO:0070509","count":2}]},{"hash":"1655138292581534776","title":"Unknown","description":"It spans multiple unrelated processes (DNA replication, nuclear autophagy, vesicle trafficking, various protein modifications, and RNA/tRNA modification), with little unifying function linking them; there is no cohesive theme to label a specific function cluster.","confidence":"","size":14,"edges":43,"triangles":42,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0034727","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0032508","count":2}]},{"hash":"625966844038814432","title":"TLR-Mediated Antiviral Innate Immunity","description":"The cluster centers on innate antiviral signaling and cytokine production, with frequent GO terms for defense against virus, innate immune response, dsRNA recognition, and Toll-like receptor pathways (TLR1 and TLR9) leading to inflammatory cytokine regulation, including IL-18.","confidence":"High","size":14,"edges":10,"triangles":0,"max_degree":3,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0034130","count":3},{"id":"GO:0043330","count":3},{"id":"GO:1905289","count":3}]},{"hash":"427444434810993278","title":"Unknown","description":"The GO terms are highly diverse, including immune evasion, ubiquitination, RISC assembly, and multiple biosynthetic/catabolic processes (alginate, pectin, fatty acids, verruculogen, ectoine), with no clear shared function or connectivity among the 14 proteins (no edges). This makes it impossible to assign a cohesive function label, so Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0020012","count":2},{"id":"GO:0016567","count":1},{"id":"GO:0070923","count":1},{"id":"GO:0042121","count":1},{"id":"GO:0045490","count":1}]},{"hash":"945279820983990953","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071042","count":1},{"id":"GO:0016973","count":1},{"id":"GO:0071051","count":1},{"id":"GO:0071038","count":1},{"id":"GO:0090502","count":1}]},{"hash":"1937716888650340355","title":"Ribosome Biogenesis & Mitochondrial Translation","description":"The cluster is dominated by GO terms for ribosome biogenesis, translation, and ribosomal large subunit assembly, with additional terms for rRNA methylation, mitochondrial translation, and assembly of mitochondrial respiratory components (e.g., complex II) and ubiquinone biosynthesis. This points to a cohesive theme around protein synthesis machinery and mitochondrial function/energy production. A few terms like neural tube closure and protein oxidation regulation appear peripheral or annotation-noise rather than central to the main theme.","confidence":"Medium","size":14,"edges":66,"triangles":167,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0006120","count":1},{"id":"GO:0034553","count":1}]},{"hash":"581119949634609004","title":"Mitochondrial Translation","description":"This cluster is characterized by GO terms tied to translation, specifically mitochondrial translation and termination, suggesting it groups proteins involved in mitochondrial protein synthesis machinery. The evidence is focused but limited (two related terms with single annotations), hence a Moderate confidence level.","confidence":"Medium","size":14,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0070126","count":1},{"id":"GO:0006412","count":1}]},{"hash":"1700149968100871915","title":"Unknown","description":"Insufficient functional signals to infer a shared role\u2014the Top Terms are not provided, so there is no common GO theme to bind these proteins. The small network (5 edges, 1 triangle) and 14 proteins offer little evidence for a specific function.","confidence":"","size":14,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[]},{"hash":"756574669007705488","title":"RNA splicing and silencing regulation","description":"The top terms cluster around post-transcriptional RNA control, including spliceosome-mediated splicing regulation (splice site recognition, small-subunit processome), ncRNA/miRNA-mediated gene silencing, and translation reinitiation plus stress-related mRNA stability. This points to a cohesive RNA processing and silencing regulatory theme.","confidence":"High","size":14,"edges":42,"triangles":60,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":10},{"id":"GO:0075525","count":10},{"id":"GO:1905663","count":10},{"id":"GO:0000381","count":10},{"id":"GO:0035278","count":10}]},{"hash":"2028668526541109268","title":"Proteostasis and Stress Response","description":"This cluster centers on ubiquitin-mediated protein quality control (ERAD, autoubiquitination, aggresome formation) and stress signaling (IL-1 response, apoptosis), with supporting links to organelle protein trafficking (peroxisome import) and DNA damage repair, all pointing to cellular proteostasis and stress maintenance.","confidence":"High","size":13,"edges":59,"triangles":136,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0070911","count":5},{"id":"GO:0016558","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0016562","count":4}]},{"hash":"978596088601392068","title":"ER-Golgi trafficking and stress-response signaling","description":"The cluster is enriched for ER-to-Golgi vesicle transport, unfolded protein response, and glucocorticoid signaling, pointing to a shared theme of secretory pathway function under cellular stress and protein quality control. While there are some development and DNA replication terms present, the core connection appears to be stress-related trafficking and signaling. ","confidence":"Medium","size":13,"edges":21,"triangles":13,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0070262","count":4},{"id":"GO:2000324","count":4},{"id":"GO:0016576","count":4}]},{"hash":"20147006044669480","title":"DNA replication and cell cycle","description":"The top terms strongly center on DNA replication, cell division, DNA recombination, and viral genome replication, suggesting a nucleic-acid replication and cell-cycle-focused cluster. Some other terms (photosynthesis, LPS metabolism, obsolete terms) appear to be noise or annotation quirks, but the dominant signals point to replication and genome maintenance. Confidence: Medium","confidence":"","size":13,"edges":15,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0019079","count":2}]},{"hash":"1447855587730651301","title":"Neural progenitor division and secretory trafficking","description":"The cluster is enriched for terms tying cell division (mitotic cleavage furrow ingression, cell division) with vesicle trafficking routes between the ER/Golgi and the plasma membrane (COPII coating regulation, Golgi to PM/transport). Also includes neural development and structural terms (radial glial scaffolds, dendrite development, tight junctions, EGFR signaling, ER stress response), suggesting a group of proteins coordinating progenitor proliferation with secretory pathway function and neural tissue organization. ","confidence":"Medium","size":13,"edges":21,"triangles":11,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1990386","count":3},{"id":"GO:0055108","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0003400","count":3},{"id":"GO:0034976","count":3}]},{"hash":"599287196523109650","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":13,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0030157","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2}]},{"hash":"1161209441639274505","title":"Mitosis: spindle assembly and checkpoint control","description":"The top GO terms cluster around mitotic processes\u2014spindle assembly and mitotic cell cycle checkpoint signaling\u2014indicating a focus on cell division regulation. While translation and certain kinase-regulation terms appear, the strongest, most coherent theme is mitotic control. Some sensory-related terms (temperature/pain detection) and other signals may reflect broader signaling roles or annotation noise rather than a unifying function of the cluster.","confidence":"Medium","size":13,"edges":31,"triangles":27,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0007093","count":2},{"id":"GO:0071446","count":2},{"id":"GO:0070213","count":2},{"id":"GO:0071901","count":2}]},{"hash":"647947861143179542","title":"Nitrogen fixation and Fe-S cluster assembly in symbionts","description":"The top GO terms are dominated by nitrogen fixation (GO:0009399) and iron-sulfur cluster assembly (GO:0016226), pointing to bacterial systems that coordinate Fe-S cofactors for enzymes like nitrogenase. While ribosome biogenesis and some stress/host-interaction terms appear, they are more general or peripheral to the core theme of metal cofactor assembly and nitrogen fixation in a symbiotic context. Therefore, the cluster is best described as centered on nitrogen fixation and Fe-S cluster biosynthesis in symbionts.","confidence":"Medium","size":13,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0030242","count":1},{"id":"GO:0006810","count":1},{"id":"GO:0050826","count":1},{"id":"GO:0052190","count":1}]},{"hash":"1178286738534624224","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0042794","count":1},{"id":"GO:0006390","count":1}]},{"hash":"1802576559716485001","title":"TLR-Mediated Innate Immune Signaling","description":"This cluster is dominated by toll-like receptor pathways (TLR1, TLR9), dsRNA response, inflammatory defense, and cytokine production (e.g., IL-18), pointing to innate immune sensing and downstream inflammatory signaling as the core theme; other terms may reflect broader regulatory links but do not override the main pattern.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034130","count":1},{"id":"GO:0043330","count":1},{"id":"GO:1905289","count":1},{"id":"GO:0032741","count":1},{"id":"GO:0034162","count":1}]},{"hash":"707006219639857491","title":"Unknown","description":"The GO terms are spread across diverse processes (cell division, meiosis, stomatal opening, transcription, ER stress, viral transcription, hormone responses) with no clear, shared function, so a cohesive cluster label cannot be determined.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0007129","count":1},{"id":"GO:1990069","count":1},{"id":"GO:0035186","count":1},{"id":"GO:0006351","count":1}]},{"hash":"693306476391211435","title":"Neurodevelopment and Stress Response","description":"This cluster centers on neural development and axon formation (forebrain development, multicellular organism development, positive regulation of axon extension), suggesting a neurodevelopmental theme. It also contains stress- and toxin-response terms (ER stress\u2013related apoptosis, cadmium response, response to toxic substances) and metabolic angle (fatty acid oxidation), indicating related cellular stress and metabolic processes accompanying development. Overall, the dominant signal is neurodevelopment with associated stress-response pathways.","confidence":"Medium","size":13,"edges":11,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006349","count":3},{"id":"GO:1900015","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0019395","count":3},{"id":"GO:0007275","count":3}]},{"hash":"571006816864548381","title":"Nucleotide salvage and catabolism","description":"This cluster centers on nucleotide metabolism, dominated by nucleobase salvage and nucleoside catabolic processes (uridine, cytidine, inosine, guanosine; purine/pyrimidine interconversion) and related salvage pathways, with supporting roles from the pentose-phosphate shunt and NAD biosynthesis salvage, indicating a cohesive nucleotide salvage/metabolism theme.","confidence":"Medium","size":13,"edges":18,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006098","count":3},{"id":"GO:0019358","count":2},{"id":"GO:0006206","count":2},{"id":"GO:0006218","count":2},{"id":"GO:0006216","count":2}]},{"hash":"926302110605580802","title":"Cardiac calcium signaling and contraction regulation","description":"The GO terms point to heart rhythm control (SA node action potential), calcium-responsive signaling, and modulation of muscle contraction (sliding speed), suggesting a core theme of calcium-dependent cardiac signaling and contraction. Some terms (nucleotide biosynthesis, miscellaneous signaling) may be less directly related, so confidence is Moderate.","confidence":"Medium","size":13,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0060830","count":1},{"id":"GO:0006183","count":1},{"id":"GO:0021795","count":1}]},{"hash":"537883061601195074","title":"Glucocorticoid-regulated neuronal signaling and plasticity","description":"This cluster links neural development and function (hippocampus and substantia nigra development, membrane depolarization during action potential) with glucocorticoid receptor signaling, protein trafficking, and regulation of synaptic plasticity, implying a coordinated, stress-responsive neuronal signaling module.","confidence":"High","size":13,"edges":13,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0021766","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0042921","count":2},{"id":"GO:0051291","count":2}]},{"hash":"1296317437113334190","title":"Nucleolar ribosome biogenesis and rRNA processing","description":"Based on the GO terms, the cluster is dominated by rRNA maturation (SSU/LSU/5.8S), assembly of preribosomes, and nucleolus organization, indicating a ribosome biogenesis function in the nucleolus. A couple of development-related terms seem incidental and do not overturn the main signal.","confidence":"High","size":13,"edges":18,"triangles":10,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0000469","count":1},{"id":"GO:0035214","count":1},{"id":"GO:0007000","count":1},{"id":"GO:0045572","count":1}]},{"hash":"2132358741729879330","title":"Transmembrane Transporters for Nutrients and Ions","description":"The dominant GO terms describe membrane transport of multiple nutrients and ions (nitrate/nitrite, arabinose, sialic acid, phosphate, potassium), plus xenobiotic export and vesicular neurotransmitter loading, indicating a cluster of transporter proteins with broad substrate specificity.","confidence":"High","size":13,"edges":24,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0015739","count":4},{"id":"GO:0015751","count":4},{"id":"GO:0071805","count":4}]},{"hash":"549145940551651748","title":"Unknown","description":"This cluster has no edges or enriched GO terms linking the 13 proteins, and despite ReCIPE re-adding 20 proteins, there is no clear functional theme to tie them together. Therefore, a specific label cannot be assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"994625908482345950","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":2},{"id":"GO:0001193","count":1},{"id":"GO:0097190","count":1},{"id":"GO:0051123","count":1},{"id":"GO:0006362","count":1}]},{"hash":"1673314750015793287","title":"Unknown","description":"There is no functional signal: Top Terms are empty and there are no edges or triangles, so there is no shared GO enrichment to base a function on. Although 13 proteins are listed, the absence of GO terms (and the note about ReCIPE re-additions) prevents defining a cohesive biological theme. Therefore the safe label is Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1626967932306208929","title":"Unknown","description":"There are no GO terms listed for this cluster (Top Terms are empty), and with only a single edge among 13 proteins, there is no clear shared function or process to tie the proteins together. Therefore I can't assign a meaningful label beyond Unknown.","confidence":"","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"1583769796640917531","title":"Steroid and lipid biosynthesis and metabolism","description":"The cluster is dominated by GO terms for testosterone biosynthetic process and androgen metabolic process, indicating steroid synthesis/metabolism. Additional terms cluster around lipid biosynthesis and metabolism (very long-chain fatty acids, retinal metabolism, 3-keto-sphinganine, mycolic acid, tropane alkaloid biosynthesis), suggesting a broader lipid/secondary metabolite biosynthetic theme. Some terms like lung development and response to methotrexate reflect wider physiological contexts, but the core shared function appears to be steroid and lipid biosynthesis and related metabolic processes.","confidence":"Medium","size":13,"edges":65,"triangles":175,"max_degree":12,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0061370","count":12},{"id":"GO:0008209","count":12},{"id":"GO:0055114","count":11},{"id":"GO:0071768","count":10},{"id":"GO:0030324","count":10}]},{"hash":"1840748632384750181","title":"TNF-NF-\u03baB immune signaling and antigen presentation","description":"The cluster is enriched for TNF-mediated signaling, non-canonical NF-\u03baB pathways, and MHC class I antigen processing/presentation, plus responses to metal ions (zinc, cadmium) and inflammatory regulation. This combination points to a coherent immune-regulatory module focused on inflammatory signaling and antigen presentation, with some ancillary metal ion response and protease activity regulation.","confidence":"High","size":13,"edges":69,"triangles":223,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0002862","count":12},{"id":"GO:0006521","count":12},{"id":"GO:0038061","count":12},{"id":"GO:0090090","count":12},{"id":"GO:0010043","count":12}]},{"hash":"1956286064527575776","title":"Unknown","description":"No GO terms or edges are provided to indicate a shared function, and with 13 proteins and no interactions, there is no cohesive theme to label beyond Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1879290810525872007","title":"Ubiquitin Signaling and Proteasome Regulation","description":"This cluster centers on ubiquitin-related processes: multiple deubiquitination terms (histone H2A, K11-linked), COP9 signalosome assembly, and proteasome-related activity (storage granule assembly), implying coordinated control of protein turnover and chromatin regulation. Some terms are outliers or obsolete, but the dominant theme is ubiquitin-mediated regulation of protein fate.","confidence":"Medium","size":12,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0070537","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0014067","count":1},{"id":"GO:1902906","count":1},{"id":"GO:0035522","count":1}]},{"hash":"1924964161530478768","title":"Mitotic spindle organization and chromosome alignment","description":"This cluster is dominated by mitosis- and microtubule-related terms: metaphase chromosome alignment, centrosome separation, spindle midzone assembly, and chromosome recapture, all pointing to spindle organization and chromosome handling. Additional terms about microtubule depolymerization, stress granule disassembly, and neuron/root development suggest broader cytoskeletal/mRNA regulation roles linked to development. Confidence: High","confidence":"High","size":12,"edges":61,"triangles":180,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035617","count":8},{"id":"GO:0007080","count":7},{"id":"GO:1990535","count":6},{"id":"GO:0010938","count":6},{"id":"GO:0007100","count":6}]},{"hash":"1367315434749284960","title":"Spliceosome-driven mRNA processing and silencing","description":"This cluster is dominated by terms for mRNA export and splicing via the spliceosome, regulation of alternative splicing, and ncRNA-mediated silencing (including miRNA-mediated translational repression). The convergence on post-transcriptional RNA processing and RNA-silencing pathways suggests a cohesive module of spliceosome-associated processing and gene-silencing regulation.","confidence":"High","size":12,"edges":21,"triangles":22,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006406","count":6},{"id":"GO:0031047","count":5},{"id":"GO:0048026","count":5},{"id":"GO:0045292","count":5},{"id":"GO:0006446","count":5}]},{"hash":"2263333306185345948","title":"Mitochondrial Fe-S cluster assembly and respiration","description":"The GO terms cluster around iron-sulfur (Fe-S) cluster biogenesis in mitochondria, including iron homeostasis, regulation/assembly of Fe-S clusters, and iron incorporation into metallo-sulfur clusters, plus mitochondrial electron transport (succinate dehydrogenase) and oxidative stress response. This suggests a cohesive function linking Fe-S cluster assembly with mitochondrial respiration.","confidence":"High","size":12,"edges":31,"triangles":38,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006879","count":1},{"id":"GO:1903329","count":1},{"id":"GO:0090201","count":1},{"id":"GO:0010040","count":1},{"id":"GO:0010722","count":1}]},{"hash":"587940754110715509","title":"Genome maintenance during cell division","description":"The top terms cluster around DNA replication, mitotic processes (mitotic cytokinesis, sister chromatid biorientation, exit from mitosis), and DNA repair (HR repair regulation and UV-damage repair), suggesting a cohesive role in maintaining genome integrity during cell division. A few vesicle trafficking terms (vacuole inheritance, multivesicular body assembly) may reflect coupling of organelle inheritance with mitosis in certain organisms, reinforcing a cell-cycle\u2013linked maintenance theme. Overall, the cluster appears to reflect genome maintenance during cell division.","confidence":"Medium","size":12,"edges":12,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0000281","count":2},{"id":"GO:0000011","count":2},{"id":"GO:0070527","count":2},{"id":"GO:0006479","count":1}]},{"hash":"1918098492012187916","title":"Meiosis and Germ Cell Genome Maintenance","description":"This cluster is dominated by terms related to germ cell development, embryonic development, and meiotic processes (meiotic gene conversion), along with DNA repair and replication stress responses (interstrand cross-link repair, replication fork arrest, helicase activity) and genome maintenance (maintenance of DNA repeat elements). These together point to roles in germ cell formation and meiotic genome integrity. A minority of terms (e.g., isotype switching) appear less directly linked but may reflect broader DNA recombination or chromatin remodeling contexts. Overall, the primary theme is meiosis with genome maintenance in the germ line.","confidence":"Medium","size":12,"edges":43,"triangles":99,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001701","count":6},{"id":"GO:0045190","count":5},{"id":"GO:0007281","count":5},{"id":"GO:0036297","count":5},{"id":"GO:0006311","count":5}]},{"hash":"174786529574844720","title":"Ubiquitin-Proteasome Pathway & Cell Cycle Regulation","description":"The top GO terms cluster around ubiquitin-dependent degradation pathways (ERAD, K11-linked ubiquitination, ubiquitin-dependent proteolysis) and cell cycle processes (mitotic transition, cell division). This suggests a coherent theme where ubiquitin-mediated proteolysis governs cell cycle progression, with additional links to hormone receptor assembly and interferon signaling that can be modulated by ubiquitin pathways.","confidence":"High","size":12,"edges":45,"triangles":84,"max_degree":11,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0000492","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0006463","count":4},{"id":"GO:0046661","count":4}]},{"hash":"274340576070835941","title":"Viral life cycle and host interactions","description":"The terms cluster around key viral infection processes\u2014uncoating, virion assembly, viral release, and fusion with the host membrane\u2014i.e., the viral life cycle, with an immune component (leukocyte migration) and chaperone-related protein folding/PPIase activities that can assist viral proteins. This suggests a focus on viral replication/assembly and host response mechanisms.","confidence":"Medium","size":12,"edges":39,"triangles":78,"max_degree":9,"top_function":"protein folding","top_go_terms":[{"id":"GO:0019076","count":10},{"id":"GO:2000276","count":10},{"id":"GO:0010849","count":10},{"id":"GO:0006457","count":10},{"id":"GO:0000413","count":10}]},{"hash":"259237233280020064","title":"Ubiquitination-Driven Chromatin Regulation","description":"The cluster prominently features protein ubiquitination (GO:0016567) alongside transcription (GO:0006351) and histone methylation (GO:0061087, GO:0051568), pointing to control of gene expression via ubiquitin-related chromatin modification. Additional terms touch on translation initiation and cell-cycle regulation, but the dominant signal is nuclear regulation of transcription through ubiquitin signaling and chromatin state.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0045842","count":2},{"id":"GO:1903071","count":2},{"id":"GO:1903070","count":2}]},{"hash":"2243722082910995552","title":"Cell Division and Chromosome Segregation","description":"This cluster is best captured by GO terms related to the cell cycle, chromosome segregation, and plasmid partitioning, which together point to the machinery that distributes genetic material during cell division. While other terms indicate metabolic or biosynthetic roles, the strongest and most coherent signal across the top terms is coordinated DNA distribution and cell division processes.","confidence":"Medium","size":12,"edges":29,"triangles":27,"max_degree":9,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0007049","count":5},{"id":"GO:0009236","count":4},{"id":"GO:0018108","count":3},{"id":"GO:0007059","count":3},{"id":"GO:0006541","count":3}]},{"hash":"1929656977025531179","title":"Unknown","description":"There are no top GO terms to guide a functional label, and the interaction network shows no edges or triangles, despite 12 proteins and 20 re-added by ReCIPE. Without shared functional terms or connections, a cohesive, specific function cannot be inferred.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2183293781019199399","title":"Unknown","description":"The GO terms are highly diverse, ranging from mRNA decay (deadenylation-dependent and independent) to cellular responses to growth factors and hormones, plus developmental processes. There is no single, cohesive function that clearly binds these proteins, so a precise functional label cannot be confidently assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902172","count":1},{"id":"GO:0044344","count":1},{"id":"GO:0071385","count":1},{"id":"GO:0000288","count":1},{"id":"GO:1904628","count":1}]},{"hash":"1926837902476709509","title":"Unknown","description":"The top terms are a mix of DNA replication and meiotic processes, kinetochore localization, and various stress- and development-related terms (xenobiotic response, autophagy, sumoylation, lung and substantia nigra development, cardiac hypertrophy). This heterogeneous set lacks a single cohesive theme, so a concise, representative label can\u2019t be confidently assigned.","confidence":"","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0014883","count":3},{"id":"GO:0014898","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0016236","count":2}]},{"hash":"1555321405214451930","title":"Membrane Transporters for Ions and Nutrients","description":"The top GO terms center on transmembrane transport of various solutes\u2014potassium, nitrate/nitrite, sialic acid, arabinose, xenobiotics\u2014and a process for loading neurotransmitters into synaptic vesicles. This cohesive theme points to a cluster of transporter proteins mediating diverse solute movement across membranes, with a vesicular transport component, hence the label.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010197","count":6},{"id":"GO:0042128","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0015739","count":4},{"id":"GO:0015751","count":4}]},{"hash":"282789354145896358","title":"Ribosome Biogenesis and Cell Division","description":"The top GO terms are dominated by ribosome biogenesis and cytoplasmic translation, with additional terms for cell division and septum assembly, pointing to a module of proteins involved in ribosome assembly/translation that is coordinated with cell cycle processes. Peripheral stress-response terms are present but not central, so the core theme is ribosome-related biosynthesis coupled to division.","confidence":"High","size":11,"edges":4,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0042274","count":3},{"id":"GO:1901001","count":3}]},{"hash":"1341709451077891614","title":"Mitotic spindle assembly and microtubule dynamics","description":"The cluster centers on mitosis-related processes: cell division, mitotic cell cycle, mitotic spindle assembly, and microtubule-based movement, with supporting microtubule severing and CENP-A chromatin assembly. A few vesicle transport and peroxisomal import terms appear but are less represented, suggesting secondary roles. Thus the predominant function is spindle organization and chromosome segregation during cell division.","confidence":"High","size":11,"edges":12,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0007018","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0006888","count":2}]},{"hash":"48808681812967046","title":"Centromere assembly and mitotic chromosome segregation","description":"The cluster is dominated by GO terms related to mitosis, cell cycle progression, centromere assembly (CENP-A), sister chromatid segregation, and microtubule dynamics, with supporting ubiquitin-proteasome\u2013mediated regulation. These strongly point to a mitotic centromere/spindle\u2013associated function, even though some trafficking-related terms appear peripherally. ","confidence":"High","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0000070","count":4},{"id":"GO:0006888","count":4}]},{"hash":"150431862965755722","title":"Membrane Biogenesis","description":"These terms highlight membrane insertion and assembly across different contexts (mitochondrial cristae and Gram-negative outer membrane), indicating a common theme of membrane biogenesis. Hence a concise label \"Membrane Biogenesis\" reflects the cluster's functional theme.","confidence":"Medium","size":11,"edges":23,"triangles":29,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051205","count":1},{"id":"GO:0042407","count":1},{"id":"GO:0043165","count":1}]},{"hash":"197452703899797282","title":"Membrane organization and ECM remodeling","description":"The cluster centers on membrane- and matrix-related processes: protein localization to membrane rafts, extracellular matrix disassembly, and regulation of cell adhesion molecule production, plus podocyte development which depends on basement membrane interactions. Additional terms touch on vesicle trafficking at membranes (dopaminergic synaptic transmission) and organelle maintenance (mitochondrial inheritance), reinforcing a broader theme of membrane organization and cell-matrix dynamics, despite some obsolete terms. ","confidence":"Medium","size":11,"edges":52,"triangles":141,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:1901585","count":1},{"id":"GO:0060355","count":1},{"id":"GO:0072249","count":1},{"id":"GO:0045541","count":1},{"id":"GO:0070584","count":1}]},{"hash":"1944845991172181245","title":"Nucleic Acid Repair and tRNA Modification Under Stress","description":"This cluster's prominent GO terms center on DNA repair, RNA repair, mRNA processing, and tRNA wobble uridine modification, plus a link to mitochondrial membrane permeability in programmed necrotic cell death; collectively they point to maintenance of nucleic acid integrity and RNA metabolism under stress, with possible ties to cell death pathways.","confidence":"High","size":11,"edges":42,"triangles":80,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0012501","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0035553","count":1},{"id":"GO:0042245","count":1},{"id":"GO:1990983","count":1}]},{"hash":"682913916471793046","title":"Transcription Machinery and Ribosome Biogenesis","description":"The proteins show GO terms across RNA polymerase I/II/III transcription (initiation, termination, elongation) and ribosome biogenesis, suggesting a shared role in transcriptional machinery and ribosome production; a single apoptotic signaling term is present but does not alter the main theme.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001193","count":1},{"id":"GO:0042790","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0097190","count":1},{"id":"GO:0006363","count":1}]},{"hash":"1683290571863389436","title":"Methyltransferases: histone, rRNA, and peptide methylation","description":"The cluster is strongly enriched for various methylation activities, including N-terminal peptide methylation, arginine/lysine methylation on proteins, and RNA methylation (rRNA and histone methylation), plus rDNA heterochromatin formation. This pattern suggests a group of methyltransferases involved in chromatin and RNA modification, with broader support from multiple methylation-related GO terms; a minor term about cobalamin biosynthesis may reflect related methyl-transfer chemistry but does not override the core theme. ","confidence":"High","size":11,"edges":42,"triangles":84,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0018013","count":5},{"id":"GO:0000183","count":5},{"id":"GO:0009236","count":4},{"id":"GO:0090398","count":4},{"id":"GO:0016049","count":4}]},{"hash":"1608342109721872058","title":"Brain Development and Neural Function Cluster","description":"Top GO terms are largely centered on neural development and brain function\u2014forebrain development, corpus callosum development, Schwann cell development, and visual perception\u2014suggesting this cluster comprises proteins involved in nervous system development and sensory processing. Additional terms for multicellular organism development and glucose-related cellular responses reinforce a theme of brain maturation and neural signaling. A couple of terms relate to cell-cycle processes (DNA replication, protein localization to kinetochore), which may reflect proliferative phases in development or shared cellular machinery rather than neural-specific roles. Overall, the cluster appears to group proteins associated with brain development and neural function, with some non-neural annotations contributing to the signal.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034501","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0014044","count":4},{"id":"GO:0006349","count":4}]},{"hash":"1103800994185627710","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":13,"triangles":8,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007035","count":2},{"id":"GO:0043144","count":1},{"id":"GO:0001682","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0007030","count":1}]},{"hash":"2293607902907988222","title":"RNA transcription and ribosome biogenesis","description":"This cluster centers on transcription by RNA polymerases I, II, and III, including RNA-templated transcription and Pol III\u2013specific tRNA transcription, and it also includes a term for ribosome biogenesis, pointing to a cohesive theme of transcription machinery and ribosome assembly. Some other terms (nucleotide and amino acid biosynthesis, neutrophil homeostasis) appear less connected and may reflect peripheral functions or annotation noise.","confidence":"Medium","size":11,"edges":13,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006385","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0006386","count":1},{"id":"GO:0006366","count":1},{"id":"GO:0006360","count":1}]},{"hash":"1269005001596366837","title":"Unknown","description":"With no GO terms or interaction signals (edges/triangles and max degree are zero), there is no shared function to define this cluster. Therefore it cannot be confidently labeled.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2199867780599380985","title":"Unknown","description":"There are 11 proteins with no observed interactions (edges/triangles/max degree all zero) and no top GO terms to suggest a shared function. Without evidence of a common process or molecular function, a reliable.label cannot be assigned; the note about ReCIPEAdding proteins does not establish a theme.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"764058085857366430","title":"Unknown","description":"There is no GO term enrichment or interaction signal for this cluster: Edges 0, Triangles 0, Max Degree 0 and Top Terms empty, so no common function can be inferred from the data provided.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1178778322317056681","title":"Plant plastid RNA processing and metabolism","description":"The cluster combines RNA-centric processes (DNA-templated transcription, mRNA capping, rRNA methylation, histone and lysine dimethylation) with plastid-associated biosynthesis (chlorophyll and vitamin E) and related metabolism, suggesting a theme of plant gene expression coordination with plastid metabolism. Some terms (e.g., response to amine, ER-Golgi transport) are less specific to this theme, so the link is partial.","confidence":"Medium","size":11,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0014075","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006370","count":1},{"id":"GO:0006596","count":1}]},{"hash":"1375581618050760133","title":"Unknown","description":"The GO terms are heterogeneous: neural development and neuron apoptotic regulation appear but are surrounded by lipid transport, ergosterol biosynthesis, GPCR signaling, miRNA regulation, viral suppression, and other unrelated processes. With no edges connecting terms and no clear cohesive function, there is no single theme to label the cluster beyond Unknown.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043523","count":1},{"id":"GO:0006869","count":1},{"id":"GO:0070207","count":1},{"id":"GO:0006696","count":1},{"id":"GO:0038003","count":1}]},{"hash":"1007063216182597867","title":"Ubiquitin-Proteasome Degradation and Cell Cycle Regulation","description":"This cluster centers on ubiquitin-dependent proteolysis and proteasome activity (ERAD, SCF-based degradation, proteasome assembly, aggresome formation) with links to protein quality control and turnover. The presence of peroxisomal protein import hints at ubiquitin signaling involvement, and TNF signaling connections reflect broader stress/immune regulation, but the dominant theme is regulated protein degradation and cell-cycle-related processes.","confidence":"High","size":10,"edges":28,"triangles":34,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0016558","count":4},{"id":"GO:0033209","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0031146","count":3}]},{"hash":"610815555914820410","title":"TLR-Driven Antiviral Immune Signaling","description":"The cluster is dominated by GO terms related to toll-like receptor pathways (TLR3 signaling, MyD88-independent signaling), dsRNA response, interferon production, and chemokine induction, which together indicate innate immune sensing of viral RNA and downstream antiviral signaling. B cell proliferation and chemokine production further support an activated immune response, though a couple of terms (tRNA export, actin regulation) may reflect multifunctionality or annotation noise. Overall, the core theme is innate antiviral immune signaling through TLR pathways.","confidence":"Medium","size":10,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0002322","count":2},{"id":"GO:0034138","count":1},{"id":"GO:0045078","count":1},{"id":"GO:0007352","count":1},{"id":"GO:0002756","count":1}]},{"hash":"1537068180968749201","title":"DNA replication and chromosome segregation","description":"The cluster is enriched for DNA replication, DNA repair, spindle assembly regulation, and kinetochore localization, pointing to a core role in chromosome maintenance and mitosis. Peripheral terms (hippocampus development, VEGF response, calcium import, TORC1 signaling) do not override this central theme but suggest broader regulatory contexts. ","confidence":"Medium","size":10,"edges":10,"triangles":3,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0021766","count":3},{"id":"GO:0010800","count":2}]},{"hash":"403080653396338973","title":"TLR Signaling and Inflammatory Cytokine Regulation","description":"The cluster is dominated by GO terms for toll-like receptor signaling (TLR1, TLR9), response to dsRNA, inflammatory response, and regulation of cytokine production, pointing to innate immune recognition and downstream inflammatory signaling. Some terms appear as unrelated noise (tooth mineralization, kidney size), but the core theme is clear TLR-driven immune signaling and cytokine regulation.","confidence":"High","size":10,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0034130","count":2},{"id":"GO:0043330","count":2},{"id":"GO:1905289","count":2},{"id":"GO:0032741","count":2}]},{"hash":"2171604055650421371","title":"Oxidative Stress and Aging Response","description":"The terms center on reactive oxygen species handling (removal of superoxide radicals, oxidation-reduction) and aging-related processes, including selenium ion response, suggesting a theme of oxidative stress defense and aging. Some terms related to hippocampus development and sound perception may reflect broad annotation rather than core function.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001320","count":2},{"id":"GO:0071291","count":2},{"id":"GO:0001302","count":2},{"id":"GO:0003069","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1789645186981457040","title":"Ribosome biogenesis and translation","description":"The dominant GO terms point to ribosome production and protein synthesis\u2014translation and ribosomal large subunit biogenesis/assembly\u2014suggesting a cohesive function around ribosome assembly. A few retina-related terms appear, but they are likely unrelated noise and do not override the ribosome-focused signals. Therefore, the cluster is best described as involving ribosome biogenesis and translation.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0032781","count":1},{"id":"GO:1902626","count":1},{"id":"GO:0021554","count":1},{"id":"GO:0010458","count":1}]},{"hash":"2047337215693160522","title":"Neuronal development and cell cycle control","description":"The terms emphasize nervous system development and axon extension along with mitotic cell cycle transitions (G1/S, G2/M) and hemopoiesis, indicating a theme of developmental signaling coupled with cell proliferation. Additional signals like VEGF response and calcium import point to broader signaling dynamics during development. This supports a combined label of neuronal development intertwined with cell cycle regulation.","confidence":"Medium","size":10,"edges":8,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045773","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0030097","count":3},{"id":"GO:0000082","count":3}]},{"hash":"2190150579578463377","title":"Membrane excitability regulators","description":"Based on the dominant themes in the terms, the cluster centers on membrane potential and ion-channel\u2013mediated excitability: neuronal action potential, cardiac conduction and atrial repolarization, membrane hyperpolarization, and regulation of potassium channel activity. A few peripheral terms (touch, UV-B response, Rho signaling, Wnt) exist but do not override the core link to excitability. Therefore, this label reflects the main functional thread linking most entries.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019228","count":1},{"id":"GO:0086091","count":1},{"id":"GO:0006547","count":1},{"id":"GO:0050976","count":1},{"id":"GO:0060081","count":1}]},{"hash":"1322725495602802421","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":16,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0000398","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0090394","count":2},{"id":"GO:0000463","count":2}]},{"hash":"538223685421501079","title":"Neural and cardiac remodeling signaling","description":"This cluster centers on signaling pathways and processes linked to tissue remodeling in neural and cardiac contexts, including substantia nigra development, dendrite morphogenesis regulation, EMT, muscle fiber-type switching, and stress-induced cardiac hypertrophy via calcineurin\u2013NFAT signaling. While a few terms are broader (e.g., miRNA processing regulation), the dominant theme ties developmental signaling to remodeling across neural and muscular tissues.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021762","count":4},{"id":"GO:1905205","count":4},{"id":"GO:0050774","count":4},{"id":"GO:0051343","count":4},{"id":"GO:0033173","count":4}]},{"hash":"1665920058055636996","title":"Ribosome Biogenesis and rRNA Processing","description":"This cluster\u2019s top GO terms are dominated by ribosome-related processes: ribosome biogenesis, maturation of SSU/LSU rRNA, and maturation from the tricistronic rRNA transcript. These consistently point to proteins involved in assembling and processing ribosomal RNA, i.e., ribosome assembly factors and rRNA maturation components. Other terms like nucleotide-excision repair, SOS response, and embryonic development are present but much less represented and do not define the core function of the cluster. ","confidence":"High","size":10,"edges":14,"triangles":8,"max_degree":5,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007584","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0006289","count":5},{"id":"GO:0009432","count":5},{"id":"GO:0042254","count":4}]},{"hash":"844159696522449073","title":"Quinone biosynthesis and fatty acid metabolism","description":"Most terms cluster around biosynthesis of quinones (phylloquinone, menaquinone) and fatty acid metabolism (beta-oxidation), with related secondary metabolism (antibiotic biosynthesis) and small-molecule catabolism. A few outliers exist, but the core theme is quinone and lipid-related metabolism.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":2},{"id":"GO:0048733","count":2},{"id":"GO:0018230","count":2},{"id":"GO:0031047","count":1},{"id":"GO:0010372","count":1}]},{"hash":"276045907668898501","title":"Unknown","description":"The GO terms span a wide range of unrelated processes (fertilization, microtubule movement, hypoxia response, splicing, cadmium response, kinase regulation, cytokinesis-related septum digestion, neuron apoptosis, ribosome biogenesis, and pattern formation), and there are no evident shared functional themes or interactions among the proteins. This makes it inappropriate to assign a specific, coherent label to the cluster.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":1},{"id":"GO:0007018","count":1},{"id":"GO:0071456","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0071276","count":1}]},{"hash":"247756171653115922","title":"Chromatin Regulation and RNA Processing During Mitosis","description":"The cluster centers on chromatin-related processes (histone H3-K9 methylation, DNA-templated transcription, mRNA splicing) and interfaces with cell division mechanics (negative regulation of cytokinesis, microtubule-based movement, and general transcription). This suggests a cohesive theme where chromatin state and RNA processing are coordinated with mitotic spindle function and cytokinesis. Some terms are historical/obsolete, but the core signals point to chromatin regulation and gene expression during cell division, with cytoskeletal involvement and stress-response context (hypoxia, cadmium). ","confidence":"Medium","size":10,"edges":6,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071456","count":5},{"id":"GO:0051567","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0007338","count":4},{"id":"GO:0007018","count":4}]},{"hash":"771443177017815477","title":"Golgi-ER transport and development","description":"The cluster's top GO terms highlight vesicle trafficking between the Golgi and ER (retrograde and ER-to-Golgi transport), indicating a core role in intracellular trafficking. It also includes terms related to development (multicellular organism development, skeletal system development) and regulation of kinase activity and the mitotic cell cycle, suggesting broader roles in cell growth and organization. Additional terms such as cadmium ion response and defense against Gram-positive bacteria may reflect stress responsiveness rather than a single pathway. Overall, the strongest shared signal is Golgi-ER\u2013associated transport linked to developmental processes, justifying this label.","confidence":"Medium","size":10,"edges":8,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071276","count":4},{"id":"GO:0071902","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0006890","count":4}]},{"hash":"1252361358772349031","title":"Mitotic spindle and chromosome dynamics","description":"This cluster is dominated by GO terms tied to microtubule-based spindle formation and chromosome handling during cell division, including spindle assembly, metaphase chromosome alignment, centrosome separation, and meiotic spindle orientation, as well as microtubule depolymerization. While a few terms touch on nuclear migration or development, the strongest and most consistent signal is spindle organization and chromosome dynamics.","confidence":"High","size":10,"edges":27,"triangles":38,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":5},{"id":"GO:0007080","count":5},{"id":"GO:1990535","count":4},{"id":"GO:0010938","count":4},{"id":"GO:0007100","count":4}]},{"hash":"1946715227151902563","title":"Actin Cytoskeleton Dynamics","description":"This cluster is dominated by actin-related processes: thin filament assembly, cortical actin localization, and regulation of cell shape/polarity, pointing to actin-mediated cytoskeletal organization; other terms touch on cytokinesis and chromosome movement in cell division, but the core signal centers on actin dynamics.","confidence":"Medium","size":10,"edges":11,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010628","count":1},{"id":"GO:0043983","count":1},{"id":"GO:1904623","count":1},{"id":"GO:0016344","count":1},{"id":"GO:0030240","count":1}]},{"hash":"625264221552555373","title":"Membrane Lipid Biosynthesis and Immune Signaling","description":"The cluster centers on lipid-related processes: unsaturated fatty acid biosynthesis, ergosterol biosynthetic regulation, and mannosyl-inositol phosphorylceramide metabolism, with additional lipid-associated functions like CNS myelin maintenance and sebaceous gland differentiation. It also includes immune-related signaling terms (TLR1 pathway and response to dsRNA) and nitric oxide biosynthesis, suggesting a theme where membrane lipid composition and lipid-derived signals interface with immune signaling. This combination supports a cohesive label around membrane lipids and linked signaling rather than a single narrow function.","confidence":"Medium","size":10,"edges":13,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":1},{"id":"GO:0006636","count":1},{"id":"GO:0006675","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0032443","count":1}]},{"hash":"786073399990311221","title":"Peroxisome Dynamics and Protein Homeostasis","description":"The GO terms emphasize peroxisome organization, size regulation, and fission, suggesting a focus on peroxisome biogenesis and dynamics. Additional terms related to translation initiation, proteasomal degradation, and ER-Golgi transport imply broader protein quality control and trafficking roles that can intersect with peroxisomal maintenance. Overall, the cluster seems best described by peroxisome dynamics with supporting protein homeostasis processes, though some terms are peripheral.","confidence":"Medium","size":10,"edges":12,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032435","count":1},{"id":"GO:1901194","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006888","count":1},{"id":"GO:2000269","count":1}]},{"hash":"1032756513538615716","title":"Catabolic Metabolism and Proteolysis","description":"The cluster is enriched for several catabolic and protein-degradation related GO terms, including proteolysis, carbohydrate metabolic process, and glycosphingolipid/oligosaccharide catabolism, suggesting a focus on breakdown and recycling of macromolecules. There are also terms tied to detoxification and autophagy regulation, indicating involvement in cellular quality control and metabolic turnover. This points to a cohesive theme around catabolic metabolism and proteolysis, with supporting autophagy regulation signals.","confidence":"Medium","size":10,"edges":34,"triangles":63,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0009405","count":5},{"id":"GO:0006689","count":3},{"id":"GO:0051692","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0098869","count":2}]},{"hash":"864922854462698354","title":"Unknown","description":"The top GO terms span neural development (lung and substantia nigra development, dendrite morphogenesis), brain-related drug response (response to cocaine), cell division (kinetochore localization, meiotic DSB formation), and metabolism (AMP catabolic process, glucose signaling). This mix doesn\u2019t reveal a single coherent function or pathway linking all proteins, so there isn\u2019t a clear, representative label beyond Unknown.","confidence":"","size":9,"edges":27,"triangles":40,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042220","count":6},{"id":"GO:0030324","count":4},{"id":"GO:0021762","count":4},{"id":"GO:0010780","count":4},{"id":"GO:0034501","count":4}]},{"hash":"270703440833871378","title":"Innate immune signaling and xenophagy","description":"Most of the top GO terms relate to innate immune defense and autophagy: defense against Gram-positive bacteria, dsRNA response, LPS response, interferon-beta production, and positive regulation of xenophagy. This points to antimicrobial signaling and autophagic defense as the core theme of the cluster, with a few outliers (insulin signaling, axonogenesis, pain) likely reflecting multifunctionality or annotation spillover. ","confidence":"High","size":9,"edges":25,"triangles":32,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":4},{"id":"GO:0008286","count":4},{"id":"GO:0043330","count":3},{"id":"GO:0045359","count":3},{"id":"GO:0071222","count":3}]},{"hash":"2103863527242961929","title":"Telomeric Heterochromatin Silencing","description":"The terms cluster around chromatin silencing and heterochromatin formation, especially at subtelomeric regions and the silent mating-type cassette, indicating a shared function in telomeric/subtelomeric heterochromatin silencing. A few other terms appear but do not define the main theme.","confidence":"High","size":9,"edges":14,"triangles":7,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0061186","count":2},{"id":"GO:0031939","count":2},{"id":"GO:0006348","count":2},{"id":"GO:0030466","count":2},{"id":"GO:0006344","count":2}]},{"hash":"1168387060123329722","title":"Two-Component signaling and transcription regulation","description":"This cluster centers on phosphorelay signal transduction (two-component systems) and transcriptional regulation, with multiple GO terms pointing to regulation of DNA-templated transcription and signal transduction. The presence of chemotaxis and xenobiotic response terms supports a theme of environmental sensing leading to gene regulation and movement. Some peripheral terms (protein folding, light detection, NO biosynthesis) may reflect broader regulatory or ancillary roles, but the core link is signaling-driven transcriptional control in response to stimuli.","confidence":"Medium","size":9,"edges":9,"triangles":1,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0006935","count":2},{"id":"GO:0000160","count":2},{"id":"GO:2000010","count":2}]},{"hash":"891994238969564416","title":"Growth and cell division signaling","description":"The cluster shows a theme around developmental/growth processes (spinal cord development, multicellular organism growth) and growth-regulating signaling (TORC1), complemented by cytoskeleton-associated mitosis/cytokinesis activity (microtubule-based movement, septum digestion after cytokinesis). While there are some ancillary stress and splicing terms, the core signal points to growth control and cell division regulation.","confidence":"Medium","size":9,"edges":7,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0007338","count":1},{"id":"GO:0007018","count":1}]},{"hash":"32508629459147657","title":"DNA repair and genome maintenance","description":"This cluster is dominated by GO terms tied to DNA damage recognition and repair (interstrand cross-link repair, UV-damage excision repair, response to X-ray) and recombination-related processes (t-circle formation, homologous chromosome pairing at meiosis), indicating a cohesive theme of genome maintenance and repair\u2014despite a few peripheral terms that may reflect annotation noise.","confidence":"High","size":9,"edges":28,"triangles":44,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0036297","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0010165","count":2},{"id":"GO:0090656","count":2},{"id":"GO:0070914","count":2}]},{"hash":"1906323743650521611","title":"Mitosis and Chromosome Segregation","description":"This cluster is dominated by GO terms tied to cell division and mitosis (mitotic cell cycle, cell division) plus chromatin and spindle-related processes (CENP-A chromatin assembly, microtubule severing), suggesting a cohesive role in mitotic chromosome segregation. While some terms touch broader cellular processes, the recurring mitotic theme makes this label representative.","confidence":"High","size":9,"edges":33,"triangles":65,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0051260","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0006351","count":5}]},{"hash":"976895585087863249","title":"Innate immune and cellular stress response","description":"The top GO terms are dominated by innate immune reactions to pathogens (response to dsRNA, LPS, Gram-positive defense, interferon-beta production) and cellular stress/damage pathways (DNA repair, ethanol response). Although there are a few neuron-related terms, the shared theme across most terms points to a module of defense signaling and stress response rather than a single specific process. ","confidence":"Medium","size":9,"edges":17,"triangles":8,"max_degree":6,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0071361","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0043330","count":3},{"id":"GO:0050830","count":3}]},{"hash":"998917675904690328","title":"Neural signaling and synaptic regulation","description":"Based on the prevalent GO terms, the cluster centers on nervous system function and neuronal communication, including regulation of synaptic vesicle exocytosis, regulation of excitatory postsynaptic potential, and dopamine signaling. Developmental terms (nervous system development, branching morphogenesis of a nerve, Wnt signalosome assembly) reinforce a neural development/regulation theme, while a few peripheral terms (kidney size, manganese response) are less central. Overall, the proteins appear to function together in neuronal signaling and development.","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000300","count":3},{"id":"GO:0007399","count":3},{"id":"GO:1905289","count":3},{"id":"GO:0035564","count":3},{"id":"GO:1904887","count":3}]},{"hash":"2145929167879458774","title":"Phosphorylation-driven signaling and TORC1 regulation","description":"The GO terms cluster around regulation of phosphorylation and catalytic activity, signaling pathways (including VEGF response and calcium import), and growth/translation control via TORC1, as well as cell-cycle aspects like spindle assembly. This pattern suggests a cohesive module where phosphorylation state governs signaling networks and TORC1-mediated growth and translation, with metabolic cues. The glycogen term is a minor cue toward energy status, fitting TORC1-linked regulation but less central. Overall, these terms point to a theme of phosphorylation-regulated signaling and growth control, though the component terms are diverse. ","confidence":"Medium","size":9,"edges":23,"triangles":24,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0005977","count":1},{"id":"GO:0043086","count":1},{"id":"GO:0009966","count":1},{"id":"GO:0043666","count":1}]},{"hash":"1358326862150140409","title":"DNA replication and repair","description":"Many top terms relate to DNA synthesis and maintenance, including DNA replication, lagging strand elongation, and Okazaki fragment processing during mitotic replication, as well as double-strand break repair via classical NHEJ. A couple of terms reference V(D)J recombination in immunoglobulin and T cell receptors, which are driven by DNA rearrangement processes that share the same repair machinery, so they still align with DNA processing. Overall, the cluster appears to group proteins involved in DNA replication and repair pathways.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000685","count":1},{"id":"GO:0033152","count":1},{"id":"GO:0051301","count":1},{"id":"GO:1903461","count":1},{"id":"GO:0033153","count":1}]},{"hash":"949333053930521369","title":"RNA Splicing and Silencing Machinery","description":"The cluster shows a clear connection to post-transcriptional RNA regulation, with terms for mRNA splice site recognition and spliceosome-mediated splicing as well as miRNA- and ncRNA-mediated gene silencing. Although a few viral-related terms appear, the dominant signals point to RNA processing and regulation rather than viral replication, making this a coherent RNA processing/silencing cluster.","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019076","count":1},{"id":"GO:2000276","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0010849","count":1},{"id":"GO:0075525","count":1}]},{"hash":"1260650920611516796","title":"Unknown","description":"The GO terms are highly diverse (hormone receptor assembly, chlorophyll biosynthesis regulation, oxidative stress response, fat pad development, metal ion response, gluconeogenesis regulation, innate immunity, sex differentiation, centrosome microtubule anchoring, and protein isomerization), with little overlap pointing to a single cohesive function. This lack of a unifying theme makes it not possible to ascribe a specific, representative label beyond Unknown.","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006463","count":1},{"id":"GO:1902325","count":1},{"id":"GO:0070301","count":1},{"id":"GO:0060613","count":1},{"id":"GO:0071276","count":1}]},{"hash":"211101801761883663","title":"Unknown","description":"No top GO terms, no edges, and no triangles are present, so there is no clear shared function to define a label. With no functional signal, a cohesive theme cannot be inferred; thus the cluster is Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"496958816760344238","title":"DNA Damage Checkpoint and G2/M Regulation","description":"The top GO terms center on regulating DNA damage checkpoints and the G2/M transition of the cell cycle, with an additional note on fibroblast proliferation and a developmental term. This points to a cluster of proteins involved in cell cycle control and growth rather to a single pathway, though the signal is modest (few proteins per term), hence a cautious but coherent label.","confidence":"Medium","size":9,"edges":11,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:2000001","count":1},{"id":"GO:0001701","count":1},{"id":"GO:0010389","count":1},{"id":"GO:0048146","count":1},{"id":"GO:0090502","count":1}]},{"hash":"701055787294700166","title":"Unknown","description":"The GO terms for this cluster are highly diverse, including chemotaxis and regulation of cell migration (motility), immune response, bone remodeling, various lipid-related processes, and several metabolism and signaling terms. With only 3 edges and a single occurrence for each term, there is no clear, cohesive biological function uniting the proteins. Thus a concise, representative label cannot be reliably assigned beyond Unknown.","confidence":"","size":9,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":1},{"id":"GO:0030505","count":1},{"id":"GO:0006935","count":1},{"id":"GO:0046849","count":1},{"id":"GO:0006955","count":1}]},{"hash":"980353215445246909","title":"Unknown","description":"This cluster shows no edges, no triangles, and no top GO terms to anchor a shared function, so a coherent functional label cannot be inferred.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2277962443059448507","title":"Vacuolar trafficking and ion transport","description":"The terms converge on vacuolar biology (vacuole organization, protein targeting to vacuole, vacuolar acidification) and ion/proton transport (sodium transport, proton transmembrane transport, proton motive force\u2013driven ATP synthesis), with copper homeostasis suggesting metal ion handling tied to vacuoles. Some annotations are obsolete or reference mitochondria, but the core signal points to a vacuole-centered function with associated ion transport.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000746","count":1},{"id":"GO:0006627","count":1},{"id":"GO:0007033","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0006814","count":1}]},{"hash":"2182203932635636448","title":"DNA replication and damage response","description":"The dominant GO terms indicate core DNA replication and recombination processes (DNA replication, DNA recombination, meiotic recombination repair, DNA strand displacement) along with stress-induced DNA damage responses (heat, cisplatin, SOS response, hydroxyurea). This points to a cohesive cluster of proteins involved in replication and repair under stress, with a few unrelated terms likely representing noise.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006310","count":3},{"id":"GO:1990918","count":3},{"id":"GO:0009408","count":3},{"id":"GO:0072719","count":2}]},{"hash":"1967579214942190147","title":"DNA replication and cell cycle proteins","description":"The cluster is dominated by GO terms tied to DNA replication, recombination, and cell division (DNA synthesis, RNA primer removal in mitotic replication, and mtDNA replication regulation). Some terms point to chaperone-mediated assembly of protein complexes and stress responses that commonly accompany replication machinery, supporting a cohesive theme around DNA replication and cell-cycle progression.","confidence":"High","size":8,"edges":11,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0032508","count":2},{"id":"GO:0090305","count":2}]},{"hash":"251414506140459871","title":"RNA Splicing and mRNA Processing","description":"The top GO terms cluster around RNA processing, especially pre-mRNA splicing (spliceosome activity, disassembly, and regulation of alternative splicing) and mRNA maturation (7-methylguanosine cap), with related helicase regulation and nucleolar localization, indicating a group of proteins involved in post-transcriptional RNA processing and spliceosome dynamics.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903070","count":2},{"id":"GO:0097309","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0032211","count":1},{"id":"GO:1904744","count":1}]},{"hash":"1288348104474109824","title":"Developmental signaling and RNA processing with stress responses","description":"The top terms point to developmental processes (multicellular organism development, single fertilization) combined with signaling and gene-expression control (SREBP signaling, positive regulation of protein kinases, ubiquitin ligase regulation, mRNA splicing, translation initiation). Additional terms underscore cellular stress responses (hypoxia, cadmium) and cytoskeletal dynamics (microtubule movement), suggesting a cluster focused on development linked to regulation of RNA processing and protein turnover under stress.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":5},{"id":"GO:1904668","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0032933","count":5},{"id":"GO:0007338","count":4}]},{"hash":"1799311488388289412","title":"Signaling and Protein Oligomerization","description":"The top GO terms cluster around cellular signaling (insulin receptor signaling; negative regulation of calcineurin-NFAT signaling), development/growth (cerebral cortex development; positive regulation of cell size), and protein assembly (protein homotetramerization; protein heterooligomerization), with additional metabolism-related terms. This suggests a common theme of signal transduction modulated by protein\u2013protein interactions and complex formation that influence growth and development, hence the proposed label.","confidence":"Medium","size":8,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0048240","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0051534","count":2}]},{"hash":"1166144936593583720","title":"Neural development and transcriptional regulation","description":"Based on strong signals for forebrain development, neural tube closure, and multicellular/skeletal development, the cluster appears dominated by transcriptional regulators guiding neural development. DNA-templated transcription is a core theme, with accompanying signals of proliferation (mitotic cell cycle). A subset of stress-related terms (ER stress\u2013associated apoptosis, cadmium response) suggests additional cellular stress responsiveness but does not override the central developmental transcriptional pattern.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006349","count":4},{"id":"GO:0030900","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0001501","count":4}]},{"hash":"2188438482164838285","title":"Immune signaling and endocytic regulation","description":"Based on the top GO terms, the cluster centers on dampening or modulating immune signaling (negative regulation of TLR5 and IL-1\u03b2 production, LPS tolerance) coupled with endocytic and trafficking processes (synaptic vesicle endocytosis, endocytic recycling, Rab/GTPase regulation). A deubiquitination term (K27-linked) further supports a regulatory, post-translational control role that can link trafficking with immune signaling. This combination suggests a coherent theme of immune regulation mediated through endocytic and trafficking pathways.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035745","count":1},{"id":"GO:0097194","count":1},{"id":"GO:0048488","count":1},{"id":"GO:0032456","count":1},{"id":"GO:0032483","count":1}]},{"hash":"1307429304383414336","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":13,"triangles":13,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006223","count":5},{"id":"GO:0007625","count":4},{"id":"GO:0019835","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0046038","count":4}]},{"hash":"383420906852231377","title":"DNA Replication Fork Dynamics and Telomere Regulation","description":"The top GO terms cluster around DNA replication and genome maintenance, including replication fork progression and reversal, DNA recombination, RNA primer processing, and telomere maintenance/regulation, plus mitochondrial DNA repair. This combination points to a cohesive theme of replication fork dynamics and telomere integrity maintenance, with a broader role in genome stability across nuclear and mitochondrial DNA.","confidence":"High","size":8,"edges":24,"triangles":34,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1903469","count":2},{"id":"GO:0044806","count":2},{"id":"GO:0051974","count":2},{"id":"GO:0043504","count":2},{"id":"GO:0097046","count":2}]},{"hash":"391543487581869608","title":"Meiotic recombination and chromosome segregation","description":"The top GO terms are dominated by meiotic processes\u2014meiotic heteroduplex formation, reciprocal meiotic recombination, meiotic mismatch repair, meiotic metaphase I chromosome alignment, meiotic spindle midzone assembly, and chromosome segregation in meiosis (both male and female). There are a couple general terms (protein folding, somatic hypermutation) that are not core to meiosis, but the strongest signal is meiosis and homologous recombination, supporting a cohesive label. ","confidence":"High","size":8,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000713","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0006298","count":2},{"id":"GO:0007144","count":2},{"id":"GO:0043060","count":2}]},{"hash":"141540936669091333","title":"Unknown","description":"The top GO terms cover a wide mix of processes: cytoskeletal remodeling (myosin II filament disassembly) and adhesion, protein phosphorylation and its regulation, necroptotic cell death, hypoxic/anoxic response, ion homeostasis (Mg2+), protein tetramerization, and responses to growth factors (prolactin, BDNF). There isn\u2019t a single cohesive biological theme tying these together, suggesting the cluster may be functionally diverse or multi-tasking rather than representing one clear pathway or process.","confidence":"","size":8,"edges":12,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0031037","count":2},{"id":"GO:0046777","count":2},{"id":"GO:0070266","count":2},{"id":"GO:0071454","count":2},{"id":"GO:0010961","count":2}]},{"hash":"349037802710556185","title":"Unknown","description":"The terms span peroxisomal import and lipid metabolism (peroxisome-related processes) as well as plant-specific interactions (peroxisome\u2013chloroplast tethering and photomorphogenesis) alongside animal reproductive processes (meiosis/spermatocyte division). This mix suggests no single cohesive function linking all proteins, so Unknown is the most appropriate label.","confidence":"","size":8,"edges":15,"triangles":13,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0048147","count":1},{"id":"GO:0016558","count":1},{"id":"GO:0010381","count":1},{"id":"GO:0007112","count":1},{"id":"GO:0006513","count":1}]},{"hash":"88731256996401151","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030836","count":1},{"id":"GO:0032361","count":1},{"id":"GO:0046050","count":1},{"id":"GO:0071318","count":1},{"id":"GO:0006114","count":1}]},{"hash":"642720829573202739","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":1},{"id":"GO:0009060","count":1},{"id":"GO:0022904","count":1},{"id":"GO:0044780","count":1},{"id":"GO:0045041","count":1}]},{"hash":"445368753353395506","title":"RNA Splicing and Translational Regulation","description":"The dominant GO terms center on RNA processing and post-transcriptional control: splicing (mRNA splice site recognition, regulation, and spliceosome assembly), small-subunit processome assembly, and stress-related mRNA stability, together with miRNA- and regulatory ncRNA-mediated gene silencing and translation reinitiation. This points to a cohesive cluster of RNA processing and translational regulation functions.","confidence":"High","size":8,"edges":16,"triangles":16,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0075525","count":4},{"id":"GO:1905663","count":4},{"id":"GO:0000381","count":4},{"id":"GO:0035278","count":4}]},{"hash":"1279140418573609488","title":"Unknown","description":"No GO terms are provided for this cluster, so there isn\u2019t a clear shared function to label. The cluster has 8 proteins with 13 edges and 7 triangles, indicating moderate connectivity, but without functional terms a specific label cannot be inferred.","confidence":"","size":8,"edges":13,"triangles":7,"max_degree":7,"top_function":null,"top_go_terms":[]},{"hash":"966731320032061095","title":"Ribosome biogenesis and translation regulation","description":"The top GO terms show a strong emphasis on translation and ribosomal RNA maturation (translation GO:0006412 with 5 proteins; SSU-rRNA maturation GO:0000462 with 2), plus a signal for regulation of translation initiation. This indicates a cluster focused on ribosome assembly and control of protein synthesis. Additional terms touch on transcription-related processes and stress responses (antibiotic exposure, heat), which may reflect broader RNA metabolism and regulatory connections but do not outweigh the primary ribosome/translation signal. ","confidence":"Medium","size":8,"edges":11,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006351","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0000902","count":2}]},{"hash":"703519928973827233","title":"Mitochondrial energy metabolism and insulin signaling","description":"The cluster is enriched for GO terms tied to mitochondria (membrane fission, ATP transport, nucleotide import, CoA transport) and energy-related processes (adaptive thermogenesis), along with insulin- and glucose-related signaling responses. This combination suggests a cohesive theme around mitochondrial energy production and metabolic regulation in response to insulin/glucose.","confidence":"High","size":8,"edges":12,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1990314","count":6},{"id":"GO:0030302","count":6},{"id":"GO:0090149","count":6},{"id":"GO:1990519","count":6},{"id":"GO:0034198","count":6}]},{"hash":"1569344049560044392","title":"Ribosome Biogenesis and LSU Maturation","description":"The top GO terms cluster around maturation of LSU rRNA, assembly of the large subunit preribosome, and overall ribosome biogenesis, with supporting signals from mRNA transport and TORC1 pathways that coordinate ribosome production with growth. This points to a cohesive function in ribosome assembly and rRNA processing, especially for the large subunit.","confidence":"High","size":7,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0051301","count":2},{"id":"GO:1902626","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0070262","count":2}]},{"hash":"1184288927670658472","title":"Viral entry and virion assembly","description":"The top GO terms are dominated by virus-related processes: pore complex assembly, translocation of proteins into host cells, and virion assembly, pointing to viral particle formation and entry into host cells as the core theme; a few immune response terms may reflect host-pathogen interactions. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046931","count":7},{"id":"GO:0044053","count":7},{"id":"GO:1904871","count":7},{"id":"GO:0052212","count":7},{"id":"GO:1901998","count":7}]},{"hash":"930817092436848496","title":"Meiosis spindle assembly and microtubule dynamics","description":"This cluster is dominated by GO terms tied to meiotic cell division: male meiosis cytokinesis and spindle assembly in female meiosis I, plus microtubule polymerization. Together, these indicate a module involved in meiotic spindle formation and microtubule dynamics. A few other terms (cadmium response, circadian rhythm regulation, brain development, synapse assembly, ubiquitination regulation) are present but represent a minority of annotations and are less central to the cluster's core function. Therefore, the label reflects the primary meiotic/spindle function of this cluster.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007112","count":2},{"id":"GO:0042752","count":1},{"id":"GO:0007057","count":1},{"id":"GO:0071276","count":1},{"id":"GO:0046785","count":1}]},{"hash":"1965607262491952825","title":"Protein quality control and ER stress response","description":"The top GO terms center on managing misfolded proteins and cellular stress: aggresome assembly and stress granule disassembly reflect cleanup of protein aggregates; ER unfolded protein response and ER polarization indicate ER stress handling; SNARE complex disassembly and microtubule-based movement point to vesicle trafficking and protein turnover; regulation of ubiquitin-specific protease activity suggests ubiquitin-mediated quality control. Overall, the cluster seems to collect proteins involved in stress-induced protein quality control and associated trafficking.","confidence":"Medium","size":7,"edges":16,"triangles":15,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0070842","count":2},{"id":"GO:0035617","count":2},{"id":"GO:0006919","count":2},{"id":"GO:0007018","count":1},{"id":"GO:0070914","count":1}]},{"hash":"1175009714511543519","title":"Seed lipid metabolism and germination","description":"The cluster shows strong signals for lipid-related processes (long-chain fatty acid import, fatty acid biosynthesis, bile acid metabolism) together with seed development signals (seed coat development and positive regulation of seed germination), suggesting a functional theme tied to lipid biosynthesis/import in seeds and their germination. Some terms (bioluminescence, malonate catabolic process, nonribosomal peptide biosynthesis) appear as outliers, but do not override the core lipid-seed signal.","confidence":"Medium","size":7,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0090410","count":6},{"id":"GO:0008218","count":6},{"id":"GO:0044539","count":6},{"id":"GO:1902987","count":6},{"id":"GO:0008206","count":6}]},{"hash":"1168429390836779261","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0045451","count":4},{"id":"GO:0000480","count":4},{"id":"GO:0060213","count":4}]},{"hash":"1052160379292677478","title":"Ubiquitin-mediated cell cycle regulation","description":"Most of the top GO terms describe mitotic cell cycle progression and ubiquitin signaling (mitotic cell cycle, cell division, positive regulation of mitotic metaphase/anaphase transition, protein K11-linked ubiquitination). This strongly suggests the cluster's function relates to ubiquitin-mediated control of mitosis. Additional terms about ER stress\u2013related translation initiation and innate immune response may reflect broader stress signaling interactions with cell-cycle checkpoints, but the core theme remains cell-cycle regulation by ubiquitin.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090526","count":2},{"id":"GO:0016570","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0045087","count":1},{"id":"GO:0008277","count":1}]},{"hash":"2080104197774530898","title":"TLR- and interferon-mediated innate immune signaling","description":"The cluster is dominated by terms related to innate immune sensing and inflammatory signaling: TLR1 and TLR9 signaling, dsRNA response, type I interferon signaling, and cytokine production (including IL-18) plus inflammatory response. A few terms about tooth mineralization and kidney size are peripheral, but the core pattern points to TLR-driven interferon and cytokine-mediated immunity.","confidence":"High","size":7,"edges":10,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0060340","count":2},{"id":"GO:0034130","count":1},{"id":"GO:0043330","count":1},{"id":"GO:1905289","count":1},{"id":"GO:0032741","count":1}]},{"hash":"273701983718743939","title":"Unknown","description":"The top GO terms are highly diverse, spanning epithelial maturation, SNARE regulation, pain response, telomere maintenance, chloroplast protein import, salicylic acid response, NOD1 signaling, ADP-ribosylation, calcium signaling, and endothelial delamination. There is no clear, common biological process or pathway linking these terms, so a coherent, specific label isn\u2019t supported.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060743","count":1},{"id":"GO:0035544","count":1},{"id":"GO:0048265","count":1},{"id":"GO:1904357","count":1},{"id":"GO:0045038","count":1}]},{"hash":"860200007104492087","title":"Mitochondrial Complex IV Assembly and Regulation","description":"The top GO terms point strongly to mitochondrial function, especially complex IV (cytochrome c oxidase) assembly and regulation of its activity, with supporting hints from copper ion transfer and protein maturation. While development-related terms (heart/brain development) appear, they are likely secondary or pleiotropic in this small cluster, and do not define the primary function. Confidence: Medium","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018343","count":1},{"id":"GO:1904960","count":1},{"id":"GO:0007507","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0015680","count":1}]},{"hash":"1903160697068759080","title":"Proteoglycan biosynthesis","description":"The top GO terms highlight chondroitin sulfate and heparan sulfate proteoglycan biosynthesis, pointing to a core theme of glycosaminoglycan production. While other terms touch on broader lipid and phosphate metabolism, proteoglycan biosynthesis is the strongest and most representative function among the cluster\u2019s terms.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2001311","count":1},{"id":"GO:0016036","count":1},{"id":"GO:0032958","count":1},{"id":"GO:0050650","count":1},{"id":"GO:0071454","count":1}]},{"hash":"1825778974449490783","title":"Developmental signaling and cytoskeletal remodeling","description":"This cluster features GO terms that converge on signaling pathways (insulin receptor signaling, hepatocyte growth factor response), tissue development (adipose tissue development, organ morphogenesis), and cytoskeletal dynamics (actin filament organization), suggesting a theme of signaling-driven developmental growth and structural remodeling. Immune-related terms and ubiquitination regulation appear but seem less central to the core theme, which is why the label emphasizes development and cytoskeletal signaling. ","confidence":"Medium","size":7,"edges":11,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1901076","count":1},{"id":"GO:0035176","count":1},{"id":"GO:0007015","count":1},{"id":"GO:0008286","count":1},{"id":"GO:0061847","count":1}]},{"hash":"1296651277408654936","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":10,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071038","count":2},{"id":"GO:0045006","count":2},{"id":"GO:0034475","count":2},{"id":"GO:0070481","count":2},{"id":"GO:0000467","count":2}]},{"hash":"472569856559653596","title":"Organelle Protein Import and Proteostasis","description":"The terms cluster around protein trafficking into mitochondria and peroxisomes (import into peroxisome matrix, receptor recycling, insertion into mitochondrial inner membrane) and related quality-control processes (intralumenal vesicle formation, aggresome assembly, oxidation-dependent proteolysis), suggesting a shared theme of organelle protein handling and proteostasis, rather than a single signaling pathway. DNA replication and ERBB signaling appear only tangentially, reinforcing that the core signal is organelle-associated protein management.","confidence":"Medium","size":6,"edges":7,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0038127","count":2},{"id":"GO:0090296","count":1},{"id":"GO:0070407","count":1},{"id":"GO:0016562","count":1}]},{"hash":"1737384996319633910","title":"Vesicle Trafficking and Endosomal Sorting","description":"The cluster is dominated by GO terms for intracellular transport: ER-Golgi and Golgi-ER vesicle trafficking, endocytosis, vacuole targeting, and multivesicular body assembly, which together indicate a cohesive vesicle trafficking/endosomal sorting theme. Protein ubiquitination also appears, likely reflecting regulation of trafficking or turnover. A minor item, pre-miRNA export, reflects general RNA/nuclear-cytoplasmic transport but does not disrupt the central trafficking pattern. Overall, these terms point to proteins that coordinate vesicle traffic, endosomal maturation, and related quality control processes.","confidence":"High","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006623","count":4},{"id":"GO:0006897","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0016567","count":4}]},{"hash":"20407246599002045","title":"Transcription Regulation and Developmental Signaling","description":"The cluster combines transcription regulation (RNA polymerase I/III, DNA binding) with several signaling pathways relevant to development and morphogenesis (Wnt, activin/SMAD signaling) and associated phosphorylation events, including serine/threonine sites. Endothelial tube morphogenesis hints at a vascular development context, tying transcriptional control to signaling-driven morphogenesis. The phosphatidylcholine biosynthetic term is less directly connected but may support membrane-associated signaling. Overall, these proteins seem to integrate transcriptional regulation with developmental signaling and angiogenesis.","confidence":"Medium","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006359","count":1},{"id":"GO:0061154","count":1},{"id":"GO:0006656","count":1},{"id":"GO:0006356","count":1},{"id":"GO:0032927","count":1}]},{"hash":"154500771742783103","title":"Meiosis and Germline Development","description":"The GO terms revolve around meiotic processes (DNA double-strand break formation, recombination checkpoint signaling) and germline maturation (oogenesis, blastocyst development), with supporting roles in chromosome dynamics and DNA integrity checkpoints typical of meiosis in germ cells. This cohesive theme strongly points to meiotic regulation and germline development as the cluster's core function.","confidence":"High","size":6,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000678","count":1},{"id":"GO:0000070","count":1},{"id":"GO:0042177","count":1},{"id":"GO:0042138","count":1},{"id":"GO:0051312","count":1}]},{"hash":"1356245722031031213","title":"Unknown","description":"The top GO terms span several distinct cellular processes (vacuolar/ion homeostasis, membrane transport, cytoskeletal movement, cytokinesis, splicing, stress responses, fertilization, and kinase regulation), with no clear single function tying the six proteins together. This makes it unlikely to assign a coherent, specific label beyond Unknown.","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009826","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0015991","count":1},{"id":"GO:0007338","count":1},{"id":"GO:0007018","count":1}]},{"hash":"1908847717714598347","title":"RNA processing and genome maintenance under stress","description":"Based on GO terms dominated by mRNA splicing regulation (GO:0000398, GO:0048026), DNA damage tolerance and nucleotide-excision repair (GO:0006301, GO:0006289), and stress-related localization (GO:1903608), the cluster appears to coordinate RNA processing with genome maintenance under cellular stress. Additional terms such as protein targeting and stress granule localization support a broader stress-response role, while plasmodesmata transport and chromatin regulation hint at context-specific regulation in multicellular tissues. Overall, the shared theme is RNA processing intertwined with genome integrity in stress conditions.","confidence":"Medium","size":6,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090394","count":2},{"id":"GO:0006301","count":1},{"id":"GO:1903608","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0006289","count":1}]},{"hash":"1686936704107526055","title":"COPI-mediated ER-Golgi transport","description":"The GO terms cluster around COPI-coated vesicles, ER-to-Golgi transport, and Golgi ribbon formation, plus regulation of protein exit from the ER and secretion-related processes (e.g., Wnt). This points to a cohesive function in early secretory vesicle trafficking and Golgi organization, making a COPI-ER-Golgi transport label appropriate.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070863","count":2},{"id":"GO:1902003","count":2},{"id":"GO:0061357","count":2},{"id":"GO:0035964","count":2},{"id":"GO:0001893","count":2}]},{"hash":"554398939844951949","title":"Unknown","description":"No GO terms are provided for this cluster (the Top Terms section is empty), so there is no clear shared function to base a label on. The network metrics alone suggest connectivity but not a specific biological role, making an accurate name impossible with the given data.","confidence":"","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[]},{"hash":"1533612073436245299","title":"Vacuolar Autophagy and TORC1 Signaling","description":"The terms cluster around autophagy-related processes and vacuolar localization, including microautophagy, regulation of autophagy, TORC1 signaling, and responses to amino acid starvation, with supporting vesicle trafficking (GTPase activity). Although transcription-related terms appear, the strongest common theme is vacuole-associated autophagy and nutrient-sensing pathways, likely in yeast. ","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903778","count":1},{"id":"GO:1904263","count":1},{"id":"GO:0006348","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0010507","count":1}]},{"hash":"20029400014217095","title":"Unknown","description":"The two GO terms present (ER protein folding and olfactory learning) do not share a clear biological theme, and there are no network connections to tie the proteins into a common function. This makes it inappropriate to assign a specific, coherent label beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":1},{"id":"GO:0008355","count":1}]},{"hash":"997225802016736636","title":"Unknown","description":"There are no GO terms in the Top Terms to define a shared function for these six proteins, so no specific label can be inferred from the data. The cluster may reflect a generic interaction group rather than a cohesive biological process or function.","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[]},{"hash":"178764994326632160","title":"RNA modification and ribosome biogenesis","description":"This cluster centers on RNA processing: tRNA acetylation, tRNA wobble modification, rRNA acetylation for SSU maturation, and ribosomal small subunit biogenesis, suggesting a cohesive theme of RNA modification and ribosome assembly. A couple of terms about telomere maintenance and cell-cycle regulation are present but less representative.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051391","count":1},{"id":"GO:0032211","count":1},{"id":"GO:1904812","count":1},{"id":"GO:0070317","count":1},{"id":"GO:0042274","count":1}]},{"hash":"1057292787598544395","title":"Antiviral Innate Immunity and Ubiquitin-Dependent Degradation","description":"The cluster is dominated by GO terms for innate immune response and defense response to virus, indicating an antiviral innate immunity theme. The presence of ubiquitin-dependent pathways (ERAD and ubiquitin-dependent protein catabolic process) supports a role in proteostasis and degradation of viral or misfolded proteins during immune responses. A few metabolic terms are present but appear incidental to the main antiviral/proteostasis signal. ","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0061615","count":1}]},{"hash":"207730067577013010","title":"Cytokine signaling and transcription regulation","description":"This cluster centers on immune signaling and transcription, with terms like positive regulation of interleukin-2 production, positive regulation of type II interferon production, and neutrophil homeostasis, plus DNA-templated transcription. Some included terms related to cardiac and retinal development may reflect broader signaling roles or annotation overlap, reducing strict specificity but not overturning the main immune/transcription theme.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032743","count":2},{"id":"GO:0019934","count":2},{"id":"GO:0000160","count":2},{"id":"GO:0055119","count":2},{"id":"GO:0001780","count":2}]},{"hash":"1479105958316360325","title":"Innate Immune TLR Signaling Cluster","description":"Dominant GO terms cluster around Toll-like receptor signaling and innate immunity (TLR3 signaling, MyD88-independent TLR signaling, LPS-mediated signaling, dsRNA response, muramyl dipeptide response, and innate immune response), with additional downstream chemokine regulation. A few outliers (tRNA export, actin filament regulation) do not define the core function. Overall, this cluster represents innate immune recognition via TLR pathways. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051770","count":2},{"id":"GO:0034138","count":1},{"id":"GO:0002756","count":1},{"id":"GO:2000813","count":1},{"id":"GO:0006409","count":1}]},{"hash":"1344551468281742305","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001680","count":1},{"id":"GO:0042245","count":1},{"id":"GO:0015969","count":1},{"id":"GO:0006808","count":1},{"id":"GO:0006203","count":1}]},{"hash":"599598345626141152","title":"TLR-Mediated Innate Immune Signaling","description":"The GO terms are dominated by Toll-like receptor\u2013related pathways and innate defense, including TLR3 signaling, MyD88-independent TLR signaling, LPS signaling, dsRNA response, and detection of muramyl dipeptide, all pointing to pathogen recognition and activation of innate immune signaling. Despite the sparse edges, this coherent set of terms supports labeling the cluster as TLR-mediated innate immune signaling.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034138","count":1},{"id":"GO:0002756","count":1},{"id":"GO:2000813","count":1},{"id":"GO:0006409","count":1},{"id":"GO:0032722","count":1}]},{"hash":"330590695443878798","title":"Electrical signaling in neurons and cardiac tissue","description":"This cluster's top GO terms point to action potential dynamics and conduction in excitable cells (neurons and heart), including neuronal action potential, membrane repolarization in atrial cardiomyocytes, and regulation of heart rate by cardiac conduction. Additional terms cover mechanosensory detection (touch and pain) and optic nerve organization, aligning with sensory-neural pathways. Some items like stress fiber assembly and circadian regulation are less central but may reflect broader cytoskeletal and neuronal signaling contexts. Overall, the proteins likely participate in electrical signaling and related sensory/cardiac functions.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019228","count":1},{"id":"GO:0050966","count":1},{"id":"GO:0051260","count":1},{"id":"GO:0043149","count":1},{"id":"GO:0021633","count":1}]},{"hash":"1411321822575536314","title":"Megakaryocyte/Platelet Vesicle Exocytosis","description":"The cluster is best described by vesicle trafficking and exocytosis processes tied to platelets and megakaryocytes, as shown by GO terms for platelet degranulation, megakaryocyte development, and dense core vesicle exocytosis, along with Golgi-to-endosome/vacuole transport and SNARE complex regulation. This points to regulated secretion and vesicle fusion in the megakaryocyte\u2013platelet axis, with phosphorylation providing regulatory control.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002576","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0009405","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0035544","count":1}]},{"hash":"2036729564941417156","title":"Mitotic DNA replication machinery","description":"The top GO terms are centered on mitotic DNA replication initiation, preinitiation complex assembly, GINS complex assembly, and DNA strand elongation in mitosis, pointing to core replication machinery. A couple of terms like fermentation and bacterial-type flagellum assembly appear as potential noise or annotations, but the dominant signal reflects replication machinery during mitosis.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902975","count":1},{"id":"GO:0032508","count":1},{"id":"GO:1902969","count":1},{"id":"GO:0071165","count":1},{"id":"GO:0001833","count":1}]},{"hash":"1417666178363408252","title":"Unknown","description":"There is no GO term information to define a shared function for this cluster; five proteins with a small edge set and no common top GO terms implies no recognizable shared pathway or molecular function. Therefore the appropriate label is Unknown with None confidence.","confidence":"","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"712857835484108212","title":"Unknown","description":"No identifiable shared function or terminology is observed: there are no GO terms, no interactions (edges), and no clustering signal to tie these proteins together, so a meaningful label cannot be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1774684717198151328","title":"Unknown","description":"No GO terms are provided for this cluster (Top Terms list empty), and with only 5 proteins and a single edge, there is no clear shared function to name it. Therefore the appropriate label is Unknown with no confidence.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"664631453525578270","title":"Actomyosin contraction and calcium signaling","description":"This cluster\u2019s strongest GO terms point to cytoskeletal regulation and contraction, including mitotic actomyosin contractile ring assembly, actin filament organization, regulation of muscle filament sliding speed, and cellular response to calcium ion, all indicating calcium-driven cytoskeletal dynamics. While other terms touch on metabolism and regulation, the cytoskeleton- and calcium-related terms are most representative of the cluster\u2019s shared function. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":1},{"id":"GO:0008216","count":1},{"id":"GO:0006749","count":1},{"id":"GO:0032972","count":1},{"id":"GO:0071277","count":1}]},{"hash":"213195224435935388","title":"Lipid Biosynthesis and Signaling","description":"The top GO terms cluster around lipid metabolism (fatty acid elongation, very long-chain fatty acid biosynthesis, sphingolipid biosynthesis) and signaling cascades (NF-kappaB, JNK, Rho). This suggests a cohesive theme where lipid biosynthesis interfaces with cellular signaling and remodeling, even though a few terms related to development are present as broader context.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030497","count":1},{"id":"GO:0045070","count":1},{"id":"GO:0007249","count":1},{"id":"GO:0007254","count":1},{"id":"GO:0046726","count":1}]},{"hash":"1501190076136758060","title":"Unknown","description":"The top GO terms are highly diverse, each appearing only once, and there are no edges or triangles linking the proteins. This lack of a shared functional theme or pathway makes it impossible to assign a cohesive label; the terms reflect a mixed set of annotations rather than a single biological function.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032435","count":1},{"id":"GO:0043058","count":1},{"id":"GO:0007033","count":1},{"id":"GO:0014898","count":1},{"id":"GO:0031642","count":1}]},{"hash":"2232743906974135633","title":"Unknown","description":"Cannot infer a common function: there are no GO terms or interactions to guide a meaningful label for these five proteins.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1034192951038116099","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0070409","count":1},{"id":"GO:0044344","count":1},{"id":"GO:0006526","count":1},{"id":"GO:0071377","count":1}]},{"hash":"1213654818670098402","title":"DNA replication and ribosome biogenesis","description":"The GO terms point strongly to core nuclear processes like nucleotide-excision repair, DNA replication, and cell division, together with ribosome biogenesis, suggesting a cluster tied to genome maintenance and protein synthesis. The transport-related terms may reflect multifunctional proteins but are less central to the dominant theme.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":2},{"id":"GO:0099133","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0010949","count":2},{"id":"GO:0060702","count":2}]},{"hash":"1316261226734543759","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":2},{"id":"GO:0000413","count":2},{"id":"GO:0006458","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1516127257495522091","title":"Unknown","description":"The GO terms cover fertilization, microtubule movement, hypoxia response, splicing, cadmium response, kinase activity regulation, cytokinesis, neuron apoptosis, ribosome biogenesis, and plant patterning, which span diverse biological processes. There isn\u2019t a single cohesive function that ties all proteins together, so a specific, representative label isn\u2019t apparent. ","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":2},{"id":"GO:0007018","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0071276","count":2}]},{"hash":"977831046129440205","title":"Fungal secretory trafficking and morphogenesis","description":"The GO terms cluster around the secretory pathway (positive regulation of ER exit, protein localization to the cell surface, secretion of lysosomal enzymes) and morphogenetic programs (pseudohyphal and invasive growth), suggesting a functional module linking protein trafficking with growth form changes in fungi. Ion homeostasis terms likely reflect the metabolic support for these processes, reinforcing the general link between secretion, surface remodeling, and morphogenesis.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030026","count":1},{"id":"GO:0010960","count":1},{"id":"GO:0070863","count":1},{"id":"GO:0061060","count":1},{"id":"GO:2000010","count":1}]},{"hash":"1526246981164456327","title":"Terpenoid and cholesterol biosynthesis","description":"This cluster is enriched for multiple terpenoid biosynthetic processes (geranyl diphosphate, farnesyl diphosphate, geranylgeranyl diphosphate, monoterpene biosynthesis) and cholesterol biosynthesis, pointing to an isoprenoid/sterol biosynthesis module. A few other terms (protein transport/heterotetramerization, occasional immune signaling terms) are present but do not define the core function; the terpenoid/sterol biosynthesis theme best explains the composition.","confidence":"High","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901663","count":2},{"id":"GO:0033384","count":2},{"id":"GO:0033386","count":2},{"id":"GO:0015031","count":2},{"id":"GO:0045337","count":2}]},{"hash":"1702278384616771082","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0072715","count":1},{"id":"GO:0006301","count":1},{"id":"GO:1903608","count":1},{"id":"GO:1902626","count":1},{"id":"GO:0071038","count":1}]},{"hash":"17430962547458596","title":"Iron-sulfur cluster assembly","description":"The strongest signal is Fe-S cluster biogenesis: [2Fe-2S] cluster assembly and maturation by Fe-S cluster transfer, suggesting these proteins function in assembling and maturing iron-sulfur cofactors. Some transcription-regulation and apoptosis-related terms are present but are peripheral or historical annotations; the core theme remains Fe-S cluster biosynthesis. ","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0044571","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0097428","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0051220","count":1}]},{"hash":"1308058582341807749","title":"RNA splicing and silencing machinery","description":"The top GO terms center on spliceosome-mediated regulation of mRNA splicing, splice site recognition, and small-subunit processome assembly, combined with miRNA- and ncRNA-mediated gene silencing and translation reinitiation. This points to a cohesive theme of RNA processing and post-transcriptional regulation, including splicing control and RNA silencing mechanisms.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1905663","count":1},{"id":"GO:0000381","count":1},{"id":"GO:0035278","count":1}]},{"hash":"734927052780758015","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":4},{"id":"GO:0006356","count":3},{"id":"GO:1990258","count":3},{"id":"GO:0048254","count":3},{"id":"GO:0000494","count":3}]},{"hash":"1353680858555557844","title":"Diphthamide formation and tRNA wobble modification","description":"This cluster is defined by GO terms for histidyl modification to diphthamide (elongation factor-related) and tRNA wobble uridine modification, both tied to translation; the budding growth term may reflect growth-related consequences of translation regulation, supporting a translation-modification theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017183","count":1},{"id":"GO:0007117","count":1},{"id":"GO:0002098","count":1}]},{"hash":"682074081685656726","title":"Actin Cytoskeleton Regulation and Lamellipodium Dynamics","description":"This cluster aggregates GO terms tied to actin filament depolymerization, lamellipodium assembly regulation, localization to the cell leading edge, and Rho signaling, indicating a shared theme of actin cytoskeleton remodeling and cell motility, with some broader signaling responses (IGF stimulus, oxidative stress) as secondary associations.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030836","count":1},{"id":"GO:0021766","count":1},{"id":"GO:0043538","count":1},{"id":"GO:1905873","count":1},{"id":"GO:0010593","count":1}]},{"hash":"214963273737817350","title":"Chloroplast and mitochondrial RNA processing","description":"Proteins in this cluster share GO annotations tied to RNA modification and processing in chloroplasts/plastids and mitochondria, including chloroplast RNA processing, plastid transcription, mitochondrial translation regulation, and RNA catabolic processes. The inclusion of chloroplast-nucleus signaling terms further reflects coordinated organellar gene expression, pointing to a cohesive role in organellar RNA maturation and expression control.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":1},{"id":"GO:0042793","count":1},{"id":"GO:0000961","count":1},{"id":"GO:0031426","count":1},{"id":"GO:0070129","count":1}]},{"hash":"104343006268156881","title":"Calcium-regulated secretion","description":"The top GO terms cluster around secretion (acetylcholine biosynthesis and secretion; insulin secretion) and calcium handling (calcium import into mitochondrion; mitochondrial calcium concentration), suggesting a common theme of calcium-dependent secretory pathways across different contexts, despite one plant-specific term and a general oligomerization term. Overall, the proteins appear to be tied to calcium-controlled secretion processes.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035786","count":1},{"id":"GO:0036444","count":1},{"id":"GO:0032024","count":1},{"id":"GO:0051561","count":1},{"id":"GO:0061526","count":1}]},{"hash":"2193206773044224202","title":"Unknown","description":"There are no GO terms or connections to tie these proteins to a shared function, and the graph has no edges, so a meaningful label can\u2019t be inferred.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1868740041430548404","title":"Calcium- and phosphorylation-driven cytoskeletal signaling","description":"The GO terms cluster around calcium-responsive signaling, actin/mitotic contractile ring organization, and various phosphorylation-regulation processes (peptidyl-threonine phosphorylation, protein serine/threonine kinase activity, and dephosphorylation), which together point to regulation of cytoskeletal dynamics in response to calcium signaling. Some terms (e.g., DNA binding, nigra development, hypoxia) are less connected, but the strongest theme is calcium- and phosphorylation-mediated control of the cytoskeleton.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071277","count":1},{"id":"GO:0032972","count":1},{"id":"GO:0010800","count":1},{"id":"GO:0006479","count":1},{"id":"GO:1903479","count":1}]},{"hash":"680081782267113605","title":"Unknown","description":"Four proteins show no interactions (Edges 0, Triangles 0, Max Degree 0) and no GO terms are listed, so there is no clear shared function to define a theme; the mention of 20 proteins re-added by ReCIPE does not establish a collapsible functional signal for this cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1282613935621311025","title":"Ribosome biogenesis and translation","description":"Although a few terms point to other processes (iron ion transport, cell septum assembly), the dominant terms describe ribosome assembly and function: ribosome biogenesis, cytoplasmic translation, tRNA modification, and export of the large ribosomal subunit from the nucleus. This pattern suggests the cluster centers on ribosome production and protein synthesis rather than a broader metabolic role.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015684","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0000747","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0002181","count":1}]},{"hash":"313401595701435364","title":"ER-phagy and autophagy machinery","description":"This cluster is strongly tied to autophagy-related processes: reticulophagy (ER-phagy), autophagosome maturation, and targeting proteins for vacuolar autophagy, along with responses to amino acid starvation and oxidative stress. The involvement of ER-to-Golgi vesicle transport and piecemeal microautophagy of the nucleus highlights roles in organelle turnover via autophagic pathways, supporting a concise label focused on ER-phagy/autophagy.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0061709","count":3},{"id":"GO:0070301","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0034727","count":3},{"id":"GO:0010940","count":3}]},{"hash":"1226016089297160778","title":"Mitosis and DNA Replication","description":"Top GO terms point to core cell division processes such as DNA replication, spindle assembly, and kinetochore localization, suggesting the cluster centers on chromosome segregation and DNA synthesis during mitosis. While there are some development-related terms, the predominant theme is mitotic machinery.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0010800","count":2},{"id":"GO:0035924","count":2},{"id":"GO:0070509","count":2}]},{"hash":"2229974472987677972","title":"Nuclear RNA Processing, Surveillance, and Decay","description":"The top GO terms point to nuclear mRNA decay and surveillance pathways (nonsense-mediated decay, nuclear mRNA surveillance, histone mRNA decay, deadenylation-independent decapping) and relate to transcription termination/elongation control by RNA polymerase II, suggesting a cohesive role in nuclear RNA quality control and processing.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000184","count":1},{"id":"GO:0070370","count":1},{"id":"GO:0031087","count":1},{"id":"GO:0000738","count":1},{"id":"GO:0071028","count":1}]},{"hash":"2218476073466819479","title":"Unknown","description":"The GO terms are highly diverse (cadmium response, nucleotide-excision repair, miRNA silencing, GPCR regulation, calcium transport, interferon signaling, rRNA maturation, action potential regulation, transcription, and morphogenesis), showing no single cohesive function or pathway linking the proteins.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0035278","count":1},{"id":"GO:1904021","count":1},{"id":"GO:1901896","count":1}]},{"hash":"2053056334129807490","title":"Unknown","description":"No GO terms or clear shared function are reported for this cluster (no edges, no topology, and empty top terms). With only a few protein IDs and no functional signals, there\u2019s no basis to assign a meaningful label beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"183977748084973425","title":"Central carbon metabolism","description":"This cluster is dominated by core energy pathways: glycolysis, the TCA cycle, 2-oxoglutarate metabolism, and gluconeogenesis, indicating functions in central carbon flux and energy production. Additional terms touch fatty acid biosynthesis and minor nucleotide-related processes, with a few obsolete terms. Overall, it represents core energy metabolism with ancillary metabolic connections.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":2},{"id":"GO:0006096","count":2},{"id":"GO:0006103","count":2},{"id":"GO:0006213","count":1},{"id":"GO:0042759","count":1}]},{"hash":"678993374750871270","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0072715","count":3},{"id":"GO:1903608","count":3},{"id":"GO:1902626","count":3},{"id":"GO:0071038","count":3},{"id":"GO:0034475","count":3}]},{"hash":"155289379711749498","title":"RNA Cap and Ribosome Methylation","description":"This cluster centers on methylation-related processes affecting RNA caps and ribosomal components; GO terms include 7-methylguanosine mRNA capping, rRNA guanine-N7 methylation, tRNA methylation, and N-terminal methylations, plus small subunit export from the nucleus, pointing to RNA processing and ribosome biogenesis. Some terms seem peripheral (e.g., nodulation, vitamin E biosynthesis), likely noise relative to the core methylation theme.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:0006596","count":2},{"id":"GO:0010189","count":2},{"id":"GO:0070476","count":2},{"id":"GO:0018012","count":2}]},{"hash":"872972009857515471","title":"Ubiquitin/SUMO-driven protein quality control","description":"The top GO terms cluster around post-translational modification by ubiquitin and SUMO (sumoylation, ubiquitin-dependent ERAD, autoubiquitination) and degradation pathways (aggresome assembly, mitophagy, autophagy regulation). Together they point to cellular protein quality control and turnover mediated by ubiquitin/SUMO pathways, with some ancillary links to ER membrane processes and translation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":2},{"id":"GO:0030433","count":2},{"id":"GO:1903265","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0071816","count":1}]},{"hash":"2245928775205024049","title":"Mitochondrial nucleotide transport and energy metabolism","description":"The GO terms point strongly to mitochondrial functions, with recurring references to nucleotide transport (deoxynucleotide transport, pyrimidine nucleotide import into mitochondrion) and energy-related transport (mitochondrial ATP transmembrane transport, coenzyme A transmembrane transport), alongside mitochondrial membrane fission and adaptive thermogenesis. This suggests a cohesive theme around mitochondrial nucleotide handling and energy homeostasis. Confidence: High","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1990314","count":3},{"id":"GO:0030302","count":3},{"id":"GO:0090149","count":3},{"id":"GO:1990519","count":3},{"id":"GO:0034198","count":3}]}]