[{"hash":"899220187483105944","title":"Neural development and synaptic vesicle regulation","description":"The top GO terms point to brain development and regulation of synaptic vesicle exocytosis, indicating a cluster enriched for neural development and synaptic signaling pathways. Additional terms about apoptosis and stress responses suggest a broader regulatory/stress-responsive context in neurons, though some terms (like mating projection growth and insulin secretion) are peripheral and reflect shared vesicle trafficking pathways. Overall, the dominant theme is neural development with regulation of vesicle release.","confidence":"Medium","size":29,"edges":2,"triangles":0,"max_degree":2,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007420","count":7},{"id":"GO:0060313","count":5},{"id":"GO:0032024","count":5},{"id":"GO:2000300","count":5},{"id":"GO:0031384","count":5}]},{"hash":"1663774292578654977","title":"Vesicle trafficking and exocytosis","description":"The top GO terms cluster around vesicle handling and regulated exocytic processes: synaptic vesicle priming, acrosome reaction, intracellular protein transport, and negative regulation of neutrophil degranulation. These point to a shared function in moving vesicles to membranes and controlling their release, with regulatory signaling (Rho/Ras pathways) affecting the cytoskeleton and exocytosis. A plant-specific term (abscisic acid signaling) appears out of place but does not override the dominant vesicle trafficking theme. Therefore the cluster is best described as vesicle trafficking and exocytosis.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0009738","count":4},{"id":"GO:0006886","count":3},{"id":"GO:0030259","count":3},{"id":"GO:0060313","count":3},{"id":"GO:0035023","count":3}]},{"hash":"1242461958353915180","title":"Actin cytoskeleton dynamics and cell polarity","description":"The cluster is dominated by GO terms for actin-based processes: filopodium assembly and its regulation, cell spreading, and small GTPase-mediated signaling that drives cytoskeletal rearrangements. Additional terms involve maintaining cell polarity and vesicle trafficking between the ER and Golgi, all pointing to coordinated cytoskeletal control of cell shape, movement, and transport. Mitochondrial fission and GABAergic synaptic transmission can be linked to cytoskeletal regulation and neuronal architecture, supporting a unifying theme of cytoskeletal dynamics guiding morphology and trafficking.","confidence":"High","size":29,"edges":52,"triangles":15,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000266","count":7},{"id":"GO:1900026","count":7},{"id":"GO:0051489","count":7},{"id":"GO:0046847","count":7},{"id":"GO:0051932","count":7}]},{"hash":"1120182150087022366","title":"Oocyte meiosis and spindle dynamics with ubiquitin regulation","description":"Based on the top GO terms, the cluster is centered on oocyte maturation and spindle assembly during female meiosis I, along with proteolytic regulation by the ubiquitin-proteasome system (SCF-mediated protein degradation) and microtubule dynamics. While some terms point to broader development (neural tube formation), the dominant signals are meiotic spindle formation and proteolysis-related processes, which justify naming it around oocyte meiosis and spindle regulation.","confidence":"High","size":29,"edges":405,"triangles":3627,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":29},{"id":"GO:0006516","count":29},{"id":"GO:0008285","count":29},{"id":"GO:0007057","count":29},{"id":"GO:0051436","count":29}]},{"hash":"412209205103098149","title":"Unknown","description":"The list of GO terms is highly heterogeneous, including mitochondrial ribosome assembly, photosynthesis, ethanol metabolism, DNA repair/recombination, cell division, and even immune receptor-related processes, with several obsolete terms. This lack of a single coherent biological theme suggests no clear, representative function for the cluster.","confidence":"","size":29,"edges":406,"triangles":3654,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0061668","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0006067","count":2},{"id":"GO:0015979","count":2}]},{"hash":"1083197504566174010","title":"Organelle RNA Editing and Processing","description":"This cluster is dominated by GO terms related to RNA modification and processing in mitochondria and chloroplasts (e.g., mitochondrial and chloroplast RNA modification/processing, cytidine-to-uridine editing, and mitochondrial mRNA processing), suggesting a cohesive function in organellar RNA metabolism and editing. Confidence: High","confidence":"","size":29,"edges":374,"triangles":2890,"max_degree":28,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0090502","count":5},{"id":"GO:0009451","count":4},{"id":"GO:0016554","count":4},{"id":"GO:0080156","count":4},{"id":"GO:0000961","count":4}]},{"hash":"52316005574006791","title":"Plant organelle RNA editing and processing","description":"The top GO terms cluster around cytidine-to-uridine editing and RNA modification/processing in mitochondria and chloroplasts, including regulation of mitochondrial translation, with a plant-specific note on seed dormancy development. This suggests a cohesive theme of organellar RNA editing and processing in plants.","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":5},{"id":"GO:0080156","count":5},{"id":"GO:0000961","count":5},{"id":"GO:1905639","count":5},{"id":"GO:1900865","count":5}]},{"hash":"2122312888567278867","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":13,"triangles":0,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071555","count":7},{"id":"GO:0009834","count":5},{"id":"GO:0010118","count":4},{"id":"GO:0006260","count":3},{"id":"GO:1903469","count":3}]},{"hash":"1373065188114591480","title":"Mitochondrial protein import and inner-membrane assembly","description":"The majority of top terms center on mitochondrial processes\u2014targeting to mitochondrion, inner-m membrane protein insertion, and respiratory chain assembly\u2014suggesting a cluster focused on mitochondrial protein handling and assembly. Other terms (cytoskeletal organization, root hair growth) may reflect broader cellular context but do not outweigh the mitochondrial theme.","confidence":"High","size":29,"edges":100,"triangles":177,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":3},{"id":"GO:0072321","count":3},{"id":"GO:0051511","count":3},{"id":"GO:0048768","count":3},{"id":"GO:0043622","count":3}]},{"hash":"919061501715464277","title":"TGF-beta/BMP Signaling Regulators","description":"Most of the top GO terms point to modulation of TGF-beta/BMP signaling: negative regulation of BMP signaling, negative regulation of TGF-beta receptor signaling, SMAD-related assembly, and cellular response to TGF-beta stimulus. Additional terms about vesicle fusion and meristem identity suggest a broader role in development, but the core pattern is clear: this cluster comprises proteins that regulate TGF-beta/BMP signaling pathways. ","confidence":"High","size":29,"edges":300,"triangles":1650,"max_degree":28,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":29},{"id":"GO:0030514","count":24},{"id":"GO:0042347","count":24},{"id":"GO:0061191","count":24},{"id":"GO:0000173","count":24}]},{"hash":"740969924346813339","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":5},{"id":"GO:0080156","count":5},{"id":"GO:0000961","count":5},{"id":"GO:0009793","count":5},{"id":"GO:0042793","count":5}]},{"hash":"2188808416970486152","title":"ABA-Activated Transcriptional Regulation and Vacuolar Amino Acid Transport","description":"The cluster is enriched for transcription-related GO terms (DNA-templated transcription and its regulation) alongside ABA-activated signaling and plant development terms (root cap and multicellular organism development). In addition, several amino acid transport terms across the vacuole (glutamine, asparagine, histidine, lysine) hint at vacuolar transport processes common in plants. Together, these terms point to a set of proteins involved in ABA-responsive transcriptional regulation and plant-specific vacuolar amino acid transport, justifying the chosen label as a cohesive theme.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0048829","count":4},{"id":"GO:0009738","count":3},{"id":"GO:0007275","count":3}]},{"hash":"1327086615856960743","title":"Neural Development and Innate Immune Signaling","description":"The top GO terms show a mix of neural development processes (axonogenesis, corpus callosum development, positive regulation of synapse assembly, response to dopamine) and innate immune responses (defense against Gram-positive bacteria, LPS signaling, innate immune response, dsRNA response). This pattern suggests a theme where certain proteins participate in both neurodevelopmental pathways and immune signaling, or reflect neuroimmune cross-talk. The name highlights this dual functional theme without overcommitting to a single pathway.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050830","count":11},{"id":"GO:0007409","count":10},{"id":"GO:1903351","count":10},{"id":"GO:0014068","count":10},{"id":"GO:0031663","count":10}]},{"hash":"2233821099831507473","title":"Mitotic DNA Replication Machinery","description":"This cluster is dominated by terms tied to mitotic DNA replication initiation and elongation (GINS complex assembly, replication initiation, preinitiation complex assembly, and DNA-templated transcription regulation), indicating a cohesive replication-focused complex active during mitosis, with some related repair processes.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:1902969","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0071165","count":2},{"id":"GO:1902975","count":2}]},{"hash":"1205585757878631312","title":"Bacterial fatty acid metabolism and siderophore biosynthesis","description":"The top GO terms are dominated by fatty-acyl-CoA biosynthesis and catabolic processes for long- and medium-chain fatty acids (including palmitic acid biosynthesis), indicating a cluster focused on lipid metabolism. The presence of enterobactin biosynthesis points to bacterial siderophore production pathways, suggesting a combined theme of lipid metabolism and iron-chelation biology in a bacterial context. Some outlier terms (e.g., transcription regulation) may reflect regulatory components, but the primary signal supports lipid metabolism and siderophore biosynthesis.","confidence":"High","size":29,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045717","count":4},{"id":"GO:0035338","count":4},{"id":"GO:0009239","count":4},{"id":"GO:0036116","count":4},{"id":"GO:1900535","count":4}]},{"hash":"2006271743722994759","title":"Plant Hormone Signaling and Chromatin Regulation","description":"This cluster combines hormone signaling terms (cytokinin, salicylic acid, gibberellin) with chromatin-related processes (rDNA heterochromatin formation, chromatin remodeling) and plant physiological responses (leaf senescence, chlorophyll biosynthesis, osmotic stress, flavonol biosynthesis, and even viral processes), suggesting a module where hormone signaling interfaces with chromatin-mediated regulation of growth, stress responses, and metabolism in plants.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":16},{"id":"GO:0000183","count":10},{"id":"GO:0009751","count":10},{"id":"GO:0009739","count":10},{"id":"GO:0043044","count":10}]},{"hash":"607758057042676214","title":"Oocyte maturation and meiosis with ubiquitin-proteasome regulation","description":"The top GO terms strongly point to SCF-dependent ubiquitin-proteasomal degradation and general ubiquitin-mediated proteolysis, coupled with processes like oocyte maturation and spindle assembly in female meiosis I. This suggests a cluster centered on ubiquitin-proteasome control of meiotic progression and meiotic spindle dynamics. While neural-development terms appear, the dominant signal is ubiquitin-regulated meiosis and cell-cycle control in oocytes, supporting this label.","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"autophagy","top_go_terms":[{"id":"GO:0031146","count":19},{"id":"GO:0042787","count":14},{"id":"GO:0001556","count":13},{"id":"GO:0006516","count":13},{"id":"GO:0008285","count":13}]},{"hash":"335163129067115582","title":"Plant growth and stress response regulation","description":"These GO terms cluster around plant development and regulation: gibberellin response, leaf senescence regulation, chlorophyll biosynthesis regulation, osmotic stress response, and secondary cell-wall aspects, plus transcriptional regulation via chromatin remodeling and snRNA transcription. The common theme is plant growth, pigment/biogenetic regulation, and stress signaling, rather than a single enzyme or pathway. Some terms like viral process appear incidental in this collection. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0016032","count":6},{"id":"GO:1901348","count":6},{"id":"GO:1900056","count":5},{"id":"GO:0010380","count":5},{"id":"GO:0009739","count":5}]},{"hash":"814409539805738405","title":"Plant cell wall remodeling and carbohydrate catabolism","description":"These proteins are enriched for pectin and polysaccharide catabolic processes and for cell wall organization, pointing to roles in plant cell wall remodeling and carbohydrate degradation. Plant-specific terms such as flower phyllotactic patterning and terpenoid biosynthesis support a plant metabolic/development context, though some terms (e.g., cerebellar cortex development) may reflect cross-organism annotation noise. Overall, the cluster appears to group polysaccharide metabolism and cell wall\u2013associated functions, with ancillary secondary metabolism in plants.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":6},{"id":"GO:0060773","count":5},{"id":"GO:0071555","count":5},{"id":"GO:0021695","count":3},{"id":"GO:0043547","count":3}]},{"hash":"708305282172326002","title":"Plant defense and cell wall remodeling with xenobiotic transport","description":"This cluster centers on plant-specific defense responses to fungi (defense response to fungus; defense response) and breakdown/remodeling of cell wall components (chitin catabolic process; cell wall macromolecule catabolic process; polysaccharide catabolic process), with auxin-mediated growth signaling and some xenobiotic transport activity, suggesting a coordinated program of immune response, cell wall turnover, and detoxification. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":5},{"id":"GO:0051781","count":2},{"id":"GO:0006032","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0006952","count":2}]},{"hash":"1607040818685779855","title":"Eye development and pigment cell differentiation","description":"This cluster features retina development in camera-type eye and pigmentation, with supporting signals for multicellular development and actin cytoskeleton remodeling (Arp2/3) that underlie morphogenesis. It also includes terms tied to transcription and translation initiation, indicating active gene expression programs driving developmental processes.","confidence":"Medium","size":28,"edges":100,"triangles":201,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0002188","count":8},{"id":"GO:0043981","count":8},{"id":"GO:0043982","count":8},{"id":"GO:0001731","count":8},{"id":"GO:0034314","count":8}]},{"hash":"703947332525972971","title":"Retina development and synaptic plasticity","description":"The top GO terms predominantly point to retina-related development (retina vasculature development in camera-type eye) and neuronal communication (glutamatergic synaptic transmission, long-term potentiation), suggesting a neural/retinal function cluster. Some terms (abscisic acid signaling, myoblast fusion) seem unrelated noise or broader cellular processes, but the core theme fits neural development and synaptic plasticity. Confidence: Medium","confidence":"Medium","size":28,"edges":15,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0061298","count":5},{"id":"GO:0001324","count":4},{"id":"GO:0034351","count":4},{"id":"GO:0060963","count":4},{"id":"GO:0009738","count":4}]},{"hash":"1377958978086607805","title":"Ubiquitin-dependent proteolysis and signaling","description":"This cluster is dominated by GO terms related to ubiquitination (K48- and K6-linked), ubiquitin-dependent ERAD, and protein catabolic processes, plus autoubiquitination, all pointing to ubiquitin-mediated protein turnover. Additional terms link to signaling pathways (JNK cascade, TNF signaling), suggesting these proteins function together in tagging substrates for degradation and modulating stress/inflammatory signaling. The presence of multiple coherent ubiquitination-related terms supports a cohesive theme, despite some obsolete annotations.","confidence":"High","size":28,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:0046328","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0070936","count":5}]},{"hash":"161100043591848645","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":378,"triangles":3276,"max_degree":27,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:1905639","count":4},{"id":"GO:0080156","count":4},{"id":"GO:0016554","count":4},{"id":"GO:1900865","count":4},{"id":"GO:0031425","count":4}]},{"hash":"204737224383016049","title":"Chloroplast and mitochondrial RNA editing and processing","description":"The cluster is enriched for chloroplast organization, chloroplast protein import into the stroma, and RNA editing/modification in chloroplast and mitochondrial transcripts, pointing to organellar gene expression and RNA processing in plants, including responses like de-etiolation. This cohesive theme explains the combination of chloroplast/mitochondrial RNA editing and organelle maintenance functions.","confidence":"High","size":28,"edges":123,"triangles":140,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006355","count":2},{"id":"GO:0009704","count":2},{"id":"GO:0009658","count":2},{"id":"GO:1904216","count":2}]},{"hash":"1892672633167492505","title":"Membrane Transporters","description":"The top GO terms are all transport-related, covering ion and sugar transmembrane transport, as well as vesicular neurotransmitter loading. This points to a cluster of transmembrane transporter proteins with diverse substrates and both uptake and vesicle-loading roles.","confidence":"High","size":28,"edges":32,"triangles":15,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035725","count":9},{"id":"GO:0015751","count":8},{"id":"GO:0042891","count":8},{"id":"GO:0015757","count":8},{"id":"GO:0042128","count":8}]},{"hash":"2110540140884161998","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0071555","count":5},{"id":"GO:0006284","count":4},{"id":"GO:0000289","count":3},{"id":"GO:0006281","count":3}]},{"hash":"642706688547403485","title":"Metal ion homeostasis and transcriptional regulation","description":"The cluster shows a blend of transcription-related terms (DNA-templated transcription; regulation of transcription by RNA polymerase II) and metal ion handling terms (cadmium, copper, mercury, zinc transport; detoxification; metal export), suggesting proteins involved in responding to metal stress via coordinated transport/detoxification and transcriptional regulation.","confidence":"Medium","size":28,"edges":19,"triangles":1,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0055114","count":3},{"id":"GO:0006357","count":2},{"id":"GO:0070574","count":2},{"id":"GO:0050787","count":2}]},{"hash":"1151382387059747562","title":"Calcium-Responsive Transcriptional Regulation","description":"The cluster is dominated by GO terms for transcription (DNA-templated transcription, RNA Pol II transcription) and cellular response to calcium, suggesting proteins coordinately regulate gene expression in response to calcium signaling. Additional terms point to SMAD signaling and development-related processes like osteoblast proliferation, reinforcing a theme of calcium- and signal-driven transcriptional regulation.","confidence":"High","size":28,"edges":363,"triangles":2915,"max_degree":27,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071277","count":16},{"id":"GO:0006351","count":15},{"id":"GO:0006366","count":12},{"id":"GO:0036091","count":10},{"id":"GO:0031063","count":9}]},{"hash":"976933400488262441","title":"Post-translational modification and mitochondrial dynamics","description":"The cluster is dominated by GO terms for protein modification (sumoylation, ubiquitination, deubiquitination, autoubiquitination) and by opposing GO terms regulating mitochondrial fusion, indicating a link between post-translational control and mitochondrial dynamics, with supporting signals of cellular stress and inflammatory signaling (toxicity response and TNF pathways). This combination supports a cohesive theme around protein modification pathways intersecting with mitochondrial regulation.","confidence":"High","size":28,"edges":109,"triangles":190,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":5},{"id":"GO:0016579","count":4},{"id":"GO:1904049","count":4},{"id":"GO:1903265","count":4},{"id":"GO:0033132","count":4}]},{"hash":"1245554876417592609","title":"Nuclear DNA maintenance and transcription regulation","description":"This cluster centers on nuclear processes: DNA repair, DNA-templated transcription, tRNA processing, and histone-related regulation of gene expression, suggesting a cohesive module of genome maintenance and transcription control. Some terms (cell wall, cerebral cortex development, cytokinin biosynthesis) appear as outliers or cross-annotation, but the dominant signals point to chromatin-associated regulation and RNA/DNA processing.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":4},{"id":"GO:0008033","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0009691","count":2}]},{"hash":"394148924738079680","title":"RNA Processing and Transcription","description":"The cluster is dominated by RNA-related processes: mRNA capping, rRNA and tRNA modification, and transcription (DNA-templated and its regulation). A few terms point to plant metabolism (sterol and chlorophyll biosynthesis) and protein degradation, but these are less central, making RNA metabolism the best cohesive theme.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016126","count":3},{"id":"GO:0006370","count":3},{"id":"GO:0042787","count":2},{"id":"GO:0006511","count":2},{"id":"GO:0006351","count":2}]},{"hash":"961969803984617425","title":"DNA Replication and Cell Cycle Machinery","description":"The cluster is dominated by GO terms related to core nuclear processes: DNA-templated transcription, DNA replication, mitotic cell cycle, and DNA repair, suggesting a cohesive group of proteins involved in DNA metabolism and cell-cycle control. While a subset of terms touches on development and signaling (neurotrophin signaling, Wnt regulation, morphogenesis), these likely reflect multifunctional proteins or secondary roles rather than defining the cluster's primary function.","confidence":"High","size":28,"edges":30,"triangles":1,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":26},{"id":"GO:0006260","count":26},{"id":"GO:0000278","count":26},{"id":"GO:0006281","count":26},{"id":"GO:0048011","count":25}]},{"hash":"2275400445918725964","title":"Plant Growth and Defense Pathways","description":"The cluster shows GO terms centered on plant development and signaling (flower phyllotactic patterning, brassinosteroid signaling) as well as cell wall dynamics (cell wall organization, pectin catabolic process) and defense-related metabolism (hypersensitive response, glucosinolate and nitrile biosynthesis). While a couple of terms like nervous system development or MHC antigen processing appear unrelated and may be annotation noise, the dominant themes tie to growth regulation and plant defense. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":6},{"id":"GO:0051260","count":5},{"id":"GO:0045490","count":4},{"id":"GO:0060773","count":4},{"id":"GO:0071555","count":4}]},{"hash":"582668566280003901","title":"TLR/Myd88 innate immune signaling and cytokine production","description":"The top GO terms are dominated by innate immune signaling and cytokine regulation (MyD88-dependent TLR signaling, defense against virus, LPS detection, and cytokine production), suggesting that the cluster represents TLR-mediated immune sensing and inflammatory responses. Some development-related terms appear but are likely incidental annotations; the primary theme is innate immune signaling and cytokine regulation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002755","count":21},{"id":"GO:0051607","count":21},{"id":"GO:0032497","count":21},{"id":"GO:0002730","count":21},{"id":"GO:0007169","count":21}]},{"hash":"544512787300175578","title":"Plant development and transcription regulation with cuticle biosynthesis","description":"The top GO terms indicate strong involvement in DNA-templated transcription regulation and transcription, alongside plant developmental processes (bract development, seed development, floral meristem growth) and cuticle-related processes (cutin and wax biosynthesis). This suggests a cluster of plant regulatory proteins coordinating transcriptional control with epidermal development and cuticle formation. Confidence: Medium","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0015031","count":2},{"id":"GO:0010200","count":2},{"id":"GO:0010432","count":2}]},{"hash":"1819854883498125668","title":"Transcriptional Regulation and Development","description":"This cluster centers on DNA-templated transcription and its regulation, plus RNA Pol I\u2013related transcription and multicellular development, suggesting a nucleus-wide gene expression regulatory module involved in development. The presence of rRNA maturation and DNA repair terms hints at broader nuclear processes (ribosome biogenesis, genome maintenance) that may accompany transcriptional control in these proteins. Overall, the dominant theme is transcriptional regulation linked to development, with some ancillary functions, possibly reflecting annotation noise. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0016575","count":2}]},{"hash":"1898657369151423071","title":"Plant membrane transport and defense biosynthesis","description":"The dominant GO terms center on transport (lipid, fatty acid, and protein transport) and membrane-related processes like plant-type cell wall assembly, coupled with defense against fungus. While heme and LPS biosynthesis appear, the strongest signal is membrane transport tied to plant defense and cell wall remodeling, justifying a label focused on membrane transport in a plant defense/metabolic context.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":4},{"id":"GO:0050832","count":3},{"id":"GO:0006869","count":3},{"id":"GO:0016049","count":2},{"id":"GO:0015031","count":2}]},{"hash":"2189597663456010757","title":"Flower development and organ boundary regulation","description":"The cluster is enriched for plant floral development terms, notably organ boundary specification between lateral organs and the meristem and petal development, plus floral organ abscission. Additional signals from transcriptional regulation and ubiquitination suggest a regulatory network governing floral morphogenesis. Overall, the set likely reflects Flower development and organ boundary regulation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0010199","count":5},{"id":"GO:0048441","count":5},{"id":"GO:0006355","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0043547","count":2}]},{"hash":"553116261357650068","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0006730","count":2},{"id":"GO:0006189","count":2},{"id":"GO:0033320","count":2},{"id":"GO:0009258","count":2}]},{"hash":"2033407697341862091","title":"Intracellular signaling and membrane localization","description":"Most represented terms point to intracellular signal transduction, including Rho signaling and GPCR-associated routes, plus membrane localization and related processes like cell migration. The presence of additional, diverse terms (NOD1 signaling, salicylic acid signaling, mRNA processing) suggests a broad, heterogeneous set of signaling-related functions rather than a single cohesive pathway. This justifies a general label reflecting signaling and membrane-associated regulation rather than a specific pathway.","confidence":"Low","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":4},{"id":"GO:0035556","count":4},{"id":"GO:0016477","count":3},{"id":"GO:0061408","count":3},{"id":"GO:0035023","count":3}]},{"hash":"460684527763438387","title":"Plant oxidative stress and cell wall remodeling","description":"The top GO terms cluster around oxidative stress response and detoxification (response to oxidative stress, cellular oxidant detoxification, hydrogen peroxide catabolic process) alongside plant-specific cell wall processes (plant-type cell wall organization, lignin catabolic process). Additional terms on lipid catabolism and cobalt transport suggest membrane remodeling and metal homeostasis during stress. Together, these point to a plant-focused response that detoxifies oxidants and remodels the cell wall and membranes, hence the label.","confidence":"High","size":28,"edges":20,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006824","count":3},{"id":"GO:0006979","count":3},{"id":"GO:0046274","count":3},{"id":"GO:0009664","count":3}]},{"hash":"219530488893960917","title":"Lymphocyte development and signaling","description":"The presence of GO terms like germinal center formation, B cell receptor signaling, and regulation of IgE isotype switching points to a theme of lymphocyte development and immune signaling, even though a few outliers may reflect annotation noise.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045497","count":1},{"id":"GO:0072156","count":1},{"id":"GO:2000176","count":1},{"id":"GO:1900477","count":1},{"id":"GO:0048294","count":1}]},{"hash":"1064873339605132655","title":"Transcription and Mitotic Cell Cycle Regulation","description":"Top terms show a strong emphasis on DNA-templated transcription and mitotic cell cycle progression (cell division, G1/S transition, syncytial blastoderm mitotic cycle). While a few terms touch on metabolism and autophagy-related assembly, the core theme is transcriptional control linked to mitosis.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0051301","count":7},{"id":"GO:0000082","count":7},{"id":"GO:0019373","count":6},{"id":"GO:0060153","count":6}]},{"hash":"847046562787653706","title":"Plant vascular development and secondary cell wall biosynthesis","description":"This cluster is enriched for plant-specific developmental processes, notably secondary cell wall biogenesis and its positive regulation, plus vascular-related differentiation (protoxylem, xylem vessel differentiation) and related organ formation steps (root cap development, callus formation, fruit dehiscence). The presence of DNA-templated transcription and its regulation supports a coordinated transcriptional program governing these developmental events.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009834","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0006355","count":6},{"id":"GO:1901348","count":5},{"id":"GO:0048829","count":4}]},{"hash":"614461302278128182","title":"Glycan and Polysaccharide Biosynthesis","description":"The top GO terms point to biosynthesis of complex polysaccharides, including plant cell wall components (xyloglucan, glucuronoxylan, xylogalacturonan, fucose) and glycosaminoglycans in proteoglycans (heparan sulfate, heparin). This suggests a shared function in glycan assembly across plants and animals, with a few development-related terms likely reflecting glycans\u2019 roles in signaling and tissue formation. Overall, the cluster seems driven by glycan biosynthesis processes.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":5},{"id":"GO:0009969","count":5},{"id":"GO:0010417","count":5},{"id":"GO:0030210","count":5},{"id":"GO:0015012","count":5}]},{"hash":"913335318181961652","title":"Ubiquitin-Proteasome System and NF-kappaB Signaling","description":"This cluster is strongly enriched for ubiquitin-dependent proteolysis, including SCF-dependent proteasomal degradation and various forms of protein ubiquitination, alongside regulators of NF-kappaB signaling, TNF-mediated pathways, and antiviral defense. The presence of histone ubiquitination and protein turnover terms further supports a theme around ubiquitin-regulated degradation and chromatin regulation that interfaces with immune signaling. Overall, the common thread is ubiquitin-proteasome\u2013mediated proteostasis linked to inflammatory/immune signaling.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0031146","count":14},{"id":"GO:0042787","count":14},{"id":"GO:0090073","count":11},{"id":"GO:1903265","count":10},{"id":"GO:0051607","count":10}]},{"hash":"2136795794396060729","title":"Plant cell wall remodeling and growth signaling","description":"The top GO terms cluster around cell wall organization/modification and pectin catabolic process, with supporting terms for auxin-activated signaling and regulation of DNA-templated transcription, suggesting a coordinated program governing cell wall remodeling during plant growth. Additional terms for copper ion response and defense against fungus indicate stress-related modulation of this growth program, while cell cycle and transcriptional regulation reflect broader control. Overall, the cluster seems to capture plant-specific cell wall remodeling coupled to growth signaling.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0071280","count":2},{"id":"GO:0045490","count":2}]},{"hash":"228979208791737578","title":"Intracellular Signaling and Cytoskeletal Dynamics","description":"Top GO terms indicate broad intracellular signaling (intracellular signal transduction, GPCR-related signaling, B cell receptor signaling) coupled with processes tied to cytoskeletal remodeling and movement (cell migration, spindle assembly, pollen tube growth/guidance) and stress responses (heat, mechanical stimulus) as well as ubiquitin-dependent protein catabolism. The common thread is proteins involved in signaling cascades that regulate cytoskeletal dynamics and cellular responses to stimuli, spanning growth, division, and stress, hence a general signaling/cytoskeletal theme.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035556","count":8},{"id":"GO:0050853","count":7},{"id":"GO:0007205","count":6},{"id":"GO:0016477","count":6},{"id":"GO:0051225","count":5}]},{"hash":"925697429475571692","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006006","count":2},{"id":"GO:0006977","count":2},{"id":"GO:0048240","count":2},{"id":"GO:0052889","count":2},{"id":"GO:2000344","count":2}]},{"hash":"1178915056221935923","title":"Ubiquitin-Dependent Signaling in Pollen Tube Growth","description":"This cluster centers on ubiquitin-related regulation, including ubiquitination and proteolysis, linked to intracellular signal transduction and transcriptional regulation. The presence of pollen tube guidance and regulation of pollen tube growth terms points to a plant reproductive context, where ubiquitin-mediated signaling likely controls growth, cell cycle, and apoptotic processes. Taken together, this cluster appears to group proteins involved in ubiquitin-dependent signaling and transcriptional modulation relevant to pollen tube development.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":6},{"id":"GO:0000122","count":5},{"id":"GO:0000209","count":5},{"id":"GO:0010183","count":4},{"id":"GO:0080092","count":4}]},{"hash":"1257978410252103961","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are heavily dominated by ubiquitin-related protein catabolism, including ubiquitin-dependent proteolysis, autoubiquitination, K48-linked ubiquitination, and SCF-mediated proteasomal degradation, indicating a core function in tagging proteins for proteasomal degradation. Other terms may reflect broader turnover processes but the dominant signal is ubiquitin-proteasome\u2013mediated degradation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":17},{"id":"GO:0051865","count":13},{"id":"GO:0070936","count":12},{"id":"GO:0031146","count":11},{"id":"GO:0030433","count":11}]},{"hash":"1399749597447555965","title":"Chloroplast and mitochondrial RNA processing and signaling","description":"The top GO terms cluster around organelle RNA metabolism in plants: chloroplast RNA processing, plastid transcription, chloroplast RNA modification, mitochondrial mRNA modification, and cytidine-to-uridine editing, plus chloroplast-nucleus signaling and regulation of mitochondrial mRNA catabolic processes. This suggests a plant-specific module focused on chloroplast/mitochondrial RNA processing and plastid-nucleus communication; the seed dormancy term aligns with plant developmental context. ","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000961","count":6},{"id":"GO:0031425","count":6},{"id":"GO:0010019","count":6},{"id":"GO:0042793","count":6},{"id":"GO:0009451","count":5}]},{"hash":"1886047191252581559","title":"Chloroplast/mitochondrial RNA editing and processing","description":"The cluster is dominated by GO terms for RNA modification and processing in chloroplasts and mitochondria, including cytidine-to-uridine editing and organelle mRNA modification/processing, as well as chloroplast-nucleus signaling. A single developmental term (seed dormancy) is present but not central to the main theme. Overall, the shared function points to organellar RNA editing/processing.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":4},{"id":"GO:1905639","count":4},{"id":"GO:0080156","count":4},{"id":"GO:0000961","count":4},{"id":"GO:0016554","count":4}]},{"hash":"743409230168638223","title":"Plant organellar RNA editing and processing","description":"This cluster centers on RNA modification and processing in plant organelles\u2014especially cytidine-to-uridine editing and mitochondrial/chloroplast RNA editing/processing\u2014with supporting signals for chloroplast-nucleus communication, indicating a cohesive theme of organellar RNA editing in plants.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":6},{"id":"GO:0016554","count":6},{"id":"GO:0080156","count":6},{"id":"GO:0000961","count":6},{"id":"GO:1905639","count":6}]},{"hash":"1953858908916381584","title":"Ribosome Biogenesis and Translation Initiation","description":"The top GO terms are dominated by ribosome biogenesis (including ribosomal large subunit biogenesis) and formation of the translation preinitiation complex, pointing to a core theme of ribosome assembly and initiation of translation. While there are other annotations (DNA-templated transcription, ubiquitination, auxin signaling, methylation, cobalamin biosynthesis), these are less cohesive with the ribosome-focused pattern, making the ribosome-centric interpretation the most representative. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0070534","count":2}]},{"hash":"1815479506093439900","title":"Bacterial polysaccharide biosynthesis","description":"The top GO terms point strongly to biosynthesis of polysaccharides and related carbohydrate metabolism, with lipopolysaccharide biosynthesis, colanic acid biosynthesis, and GDP-mannose metabolism highlighted. While there are a few plant-associated biosynthetic terms (phenylpropanoid, lignans, anthocyanin), the strongest signal centers on bacterial polysaccharide production and cell envelope components, suggesting this theme for the cluster overall.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0009242","count":2},{"id":"GO:0019673","count":2},{"id":"GO:1902132","count":2},{"id":"GO:0009699","count":2}]},{"hash":"1244186611377001233","title":"Golgi Fucosylation and GDP-Fucose Transport","description":"The top GO terms are dominated by fucosylation processes (O- and N-linked fucosylation) and GDP-fucose transport into the Golgi lumen, along with related glycan biosynthesis and sugar transmembrane transport terms. Although some developmental terms appear, the core cluster signals Golgi-based glycosylation and nucleotide-sugar transport functions, justifying this label.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001654","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0048527","count":2},{"id":"GO:0036066","count":2},{"id":"GO:0080147","count":2}]},{"hash":"1965476992953700609","title":"Actin Dynamics and Vesicle Trafficking","description":"The GO terms cluster around actin remodeling (actin filament severing, barbed-end capping), vesicle trafficking and secretion (intracellular transport, COPII vesicle coating, regulation of extracellular matrix secretion), and related developmental/wound-healing processes, suggesting a cohesive theme of cytoskeleton-driven trafficking and secretion.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":5},{"id":"GO:0051014","count":4},{"id":"GO:0003331","count":4},{"id":"GO:0016525","count":3},{"id":"GO:0060291","count":3}]},{"hash":"663569497855399638","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051568","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0043473","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0000480","count":3}]},{"hash":"2086462086101939959","title":"Developmental retinoic acid and vitamin D metabolism","description":"The top GO terms cluster around developmental processes (hepatocyte differentiation, uterus development, female gonad development) and specific metabolic pathways for retinoic acid and calcitriol (vitamin D). This suggests a coherent theme where retinoid and vitamin D metabolism intersect with developmental regulation, with some broader xenobiotic metabolism signals as ancillary, but the developmental/metabolic pattern is the strongest signal. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0070365","count":13},{"id":"GO:0071615","count":12},{"id":"GO:0042904","count":12},{"id":"GO:0060065","count":12},{"id":"GO:0008585","count":12}]},{"hash":"1713590950737198348","title":"Plant Hormone Signaling and Transcriptional Regulation","description":"This cluster is enriched for plant hormone signaling (ABA response), calcium signaling, and core transcriptional machinery, including chromatin remodeling and nucleosome assembly, suggesting a group of nuclear regulators coordinating development and hormonal responses. The presence of floral meristem identity and general transcription terms supports a developmental/regulatory theme in plants, while an animal-specific term like primitive streak formation may reflect annotation noise.","confidence":"Medium","size":27,"edges":267,"triangles":1326,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090009","count":8},{"id":"GO:0009737","count":7},{"id":"GO:0071277","count":6},{"id":"GO:0010076","count":6},{"id":"GO:0000122","count":6}]},{"hash":"374413344406735536","title":"Pectin metabolism and pollen tube growth","description":"The cluster is dominated by GO terms for pectin catabolic process, mucilage pectin biosynthetic process, and pollen tube growth, along with cell wall modification. This points to plant-specific processes governing pectin remodeling and pollen tube extension, with other terms (transcription, ER-Golgi transport) being secondary. High","confidence":"","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045490","count":5},{"id":"GO:0048358","count":5},{"id":"GO:0009860","count":5},{"id":"GO:0043086","count":5},{"id":"GO:0042545","count":5}]},{"hash":"2135984225996235517","title":"Developmental growth and mitotic processes","description":"The cluster shows a strong emphasis on developmental events (embryonic organ development, spinal cord development, seminiferous tubule development, multicellular organism growth) along with mitotic and cell division activities (cell division, mitotic spindle assembly, mitotic sister chromatid cohesion). Some terms are labeled obsolete, but the overall pattern ties development and proliferation together, suggesting proteins involved in developmental growth coordination and cell division. Confidence reflects a coherent theme across both growth and mitotic processes.","confidence":"High","size":27,"edges":9,"triangles":0,"max_degree":4,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007568","count":9},{"id":"GO:0007064","count":9},{"id":"GO:0030433","count":9},{"id":"GO:0051301","count":9},{"id":"GO:0090307","count":9}]},{"hash":"167165072313738877","title":"Stress Response and Gene Expression Regulation","description":"The cluster contains GO terms for translation and transcription, indicating core gene expression machinery, together with stress-related terms such as response to toxic substances, xenobiotic stimulus, and general stress response. It also includes links to cell cycle progression (G0 to G1) and negative regulation of apoptosis, suggesting a coordinated program where stress responses are integrated with ongoing gene expression and cell survival. This combination points to a general theme of stress-induced gene expression regulation rather than a single specific pathway, hence the label.","confidence":"Medium","size":27,"edges":351,"triangles":2925,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0042493","count":2}]},{"hash":"292018061136780935","title":"RNA and protein methylation machinery","description":"The cluster is dominated by GO terms for RNA modifications (rRNA methylation, tRNA wobble modification, mRNA capping) and protein methylation (peptidyl-lysine methylation, N-terminal glycine methylation), pointing to methyltransferase activities as a common theme. Some peripheral terms relate to developmental processes, but the core signal is methylation biology.","confidence":"High","size":27,"edges":294,"triangles":1869,"max_degree":26,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031167","count":10},{"id":"GO:0018027","count":8},{"id":"GO:0000183","count":7},{"id":"GO:0018023","count":6},{"id":"GO:0018013","count":6}]},{"hash":"1674925859972134227","title":"Ethylene signaling in plant development and defense","description":"These terms cluster around plant development (bract and seed development, floral meristem growth, multicellular development, transcription) and defense responses (response to chitin, positive regulation of defense, cutin biosynthesis), with an explicit link to ethylene-activated signaling. This suggests proteins coordinating growth and defense through ethylene signaling pathways in plants. ","confidence":"High","size":27,"edges":11,"triangles":3,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010200","count":6},{"id":"GO:0010432","count":6},{"id":"GO:0048316","count":6},{"id":"GO:0009873","count":6},{"id":"GO:0010186","count":6}]},{"hash":"1057619201667411350","title":"Pollen exine formation and flavonoid biosynthesis","description":"The cluster is dominated by sporopollenin biosynthesis and DIM/DIP cell wall layer assembly, along with chalcone and flavonoid biosynthetic processes and fatty-acyl-CoA metabolism, all characteristic of pollen exine formation and the lipid/phenylpropanoid components that accompany it. ER stress-related terms appear ancillary and do not define the main function of this group.","confidence":"High","size":27,"edges":18,"triangles":6,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045454","count":6},{"id":"GO:0006633","count":6},{"id":"GO:0071770","count":5},{"id":"GO:0080110","count":5},{"id":"GO:0009715","count":5}]},{"hash":"516917049916115670","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0016266","count":3},{"id":"GO:0000727","count":2},{"id":"GO:0031573","count":2},{"id":"GO:0006295","count":2}]},{"hash":"59475061344217883","title":"Regulation of Plant Growth and Metabolism","description":"Based on the top GO terms, most entries point to plant-specific control of growth and development (secondary cell wall biogenesis, chlorophyll biosynthesis, leaf senescence, cytokinin signaling) and metabolic regulation (proteolysis, catalytic activity, phytochelatin synthesis). Despite one outlier term (roof of mouth development) likely being an annotation artifact, the cluster predominantly reflects coordinated regulatory processes in plants rather than a single pathway. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901348","count":5},{"id":"GO:0043085","count":5},{"id":"GO:1904715","count":5},{"id":"GO:0006508","count":5},{"id":"GO:0046938","count":5}]},{"hash":"882705600000588253","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":5},{"id":"GO:0080156","count":5},{"id":"GO:0009793","count":5},{"id":"GO:0031426","count":5},{"id":"GO:0016554","count":5}]},{"hash":"1925228003993988652","title":"Muscle and neural differentiation and morphogenesis","description":"This cluster is enriched for transcription by RNA polymerase II and programs of differentiation and tissue morphogenesis across muscle and neural lineages. Top terms include skeletal muscle differentiation and muscle morphogenesis, cardioblast migration (heart development), and various neural fate commitments (subpallium neuron fate, amacrine cell differentiation), plus integrin-mediated cell adhesion. Together, these suggest coordinated developmental programs governing muscle, heart, and brain tissues under transcriptional regulation, with additional circadian and metabolic regulation that commonly accompany development.","confidence":"Medium","size":27,"edges":351,"triangles":2925,"max_degree":26,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":21},{"id":"GO:2001016","count":16},{"id":"GO:0060415","count":14},{"id":"GO:0060163","count":14},{"id":"GO:0033627","count":14}]},{"hash":"344937997807284695","title":"Craniofacial and neural morphogenesis","description":"The top GO terms cluster around development of craniofacial structures and neural/optic components (embryonic cranial skeleton morphogenesis, face development, optic nerve morphogenesis) with signaling pathways (neurotrophin TRK, FGFR, Wnt) that regulate morphogenesis. This suggests the proteins collectively participate in head/face and neural tissue formation rather than unrelated processes. The presence of related proliferative and stress-response terms may reflect concurrent developmental processes. Overall, it points to craniofacial and neural morphogenesis and associated signaling pathways.","confidence":"High","size":27,"edges":161,"triangles":389,"max_degree":20,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":27},{"id":"GO:0006260","count":27},{"id":"GO:0048011","count":23},{"id":"GO:0090090","count":23},{"id":"GO:0020021","count":23}]},{"hash":"1760915202798266848","title":"Cytokinin Signaling and Plant Development","description":"The GO terms are dominated by cytokinin-activated signaling and plant-related developmental processes, including multicellular organism development, secondary cell wall biogenesis, chlorophyll biosynthesis regulation, and leaf senescence control, suggesting a cluster of proteins involved in hormone-driven plant growth and gene regulation. Some unrelated terms may reflect annotation noise but do not overpower the main plant-development theme.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":7},{"id":"GO:0007275","count":6},{"id":"GO:1901348","count":5},{"id":"GO:0000183","count":5},{"id":"GO:0006355","count":5}]},{"hash":"1284058200763982940","title":"Developmental Regulation and Stress Response","description":"The terms cluster around developmental processes (heart, forebrain, skeletal system, multicellular organism development) and transcriptional regulation (DNA-templated transcription), suggesting regulatory roles in development. The presence of stress- and immune-related terms (defense against Gram-positive bacteria, cadmium response, ER-stress\u2013induced apoptotic signaling) indicates concomitant engagement of cellular stress pathways. Together, they point to a set of proteins coordinating development with stress responses, rather than a single, narrow function.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":16},{"id":"GO:0030900","count":16},{"id":"GO:0006351","count":16},{"id":"GO:0007275","count":16},{"id":"GO:0001501","count":16}]},{"hash":"2093970632364237319","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":32,"triangles":10,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0044205","count":5},{"id":"GO:0071244","count":4},{"id":"GO:0015976","count":4},{"id":"GO:2000122","count":4},{"id":"GO:0071548","count":3}]},{"hash":"138517287952200932","title":"Plant Hormone Biosynthesis and Fruit Ripening","description":"This cluster is dominated by GO terms tied to plant hormone biosynthesis (ethylene, gibberellin, auxin) and processes related to fruit ripening, plus related secondary metabolism and stress responses (hydrogen peroxide\u2013mediated PCD). Despite some noisy terms (penicillin biosynthesis, obsolete redox term), the strongest signals point to plant growth regulators and maturation pathways, suggesting a cohesive theme of hormone-driven biosynthesis and fruit development.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0009693","count":5},{"id":"GO:0042318","count":5},{"id":"GO:0009686","count":5},{"id":"GO:0045487","count":5}]},{"hash":"408232108525412961","title":"Plant development and cuticle biosynthesis","description":"The cluster features GO terms centering on plant organ development (bract, seed, floral meristem growth) and auxin signaling, together with regulation of cutin and wax biosynthesis, suggesting a cohesive developmental-program and surface barrier (cuticle) biology. The presence of defense-related terms to fungus and chitin hints at links between development, immunity, and surface integrity\u2014common in plants where cuticle and developmental pathways intersect. Overall this cluster appears to reflect plant development with cuticle/wax biosynthesis and associated regulatory processes.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0050832","count":3},{"id":"GO:0010200","count":2},{"id":"GO:0010432","count":2}]},{"hash":"1851746729752191967","title":"Membrane Transport and Lipid Translocation","description":"The top GO terms are centered on transport and translocation, especially of lipids and related molecules (lipid translocation, ceramide and phospholipid translocation, long-chain fatty acid import, vitamin transmembrane transport, teichoic acid transport), with additional metal ion transport (cobalt). This points to a cohesive theme of membrane-associated transport and lipid handling across diverse substrates, even though some terms (like nodulation and nutrient response) are broader. Confidence in this thematic label is Medium.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0009877","count":6},{"id":"GO:0007584","count":6},{"id":"GO:0015777","count":5},{"id":"GO:0015910","count":5},{"id":"GO:0030299","count":5}]},{"hash":"1612955658288119524","title":"Plant floral development and transcriptional regulation","description":"The prominent GO terms center on regulation of DNA-templated transcription and transcription, coupled with developmental processes such as bract and seed development, floral meristem growth, and hormone signaling (ethylene, auxin). This suggests a cluster of plant transcriptional regulators implicated in floral development and associated organ formation. Heat and chitin response terms are present but less dominant, indicating some stress responsiveness within the set.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0009873","count":3},{"id":"GO:0009408","count":3},{"id":"GO:0010200","count":2}]},{"hash":"1196623539181669643","title":"Unknown","description":"The Top Terms span many unrelated processes (immune defense, development, transcription, telomere maintenance, adipogenesis, and ER-stress\u2013induced apoptosis) with no clear shared function or connectivity, so a coherent, representative label cannot be assigned.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":15},{"id":"GO:0006349","count":15},{"id":"GO:0001403","count":15},{"id":"GO:0030900","count":15},{"id":"GO:0006351","count":15}]},{"hash":"2044869455707440176","title":"Plant growth and stress-regulated development","description":"The GO terms point to plant-specific developmental and growth-regulatory processes (gibberellin response, leaf senescence, chlorophyll biosynthesis regulation, and secondary cell wall biogenesis regulation) along with transcriptional control (chromatin remodeling, snRNA transcription). Osmotic stress response and viral process terms suggest stress signaling and potential host-virus interactions, but the core theme centers on growth and development regulation in plants.","confidence":"High","size":27,"edges":10,"triangles":0,"max_degree":3,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0043044","count":10},{"id":"GO:1901348","count":10},{"id":"GO:1900056","count":9},{"id":"GO:0010380","count":9},{"id":"GO:0009739","count":9}]},{"hash":"575898220274455498","title":"Ubiquitin-Dependent Signaling","description":"The cluster is enriched for terms on ubiquitination and ubiquitin-mediated protein turnover (protein polyubiquitination; ubiquitin-dependent protein catabolic process) along with general intracellular signal transduction, implying these proteins participate in signaling pathways regulated by ubiquitination. Some terms (pollen tube growth/guidance) are plant-specific outliers, but the overarching theme is ubiquitin-driven signaling regulation.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":5},{"id":"GO:0035556","count":5},{"id":"GO:0080092","count":4},{"id":"GO:0010183","count":4},{"id":"GO:0050853","count":4}]},{"hash":"1193413484589263559","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":344,"triangles":2763,"max_degree":26,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":16},{"id":"GO:1905869","count":16},{"id":"GO:0019236","count":16},{"id":"GO:0051301","count":16},{"id":"GO:0002098","count":16}]},{"hash":"1765692036953790840","title":"Immune Signaling and Cell Migration","description":"The top GO terms are dominated by immune-related signaling pathways (B cell receptor signaling, LPS signaling, JNK cascade regulation) and development/migration processes (thymus development, cell migration, intracellular signal transduction). These co-occur frequently, suggesting a cluster centered on immune signaling and movement. A few terms about pollen tube growth and septin ring organization might reflect cross-species annotation noise or common signaling mechanics, but the core theme remains immune signaling and cellular navigation.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0050853","count":10},{"id":"GO:0048538","count":8},{"id":"GO:0016477","count":8},{"id":"GO:0080092","count":8},{"id":"GO:0035556","count":8}]},{"hash":"1408419452188758345","title":"ER\u2013Golgi Vesicle Traffic and Stress-Induced Apoptosis","description":"This cluster is dominated by GO terms for ER-to-Golgi vesicle transport and retrograde endosome-to-Golgi transport, pointing to core intracellular trafficking through the Golgi/ER network. The inclusion of stress-related apoptotic signaling and defense signaling (salicylic acid pathway) terms suggests a link between trafficking and cellular stress responses. Peripheral transport terms (malate, glutamate) may reflect metabolic adjustments during stress. Overall, the theme centers on vesicle trafficking with a connection to stress and defense responses.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0010917","count":3},{"id":"GO:0008631","count":3},{"id":"GO:0002037","count":3},{"id":"GO:0042147","count":2}]},{"hash":"199484602083421500","title":"Oocyte Meiosis and Maturation","description":"The top GO terms are dominated by oocyte maturation and spindle assembly in female meiosis I, along with microtubule dynamics and SCF/proteasomal protein turnover. This clustering suggests proteins governing meiotic progression and oocyte development, with proteolysis and chromatin-associated processes supporting meiosis. Some neural development terms appear less central, likely annotation noise, but the primary signal is meiosis/oocyte maturation. ","confidence":"High","size":27,"edges":16,"triangles":1,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":22},{"id":"GO:0001556","count":21},{"id":"GO:0021678","count":21},{"id":"GO:0006516","count":21},{"id":"GO:0051436","count":21}]},{"hash":"70282837247149926","title":"Ubiquitin-Dependent Proteolysis and NF-kB Signaling","description":"The cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes (including K48- and K6-linked ubiquitination and autoubiquitination) and histone catabolic activity, alongside innate immune responses and positive regulation of canonical NF-kappaB signaling and TNF-mediated pathways. This points to a group of proteins that link ubiquitination-driven proteolysis with modulation of NF-kB\u2013mediated immune signaling and antiviral defense.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0070936","count":10},{"id":"GO:1903265","count":10},{"id":"GO:0036205","count":10},{"id":"GO:0085020","count":10}]},{"hash":"2178278753717735617","title":"Organelle RNA editing and processing","description":"Dominated by GO terms for RNA modification/editing, plastid transcription, and chloroplast/mitochondrial RNA processing, this cluster likely represents factors involved in organellar RNA maturation and chloroplast\u2013nucleus signaling.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":6},{"id":"GO:0000961","count":6},{"id":"GO:0010019","count":6},{"id":"GO:0042793","count":6},{"id":"GO:0016554","count":5}]},{"hash":"765386943049133517","title":"Brain and Eye Development Proteins","description":"Most terms point to neural tissue development: brain development, forebrain development, and retina development are prominent, suggesting the cluster centers on brain/eye developmental roles. While there are additional terms indicating general cellular processes (ubiquitination, actin depolymerization, nuclear pore localization, peroxisome targeting, SREBP signaling), the neural-development terms are the strongest signal, supporting a label around neural/ocular development.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0000209","count":7},{"id":"GO:0007420","count":7},{"id":"GO:2001162","count":6},{"id":"GO:0006625","count":6},{"id":"GO:0030900","count":6}]},{"hash":"59207590672554829","title":"ER-Golgi Vesicle Trafficking Regulation","description":"The cluster is dominated by GO terms for ER-to-Golgi and Golgi-to-ER vesicle transport and by positive regulation of GTPase activity, suggesting Rab-like regulation of intracellular trafficking. Ubiquitination present in the list also fits with protein turnover linked to trafficking processes. Some terms (pigmentation, spinal cord development) appear peripheral but may reflect broader roles of trafficking and modification in development. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0043473","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0021510","count":3}]},{"hash":"876923853897314469","title":"Chromatin modification and immune signaling","description":"The top GO terms cluster around chromatin dynamics (histone catabolic process, histone ubiquitination, histone acetylation) and protein turnover, with concurrent immune-related signaling (NF-kappaB activation, TNF signaling) and V(D)J recombination, suggesting a theme of chromatin regulation linked to immune response and transcriptional control.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0036205","count":10},{"id":"GO:0042787","count":10},{"id":"GO:0042981","count":9},{"id":"GO:0033151","count":9},{"id":"GO:0070535","count":9}]},{"hash":"2058171058633900848","title":"Mitotic cell cycle and developmental transcription regulation","description":"Top GO terms indicate a core theme of cell-cycle progression and transcriptional control during development (mitotic cell cycle, cell division, DNA-templated transcription, regulation of DNA-templated transcription, multicellular organism development). The pigmentation and signaling terms are peripheral but consistent with broader developmental signaling contexts. Confidence in this label is High.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0043473","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0051301","count":3}]},{"hash":"863646229666690955","title":"RNA Processing and Ribosome Biogenesis","description":"This cluster is enriched for GO terms tied to mRNA splicing regulation (spliceosome), ncRNA-mediated silencing, snoRNA release in pre-rRNA, and ribosome/preribosome assembly, along with RNA-protein cross-linking and stress granule localization\u2014together pointing to post-transcriptional RNA processing and ribosome biogenesis as core functions of the proteins.","confidence":"High","size":26,"edges":155,"triangles":691,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":17},{"id":"GO:0031047","count":16},{"id":"GO:1903608","count":14},{"id":"GO:0042255","count":11},{"id":"GO:1902626","count":11}]},{"hash":"1652619298658838094","title":"Vacuolar trafficking and autophagy","description":"Top terms are centered on protein targeting to the vacuole, Golgi-to-vacuole transport, Golgi vesicle fusion, vacuole inheritance, and autophagy, indicating a core function in vesicle trafficking to and from vacuolar/secretory compartments. The presence of related secretory processes (neuron and platelet secretion) supports a broad vesicle trafficking/secretion theme, with autophagy tying into vacuolar dynamics. A lone glucose transport term is present but does not define the cluster. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0006623","count":4},{"id":"GO:0006896","count":4},{"id":"GO:0015758","count":4},{"id":"GO:0000011","count":3},{"id":"GO:0007412","count":3}]},{"hash":"149330482348388097","title":"Oocyte Meiosis and Spindle Assembly","description":"The terms point strongly to meiosis in oocytes (oocyte maturation, spindle assembly in female meiosis I, microtubule dynamics, SCF-mediated proteolysis) indicating a core theme of meiotic progression and spindle function.","confidence":"High","size":26,"edges":292,"triangles":1911,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":23},{"id":"GO:0006516","count":23},{"id":"GO:0008285","count":23},{"id":"GO:0007057","count":23},{"id":"GO:0051436","count":23}]},{"hash":"1886959404287909814","title":"mRNA processing and translation initiation","description":"This cluster is dominated by GO terms related to RNA processing and export (splicing via the spliceosome, alternative splicing, mRNA export, and polyadenylation), together with translation initiation-related terms (formation of the preinitiation complex and translation reinitiation, including viral reinitiation). The shared theme is RNA maturation followed by the early steps of translation, implying proteins involved in post-transcriptional mRNA processing and initiation of translation. ","confidence":"Medium","size":26,"edges":40,"triangles":22,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048025","count":8},{"id":"GO:0006406","count":8},{"id":"GO:1901407","count":8},{"id":"GO:1900363","count":7},{"id":"GO:0002188","count":7}]},{"hash":"1422579250085903586","title":"Fatty acid and lipid biosynthesis","description":"The top GO terms are dominated by fatty acid\u2013related biosynthetic and metabolic processes (short-, medium-, long-, and very long-chain fatty acids, and related lipid metabolism), with additional signals for other biosynthetic pathways (lipoteichoic acid, menaquinone, siderophores, and nonribosomal peptide biosynthesis). This suggests a core theme around lipid/fatty acid production and associated metabolite biosynthesis across diverse contexts. ","confidence":"High","size":26,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006633","count":9},{"id":"GO:0043041","count":7},{"id":"GO:0009234","count":7},{"id":"GO:0036112","count":7},{"id":"GO:0009698","count":7}]},{"hash":"2237173331028095039","title":"Ribosome biogenesis and translation; cell cycle","description":"The top GO terms show ribosomal small subunit biogenesis, cytoplasmic translation, and tRNA modification, indicating a central role in ribosome assembly and protein synthesis. The inclusion of cell cycle and cell division terms suggests these processes are coordinated with proliferation. Some terms like oogenesis and conjugation with cellular fusion may reflect broader developmental annotations or unrelated connections, but the dominant signal points to ribosome biogenesis and translation as the cluster\u2019s core function.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048477","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0002181","count":2}]},{"hash":"1202098820002315532","title":"Organelle Protein Import and Membrane Biogenesis","description":"This cluster is dominated by GO terms for importing proteins into chloroplast stroma and mitochondrial matrix/inner membrane, plus cristae formation and general membrane insertion, suggesting a theme of organelle protein targeting and membrane assembly. Some noise terms exist but the core signal points to organelle import and membrane biogenesis.","confidence":"High","size":26,"edges":16,"triangles":1,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0045037","count":6},{"id":"GO:0045039","count":6},{"id":"GO:0000002","count":6},{"id":"GO:0032094","count":6},{"id":"GO:0030150","count":6}]},{"hash":"1491966163644982261","title":"Neural development and growth factor signaling","description":"The top GO terms point to neural development (optic nerve morphogenesis, face development) and growth-factor\u2013driven signaling (neurotrophin TRK signaling, FGFR signaling, PI3K/AKT pathway), with Wnt pathway regulation also implicated. A few terms about stress responses appear, but the dominant pattern supports a neural development and signaling theme for this cluster.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":26},{"id":"GO:0090090","count":26},{"id":"GO:0020021","count":26},{"id":"GO:0071469","count":26},{"id":"GO:0060324","count":26}]},{"hash":"1661458352492284973","title":"Developmental transcriptional regulators","description":"The top GO term is regulation of DNA-templated transcription (16), with many terms tied to development and differentiation across tissues (uterus, heart septum morphogenesis, inner ear morphogenesis, erythrocyte and pancreatic cell differentiation, estrogen response). This pattern points to transcriptional regulators coordinating developmental programs. An outlier plant term exists but does not override the core theme.","confidence":"High","size":26,"edges":318,"triangles":2441,"max_degree":25,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":16},{"id":"GO:2000032","count":16},{"id":"GO:0060065","count":7},{"id":"GO:0003290","count":7},{"id":"GO:0003281","count":7}]},{"hash":"1376010081304901901","title":"Plant development and hormone signaling","description":"This cluster centers on plant morphogenesis and patterning, with GO terms for axis specification, abaxial cell fate, meristem and flower development, as well as transcriptional regulation (DNA-templated transcription) and hormone signaling (auxin pathway, hormone response, and gibberellin regulation). The combination suggests a coherent developmental module controlling organogenesis and timing under hormonal control.","confidence":"High","size":26,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009942","count":3},{"id":"GO:0010262","count":3},{"id":"GO:0010158","count":3},{"id":"GO:0048507","count":3},{"id":"GO:0009908","count":3}]},{"hash":"1875962024918651984","title":"Plant organellar RNA editing and processing","description":"The GO terms cluster around RNA modification and editing in plant organelles (chloroplasts and mitochondria), including cytidine-to-uridine editing, chloroplast/mitochondrial RNA processing, and chloroplast-nucleus signaling. This points to a cohesive role in post-transcriptional regulation of organellar transcripts, with a related developmental term suggesting broader plant developmental effects. Overall, the theme is organellar RNA editing/processing in plants.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0000961","count":2},{"id":"GO:1905639","count":2}]},{"hash":"87534539869744375","title":"Meiosis and Chromosome Segregation","description":"Proteins in this cluster are enriched for meiotic chromosomal events\u2014condensation, separation, and synaptonemal complex assembly\u2014as well as related nuclear processes like transcription regulation and nuclear import. This combination points to a cohesive group of meiosis-related chromosome dynamics proteins.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0010032","count":3}]},{"hash":"442375260589710462","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0034063","count":2},{"id":"GO:0000288","count":2},{"id":"GO:0072334","count":2}]},{"hash":"1795503566281106421","title":"Plant innate immunity and hypersensitive response","description":"This cluster is enriched for plant defense terms, including plant-type hypersensitive response, defense response to bacterium, and innate immune signaling, indicating a cohesive module of plant immune signaling. There are also post-transcriptional regulation terms (mRNA stability, polyadenylation, cap-independent translation), which may relate to how defense genes are controlled during immune responses or viral interactions, but the dominant theme is plant innate immunity and hypersensitive response.","confidence":"High","size":26,"edges":41,"triangles":4,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":3},{"id":"GO:1903679","count":3},{"id":"GO:0044829","count":3},{"id":"GO:0043488","count":3},{"id":"GO:0034052","count":3}]},{"hash":"626063045050105555","title":"Plant Floral Development Transcription Regulators","description":"This cluster is dominated by GO terms related to transcription regulation in plants, especially DNA-templated transcription, alongside multiple developmental processes tied to reproductive structures (bract and seed development, floral meristem growth, and phyllotactic/auxin-related signaling). Although some terms touch on DNA repair and stress responses, the strongest and most frequent themes point to plant developmental regulation and transcription control in floral contexts.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0006469","count":2},{"id":"GO:0010200","count":2}]},{"hash":"1566839146927281914","title":"Unknown","description":"The top GO terms span several unrelated areas (ERK5/MAPK signaling, Rho signaling and cell shape, nephron differentiation, hydrogen peroxide metabolism, IL-8 and Th2 cytokine regulation, macroautophagy, and protein complex stability), with no dominant shared function. This variety makes it difficult to assign a single concise biological theme to the cluster.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070375","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0035778","count":1},{"id":"GO:0010310","count":1},{"id":"GO:0045415","count":1}]},{"hash":"2050967101122301396","title":"Yeast bud neck organization and ubiquitin-mediated degradation","description":"This cluster is dominated by terms about bud neck/septin ring organization, protein localization to the bud neck, and ubiquitin-proteasome\u2013dependent protein degradation, all characteristic of budding yeast cell cycle events at the site of division, with ancillary links to actin cable regulation and peroxisomal import. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0044810","count":12},{"id":"GO:0032186","count":12},{"id":"GO:0042787","count":12},{"id":"GO:0031146","count":12},{"id":"GO:0070936","count":11}]},{"hash":"787152083424646282","title":"Plant Hormone Signaling and Transcriptional Regulation","description":"This cluster centers on plant hormone signaling (cytokinin, gibberellin, salicylic acid) linked to growth and development processes (secondary cell wall biogenesis, chlorophyll biosynthesis, leaf senescence) and broad transcriptional control (DNA-templated transcription, chromatin remodeling), with associated stress responses (osmotic stress, viral process). The converging GO terms point to a coherent regulatory module coordinating development and stress responses through hormonal signaling and transcriptional regulation.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901348","count":8},{"id":"GO:0009736","count":8},{"id":"GO:0006351","count":6},{"id":"GO:0009739","count":6},{"id":"GO:0009751","count":6}]},{"hash":"914722639428331872","title":"Centromere Chromatin Assembly and Mitotic Regulation","description":"The cluster is strongly linked to centromeric chromatin dynamics and chromosome segregation, highlighted by terms like CENP-A containing chromatin assembly, kinetochore assembly, and mitotic cell cycle, along with histone acetylation regulation and ubiquitination\u2014together pointing to chromatin remodeling that governs mitosis/meiosis.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071442","count":2},{"id":"GO:0006351","count":2},{"id":"GO:2000617","count":2},{"id":"GO:0051382","count":1},{"id":"GO:0036297","count":1}]},{"hash":"514194717162781563","title":"Plant defense signaling and transcription regulation","description":"The top GO terms cluster around plant stress responses, including salicylic acid\u2013mediated signaling, regulation of jasmonic acid biosynthesis, and ozone response, suggesting coordinated transcriptional control during defense. Supporting terms on RNA processing and transcription regulation (splicing, RNA polymerase II regulation, helicase activity) indicate a role for general gene-expression machinery linked to these responses. Outlier terms like pollen sperm cell differentiation and brown fat differentiation are likely annotation noise rather than core cluster themes.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051096","count":2},{"id":"GO:0050873","count":1},{"id":"GO:0048235","count":1},{"id":"GO:0040015","count":1},{"id":"GO:0080141","count":1}]},{"hash":"2167245459584978358","title":"Transcription Regulation & DNA Repair","description":"The top GO terms are dominated by transcription-related processes (DNA-templated transcription; regulation of transcription by RNA polymerase II; negative regulation of transcription by RNAP II) and by protein turnover and DNA maintenance (ubiquitin-dependent proteolysis; nucleotide-excision repair). This suggests a coherent theme around nuclear gene expression control coupled with genome maintenance, with a few auxiliary terms likely reflecting broader annotations. Therefore, a label emphasizing transcription regulation along with DNA repair best captures the cluster\u2019s core functions.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009734","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0010252","count":2},{"id":"GO:0035914","count":2}]},{"hash":"471471008745781931","title":"Neuronal development and axon morphogenesis","description":"This cluster centers on neural development, with terms for axonogenesis, axonal fasciculation, and nerve branching morphogenesis, plus regulation of Rho signaling and neural trafficking. The inclusion of Golgi-to-plasma membrane transport and ER tubular network formation suggests neuron-specific trafficking and polarity, while transcription regulation and hypoxia response may coordinate developmental programs. Overall, proteins likely function together in neuronal morphogenesis and axon guidance.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0071787","count":3},{"id":"GO:0007413","count":3},{"id":"GO:2000172","count":3},{"id":"GO:0006893","count":2}]},{"hash":"701513262767497456","title":"Nuclear transcription and RNA processing","description":"This cluster is dominated by GO terms for DNA-templated transcription, transcription regulation, mRNA processing, and nucleolus organization, with additional DNA repair terms, pointing to core nuclear gene expression and RNA maturation processes. The brain/organ development terms appear incidental and do not define the main theme.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006281","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0021695","count":2},{"id":"GO:0007507","count":2}]},{"hash":"1073273038637147952","title":"Glycan biosynthesis and secretory trafficking","description":"The cluster contains GO terms tied to biosynthesis of complex glycans and proteoglycans (heparan sulfate, proteoglycans; xyloglucan, xylogalacturonan; fucose) and the ER-to-Golgi transport pathway, indicating a coherent theme around glycan production and processing through the secretory route. A couple of development-related terms may reflect roles of glycans in developmental processes, but the dominant signal is glycan biosynthesis and trafficking.","confidence":"Medium","size":26,"edges":10,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030210","count":4},{"id":"GO:0015012","count":4},{"id":"GO:0009834","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0035118","count":2}]},{"hash":"105553569675658713","title":"SCF-dependent ubiquitin proteolysis in meiosis and oocyte maturation","description":"The cluster overwhelmingly features GO terms for SCF-dependent ubiquitin-proteasomal protein degradation and ubiquitin-mediated proteolysis, with oocyte maturation and spindle assembly in female meiosis I highlighting a meiotic/oogenesis regulatory role. While some terms relate to development, the core signal is proteolysis via the ubiquitin\u2013proteasome system in meiosis.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031146","count":12},{"id":"GO:0042787","count":10},{"id":"GO:0001556","count":8},{"id":"GO:0006516","count":8},{"id":"GO:0008285","count":8}]},{"hash":"1009488336842729522","title":"Immune development and signaling","description":"This cluster shows strong representation of immune-related terms, notably thymus development (5), B cell receptor signaling pathway (5), and innate immune response (4), suggesting a focus on immune system development and signaling pathways. While other terms like face development and axon regeneration appear, they are less central to the cluster\u2019s core theme, so the dominant pattern relates to lymphoid development and immune signaling. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048538","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0043552","count":5},{"id":"GO:0050853","count":5},{"id":"GO:0045087","count":4}]},{"hash":"1901556846405353088","title":"Ubiquitin-Proteasome Mediated Degradation","description":"The cluster is dominated by GO terms describing ubiquitin-dependent proteolysis and proteasomal degradation (including SCF-dependent pathways and K48/K6-linked ubiquitination), along with histone ubiquitination and autoubiquitination, and links to apoptotic regulation and TNF signaling. This points to a cohesive function centered on tagging substrates for degradation by the ubiquitin-proteasome system, with related chromatin and signaling roles. Unknown terms like V(D)J recombination appear contextually related through ubiquitination pathways but do not override the main theme.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":14},{"id":"GO:0042787","count":14},{"id":"GO:0070936","count":11},{"id":"GO:1903265","count":11},{"id":"GO:0036205","count":11}]},{"hash":"1981310445416002879","title":"Cell Cycle Regulation and Translation Initiation","description":"The top GO terms cluster around G1/S transition of the mitotic cell cycle, chromatid cohesion and chromosome localization, and also include translation initiation steps (preinitiation complex formation and translation reinitiation). This suggests a theme of coordinating cell cycle progression with the initiation of protein synthesis, with some related cytoskeletal/chromosome organization processes, consistent with roles in cell division and chromosome dynamics. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":4},{"id":"GO:0043666","count":4},{"id":"GO:0006470","count":4},{"id":"GO:0051754","count":4},{"id":"GO:0002188","count":4}]},{"hash":"2098530293695971535","title":"Cell Envelope Polysaccharide Biosynthesis","description":"The top GO terms are dominated by lipopolysaccharide and colanic acid biosynthetic processes, along with GDP-mannose metabolic activity, all pointing to synthesis and assembly of cell surface polysaccharides and their sugar precursors. While a few terms (e.g., transcription, plant secondary metabolite biosynthesis) seem less coherent with bacteria, the overarching pattern centers on polysaccharide production relevant to the bacterial cell envelope. This makes a label focused on cell surface polysaccharide biosynthesis appropriate, with some annotation noise acknowledged.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0009242","count":2},{"id":"GO:0019673","count":2},{"id":"GO:1902132","count":2},{"id":"GO:0009699","count":2}]},{"hash":"328169604116512312","title":"Plant mitochondrial and plastid gene expression","description":"Top GO terms strongly point to transcription and RNA processing in mitochondria and plastids, including mitochondrial transcription, plastid rRNA transcription, chloroplast organization, and mitochondrial ribosome assembly, supported by RNA splicing activity. This suggests a plant-specific module dedicated to organelle gene expression and ribosome biogenesis. Some development-related terms appear, but they do not override the core organelle-focused theme. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008380","count":2},{"id":"GO:0009658","count":1},{"id":"GO:0042794","count":1},{"id":"GO:0061668","count":1},{"id":"GO:0006393","count":1}]},{"hash":"1600649151701851636","title":"TLR-MyD88 Innate Immune Signaling and Th1 Response","description":"Most prominent terms point to innate immune signaling paths: JNK cascade activation, MyD88-dependent TLR signaling and Th1-type responses, with endocytic recycling supporting TLR trafficking. While there are some neuronal development terms, the immune-related terms predominate, suggesting the cluster centers on TLR/JNK signaling and Th1 inflammation.","confidence":"Medium","size":25,"edges":37,"triangles":5,"max_degree":10,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0046330","count":6},{"id":"GO:0032707","count":6},{"id":"GO:0042088","count":6},{"id":"GO:0071260","count":6},{"id":"GO:0048813","count":4}]},{"hash":"896895902438102283","title":"ER Stress Proteostasis and Quality Control","description":"The terms cluster around a proteostasis network activated by endoplasmic reticulum stress, including regulation of translation initiation under stress, misfolded protein handling and transport, and quality control via the ubiquitin-proteasome system, with supporting roles in nuclear and organelle protein targeting.","confidence":"High","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0036494","count":3},{"id":"GO:0070843","count":3},{"id":"GO:0006626","count":3},{"id":"GO:0071630","count":3},{"id":"GO:0097428","count":3}]},{"hash":"279471397611290099","title":"Muscle and cardiac differentiation with ossification","description":"This cluster centers on skeletal muscle differentiation, ventricular cardiac muscle differentiation, endochondral ossification, and calcium signaling, with transcriptional regulation\u2014pointing to a mesoderm-derived muscle/bone development program. Some terms (primitive streak, floral development) appear as cross-species annotations but do not override the dominant muscle/heart and bone differentiation signal.","confidence":"High","size":25,"edges":270,"triangles":1716,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071277","count":14},{"id":"GO:2001016","count":13},{"id":"GO:0006351","count":13},{"id":"GO:0090009","count":12},{"id":"GO:0060947","count":12}]},{"hash":"734554091497534571","title":"Ribosome biogenesis and rRNA maturation","description":"Based on the top GO terms, especially maturation of LSU-rRNA and ribosome biogenesis, the cluster is best described by ribosome assembly and rRNA processing. Other terms appear more peripheral or unrelated to a common function, so the ribosome-related signal is the most representative. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000463","count":4},{"id":"GO:0001501","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0007568","count":3}]},{"hash":"764120793409097278","title":"Organellar RNA Modification and Translation","description":"Based on GO terms like chloroplast organization, chloroplast RNA modification, mitochondrial mRNA modification, and translation, the cluster seems enriched for proteins involved in organellar gene expression, particularly RNA processing/editing in chloroplasts and mitochondria and related translation machinery. Some terms are sparse or a bit miscellaneous, but the dominant theme is RNA modification/processing in plant organelles and associated translation.","confidence":"Medium","size":25,"edges":300,"triangles":2300,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0009658","count":2},{"id":"GO:0000746","count":2},{"id":"GO:0006627","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0009451","count":1}]},{"hash":"367098357641982896","title":"Retinoid and Steroid Metabolism with Detox Response","description":"This cluster is dominated by retinoid metabolism (retinal, retinol) and androgen/testosterone biosynthesis, pointing to a core function in processing lipophilic signaling molecules. It also features detox-related terms (cadmium ion response, naphthalene catabolic process) that suggest a broader role in xenobiotic handling. A few terms like urine volume regulation add physiological context but do not strongly contradict the core theme. Overall, the label captures the prominent metabolic and detox-related signals without overcommitting to a narrower function.","confidence":"Medium","size":25,"edges":260,"triangles":1780,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0042574","count":23},{"id":"GO:0055114","count":23},{"id":"GO:0042572","count":23},{"id":"GO:0061370","count":22},{"id":"GO:0008209","count":22}]},{"hash":"1744304756860402446","title":"Central carbon metabolism","description":"The proteins are enriched for core metabolic processes (glycolysis, TCA cycle, oxaloacetate metabolism) and multiple amino-acid catabolic pathways, pointing to energy production and carbon flow as the cluster's main function. A few terms like antibiotic biosynthesis and Notch signaling appear as secondary or annotation artifacts, but the dominant theme remains central carbon metabolism.","confidence":"High","size":25,"edges":300,"triangles":2300,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006099","count":8},{"id":"GO:0017000","count":7},{"id":"GO:0006107","count":7},{"id":"GO:0006096","count":6},{"id":"GO:0019878","count":6}]},{"hash":"2185883314458178251","title":"Redox Homeostasis and Oxidative Stress Response","description":"The top GO terms cluster around redox biology\u2014oxidation-reduction, detoxification of oxidants, and responses to oxidative stress\u2014indicating a common theme of maintaining cellular redox balance. Additional metabolism-related terms (TCA cycle and amino acid biosynthesis) likely reflect the metabolic context in which redox status is managed.","confidence":"High","size":25,"edges":169,"triangles":580,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0098869","count":3},{"id":"GO:0006099","count":2},{"id":"GO:0006979","count":2},{"id":"GO:0019878","count":2}]},{"hash":"1231744970509538691","title":"DNA-Templated Transcription Regulation","description":"The top terms cluster around transcription control, including DNA-templated transcription and its regulation, plus notes on RNA Pol II CTD phosphorylation, pointing to a core theme of gene expression regulation at the transcription level. A few terms touch on translation initiation or unrelated processes, suggesting some noise, but the dominant signal is transcriptional regulation.","confidence":"Medium","size":25,"edges":55,"triangles":35,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901407","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0010047","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0048025","count":2}]},{"hash":"2108159424130619950","title":"Organellar RNA Editing and Processing","description":"The dominant GO terms center on RNA modification and editing (including cytidine to uridine editing) and on mitochondrial and chloroplast RNA processing/modification, with an additional note on chloroplast-nucleus signaling. This pattern suggests a cohesive group of proteins involved in organellar RNA maturation and editing, spanning both mitochondria and chloroplasts.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0000961","count":3}]},{"hash":"1476549546208234230","title":"Capsule Biosynthesis and Central Metabolism","description":"The top GO terms show a clear capsule biosynthesis and cell wall organization signal, indicating a bacterial capsule production module. Alongside these, glycolysis, the TCA cycle, and thiamine biosynthesis reflect central metabolism, with additional stress-response terms (cold, xenobiotic) suggesting related environmental adaptation. Taken together, the cluster likely centers on capsule formation linked to core metabolism and stress responses.","confidence":"Medium","size":25,"edges":5,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0071555","count":8},{"id":"GO:0045227","count":7},{"id":"GO:0009228","count":6},{"id":"GO:0006099","count":5}]},{"hash":"1719747327954504763","title":"Hypoxia-Driven Kinase Signaling and Cell Cycle Regulation","description":"The cluster enriches for kinases and signaling regulation (protein autophosphorylation, serine/threonine kinase activity, GTPase activity) and for hypoxia response, alongside cell cycle, transcription, and mRNA transport terms, suggesting a cohesive module where hypoxia triggers kinase signaling that coordinates cell cycle progression and related processes, possibly with cytoskeletal remodeling via Arp2/3. ","confidence":"Medium","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031954","count":5},{"id":"GO:0071456","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0051028","count":5},{"id":"GO:0071902","count":5}]},{"hash":"831521240137437673","title":"Retinoic acid and calcitriol metabolism","description":"This cluster is dominated by GO terms for retinoic acid biosynthesis/catabolism and calcitriol biosynthesis from calciol, along with a vitamin D response term, indicating a cohesive theme around vitamin A and D metabolism. Additional developmental terms (uterus/female gonad development) may reflect downstream effects linked to these pathways, though the core signal centers on retinoid and vitamin D metabolism. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046232","count":16},{"id":"GO:0033280","count":16},{"id":"GO:0071615","count":15},{"id":"GO:0042904","count":15},{"id":"GO:0060065","count":15}]},{"hash":"1038232925452158028","title":"Diverse metabolism and cell-cycle processes","description":"The top GO terms cover a wide range of metabolic pathways (alkaloid metabolism, methanol and arabinan biosynthesis, capsule polysaccharide biosynthesis) alongside cell-cycle activities (cell division, cell cycle) and cell shape regulation. There isn\u2019t a single dominant function, suggesting these proteins participate in general metabolism and growth-related processes rather than a tightly defined pathway. Hence a label that reflects broad metabolic and cell-cycle involvement is appropriate.","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0051301","count":6},{"id":"GO:0019516","count":6},{"id":"GO:0009820","count":6},{"id":"GO:0008360","count":5}]},{"hash":"453150467734469799","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0090502","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0080156","count":3}]},{"hash":"161181926400032889","title":"Ribosome Biogenesis and TOR Signaling","description":"The cluster is dominated by terms for ribosome biogenesis, rRNA maturation (5.8S, LSU), and large subunit assembly, with a notable signal for positive TORC1 signaling and cell division, pointing to a growth-related program centered on ribosome production and its regulation. Some histone methylation terms are listed but marked obsolete, likely reflecting historical annotations rather than core function. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051568","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0000463","count":2}]},{"hash":"1708847925339587188","title":"Bacterial lipid and metabolite biosynthesis","description":"GO terms cluster around biosynthesis of lipids and small-molecule cofactors (lipopolysaccharide, mycolic acid, phylloquinone, tetrahydrobiopterin, polyhydroxybutyrate) with accompanying antibiotic response signals. This suggests a bacterial-focused theme of lipid/cofactor and polymer biosynthesis, making the label representative of the cluster\u2019s function.","confidence":"High","size":25,"edges":33,"triangles":8,"max_degree":10,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":12},{"id":"GO:0046677","count":10},{"id":"GO:0042619","count":10},{"id":"GO:0009103","count":10},{"id":"GO:0031427","count":9}]},{"hash":"1695153171224563210","title":"Cardiovascular and neural development regulators","description":"The cluster shows strong enrichment for heart development, angiogenesis, and axonogenesis, suggesting proteins that regulate development of cardiovascular and neural tissues. Transcriptional regulation terms (DNA-templated transcription, positive regulation of DNA binding) imply core gene-expression control factors driving these processes. Additional terms related to cell-cycle and apoptotic regulation align with developmental growth control, while some terms (e.g., ABA signaling) may reflect broader or organism-specific annotations. Overall, the theme is developmental regulation of heart and neural/vascular systems.","confidence":"High","size":25,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":12},{"id":"GO:0046826","count":12},{"id":"GO:0043388","count":10},{"id":"GO:0001525","count":9},{"id":"GO:0009738","count":9}]},{"hash":"1897975020820268447","title":"Membrane Ion Transport and Homeostasis","description":"The cluster's top GO terms are dominated by ion transport across the plasma membrane (potassium and sodium export/import, and proton transport) and intracellular potassium homeostasis, indicating a core theme of membrane ion transport and ionic balance. A few other terms (e.g., homogalacturonan biosynthesis, sperm capacitation, mitotic checkpoint/cell cycle) appear at lower counts and may reflect annotation noise or multifunctional proteins rather than a single cohesive function. Confidence: Medium.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0097623","count":3},{"id":"GO:0030007","count":3},{"id":"GO:0036376","count":3},{"id":"GO:0010289","count":3},{"id":"GO:0048240","count":3}]},{"hash":"491323214910292827","title":"Organellar RNA Editing and Signaling","description":"The cluster is enriched for plastid/chloroplast transcription and RNA modification/editing, including cytidine-to-uridine editing, plus chloroplast-nucleus signaling. This points to a group of proteins involved in organellar gene expression and retrograde signaling, potentially linking chloroplast function to seed dormancy programs.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":7},{"id":"GO:0009451","count":6},{"id":"GO:0016554","count":6},{"id":"GO:0080156","count":6},{"id":"GO:0000961","count":6}]},{"hash":"2190475245841435739","title":"ABA-Dependent Plant Development and Transcription","description":"The cluster centers on transcriptional regulation in plants, with strong signals for DNA-templated transcription and its regulation, plus ABA-activated signaling and developmental processes (bract/seed/floral meristem growth) and lipid biosynthesis (cutin, wax), suggesting a cohesive theme of ABA-regulated plant development driven by transcriptional control.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0006355","count":9},{"id":"GO:0009738","count":6},{"id":"GO:0010200","count":5},{"id":"GO:0010432","count":5}]},{"hash":"479254882467742543","title":"ER Stress\u2013Related Translation and Protein Quality Control","description":"The top GO terms cluster around translation initiation, ribosome biogenesis, and protein quality-control pathways (ERAD, misfolded protein transport, and ubiquitin-proteasome\u2013mediated quality control), with notes about ER-stress\u2013triggered regulation of translation. This suggests a cohesive group of proteins involved in protein synthesis and downstream quality control under ER stress.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0036494","count":1},{"id":"GO:0070843","count":1}]},{"hash":"1011420187533422155","title":"ER stress proteostasis and protein trafficking","description":"The GO terms converge on proteostasis and quality-control mechanisms\u2014misfolded-protein handling, ubiquitin-proteasome\u2013mediated QC, and stress-responsive translation\u2014together with post-translational targeting and trafficking between nucleus, ER, mitochondria, and membranes. This suggests a unified theme of maintaining protein homeostasis through coordinated trafficking under stress.","confidence":"Medium","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0036494","count":4},{"id":"GO:0070843","count":4},{"id":"GO:0006626","count":4},{"id":"GO:0071630","count":4},{"id":"GO:0097428","count":4}]},{"hash":"1032882939905153407","title":"ABA-Responsive Transcription in Plant Development","description":"Top GO terms indicate transcriptional regulation and ABA signaling driving various plant developmental processes (seed, bract, floral meristem development) with epidermal/ cutin biosynthesis, suggesting a cluster of transcriptional regulators activated by ABA governing plant development. The presence of multiple development-related terms alongside hormone signaling supports a cohesive theme of ABA-mediated transcriptional control in plant development; a minor note is the chitin response term, which may reflect auxiliary signaling but does not overturn the main theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0009738","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0010143","count":2}]},{"hash":"1198373714351046442","title":"Photoperiodic flowering regulation","description":"The terms are dominated by plant developmental processes tied to light cues and flowering timing: short-day and long-day photoperiodism, regulation of flowering, far-red light signaling, and circadian-influenced growth. While a couple of terms (e.g., brown fat cell differentiation) are tangential, the cluster overall points to photoperiodic control of flowering and related light signaling pathways.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050873","count":1},{"id":"GO:0048235","count":1},{"id":"GO:0040015","count":1},{"id":"GO:0048572","count":1},{"id":"GO:0010031","count":1}]},{"hash":"528398392975275240","title":"Plant hormone-regulated floral and seed development","description":"This cluster centers on plant reproductive development (bract and floral meristem growth, seed development) and hormone signaling (auxin, ethylene, ABA) with related cuticle processes (cutin and wax biosynthesis), suggesting a cohesive role in hormone-controlled floral/seed development and cuticle formation.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010200","count":2},{"id":"GO:0010432","count":2},{"id":"GO:0048316","count":2},{"id":"GO:0060774","count":2},{"id":"GO:0010451","count":2}]},{"hash":"1475078334430523923","title":"Unknown","description":"The top GO terms are highly varied (lipid metabolism and transport, RNA processing, plant hormone signaling, defense, and epithelial maturation), with no single coherent function tying all proteins together. This heterogeneity makes it difficult to assign a concise, representative label.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019432","count":3},{"id":"GO:0000492","count":2},{"id":"GO:0009740","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0010951","count":2}]},{"hash":"1887724765485446817","title":"Developmental transcription and Wnt signaling","description":"This cluster combines developmental gene regulation (DNA-templated transcription, organ identity maintenance, hair follicle maturation) with signaling control (negative regulation of canonical Wnt signaling), alongside core cellular processes (DNA replication, nuclear import). The pairing of development/organ identity with Wnt pathway modulation suggests a cohesive theme centered on developmental gene expression and signaling, even though some terms like vacuole inheritance and proton transport reflect general cellular functions. ","confidence":"Medium","size":25,"edges":51,"triangles":33,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000011","count":6},{"id":"GO:0048496","count":6},{"id":"GO:0006260","count":5},{"id":"GO:0015991","count":5},{"id":"GO:0048820","count":4}]},{"hash":"1107115960133461241","title":"Peptide and tRNA methylation","description":"Top GO terms are dominated by methylation-related processes, including N-terminal peptidyl-alanine trimethylation, N-terminal peptidyl-serine dimethylation, peptidyl-arginine methylation, and tRNA methylation/wobble uridine modification. This suggests a cluster centered on methyltransferase activities modifying peptides and RNA, with a few auxiliary biosynthetic terms that may reflect broader metabolic roles. Overall, the common theme is methylation of peptides and nucleic acids.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0018012","count":4},{"id":"GO:0002098","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0035572","count":3},{"id":"GO:0043985","count":3}]},{"hash":"1262769516623475441","title":"Calcium-Dependent Kinase Signaling","description":"The GO terms point to calcium-regulated signaling through phosphorylation, including protein phosphorylation, negative regulation of kinase activity, and positive regulation of calcineurin-NFAT signaling, plus calcium-related mitochondrial concentration control. While some terms reflect metabolism and development, the core shared theme is calcium-dependent modulation of kinase signaling, supporting this label with moderate confidence.","confidence":"Medium","size":25,"edges":17,"triangles":0,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":7},{"id":"GO:0000272","count":5},{"id":"GO:0007020","count":4},{"id":"GO:0006468","count":4},{"id":"GO:0048708","count":4}]},{"hash":"1948347909670365580","title":"Unknown","description":"The top terms are highly diverse (plant auxin homeostasis, methylation, RNA cleavage, cell\u2013cell adhesion, insulin response, leukocyte tethering, intestinal absorption, thyroid hormone metabolism, mucosal immunoglobulin production, UDP-xylose metabolism), and there are no edges or shared enrichment to tie them into a single coherent function, so a specific label isn\u2019t justifiable.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010252","count":2},{"id":"GO:0032259","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0034116","count":2},{"id":"GO:0032868","count":2}]},{"hash":"497790347043138576","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0055114","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0033050","count":3}]},{"hash":"1762217521522559191","title":"Organellar RNA Editing and Processing","description":"The cluster is dominated by GO terms related to RNA modification and editing in organelles (mitochondria and chloroplasts), including cytidine-to-uridine editing, mitochondrial mRNA modification/processing, and chloroplast RNA processing. The presence of chloroplast-nucleus signaling also supports a focus on organellar gene expression. Although a plant developmental term appears, the strongest signal is organellar RNA editing/processing, making the label representative. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":23},{"id":"GO:0016554","count":23},{"id":"GO:0080156","count":23},{"id":"GO:0000961","count":23},{"id":"GO:1905639","count":23}]},{"hash":"1748743765644498605","title":"Plant Cell Wall Biosynthesis and Remodeling","description":"The terms are dominated by plant-specific processes: secondary cell wall biogenesis, cell wall modification, xylan biosynthesis, and xyloglucan metabolism, indicating a coherent theme of plant cell wall formation and remodeling. Additional terms like phytochelatin biosynthesis and response to freezing suggest related abiotic stress responses in plants, but the core signal is cell wall biosynthesis/remodeling in plants.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043085","count":3},{"id":"GO:1904715","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0046938","count":3},{"id":"GO:0009834","count":3}]},{"hash":"759366950345881503","title":"Unknown","description":"This cluster lacks a single coherent function: the top GO terms span nuclear processes (DNA-templated transcription, DNA replication, mitotic spindle organization) and differentiation (keratinocyte differentiation), but also include diverse processes like glycogen and mucilage biosynthesis, signaling pathways, and host-symbiont interactions, with no clear unifying theme. The lack of network connectivity (edges/triangles) further suggests no tight functional module, supporting an Unknown label.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0030216","count":3},{"id":"GO:0007052","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0005978","count":3}]},{"hash":"1102122156352292948","title":"Unknown","description":"The terms cluster around innate immune responses and antiviral defense, with connections to NF-kappaB\u2013related transcription, apoptosis signaling, and some developmental or cell-structure processes, plus unrelated plant-specific metabolism. The mix of immune, developmental, and other seemingly disparate functions provides no clear, single cohesive theme to label the group, so the cluster is best described as Unknown.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051092","count":6},{"id":"GO:0010143","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0035372","count":5},{"id":"GO:0045087","count":5}]},{"hash":"1487084823419104098","title":"Dendritic Spine Development and Rac/Rho Signaling","description":"This cluster is dominated by terms tied to actin-based remodeling in neurons: positive regulation of GTPase activity, Rac and Rho signaling, and regulation of dendritic spine morphogenesis and development, plus lamellipodium and ruffle assembly. The Golgi to plasma membrane transport term suggests trafficking relevant to synapse formation, and hippocampus development anchors the function to brain-specific neuronal development. Together, these indicate a core theme of actin-driven dendritic spine formation mediated by Rac/Rho pathways.","confidence":"High","size":24,"edges":34,"triangles":3,"max_degree":11,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0043001","count":6},{"id":"GO:0021766","count":6},{"id":"GO:0061001","count":6},{"id":"GO:0097178","count":6}]},{"hash":"2016004839398090560","title":"Heart and Muscle Development","description":"The cluster is dominated by terms tied to muscle tissue morphogenesis and heart formation (muscle morphogenesis, cardioblast migration, atrium formation, integrin-mediated adhesion), indicating a core theme of cardiac and skeletal muscle development. Some neural differentiation terms appear but do not outweigh the cardiac/muscle signals, suggesting a primary focus on heart and muscle morphogenesis with ancillary neural differentiation involvement.","confidence":"High","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0060415","count":23},{"id":"GO:0060163","count":23},{"id":"GO:0033627","count":23},{"id":"GO:0032922","count":23},{"id":"GO:0048712","count":23}]},{"hash":"516418251629668165","title":"Carbohydrate and Ion Transporter Cluster","description":"This cluster is dominated by transmembrane transport GO terms for sugars (arabinose, galactose, fucose, sialic acid), sodium ion transport, nitrate/nitrite transport, and other metabolite transport, suggesting a group of membrane transport proteins mediating uptake of diverse substrates (primarily sugars and ions) rather than a single metabolic enzyme. The apparent outlier GO term for neurotransmitter loading does not override the overall transport theme.","confidence":"High","size":24,"edges":26,"triangles":15,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006004","count":15},{"id":"GO:0015751","count":13},{"id":"GO:0042891","count":13},{"id":"GO:0015757","count":13},{"id":"GO:0035725","count":13}]},{"hash":"815796371252245933","title":"Embryonic development and organ differentiation","description":"This cluster shows proteins associated with broad developmental regulation, including DNA-templated transcription as a core mechanism, and a range of organ- and tissue-specific development processes across species (vertebrate heart and bone formation, plant floral and ovule development, primitive streak formation). The common theme is regulation of embryogenesis and organ patterning/differentiation, making this a cohesive label.","confidence":"Medium","size":24,"edges":270,"triangles":1897,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0071277","count":8},{"id":"GO:0090009","count":8},{"id":"GO:2000111","count":7},{"id":"GO:0010582","count":7}]},{"hash":"371638579933846798","title":"Developmental transcriptional regulation","description":"The cluster is dominated by GO terms related to DNA-templated transcription and regulation of differentiation across multiple tissues (muscle, heart, bone, and plant flowers). Although a few terms (like cobalamin biosynthesis) are unrelated, the recurring theme is transcriptional control of developmental programs, suggesting a coherent role in guiding cell differentiation across lineages.","confidence":"Medium","size":24,"edges":153,"triangles":399,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:2001016","count":7},{"id":"GO:0009908","count":7},{"id":"GO:0055114","count":7},{"id":"GO:0009236","count":6}]},{"hash":"1917519277115180707","title":"Unknown","description":"The GO terms show a mix of proteostasis-related processes (ubiquitin-dependent ERAD, SCF-proteasomal degradation) with others tied to development, transcription, and vision, and no single cohesive function dominates. This heterogeneity suggests no clear, unified theme for the cluster.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070208","count":7},{"id":"GO:0030433","count":5},{"id":"GO:1905050","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0050908","count":4}]},{"hash":"1952842299581143026","title":"Unknown","description":"The top GO terms are highly diverse, including photosynthesis, DNA replication, skeletal muscle differentiation, heat response, and various regulatory or stress-related processes, with several terms marked obsolete. There is no clear, single biological function that ties these 24 proteins together, so a coherent label is not justifiable.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0015979","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1358403065932133672","title":"Developmental transcription regulators","description":"This cluster is enriched for DNA-templated transcription and regulation of transcription, with multiple development-related terms (neural development, pituitary gland development, erythrocyte differentiation, multicellular organism development). Together these indicate proteins that function as transcriptional regulators guiding developmental processes, especially neural development.","confidence":"High","size":24,"edges":9,"triangles":5,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0006355","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0051572","count":5},{"id":"GO:0032496","count":4}]},{"hash":"386433048933762938","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":27,"triangles":7,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0090615","count":3},{"id":"GO:0090502","count":3},{"id":"GO:0090617","count":3}]},{"hash":"552641142190909017","title":"Iron/Heme Metabolism and Stress Response","description":"This cluster centers on iron and heme homeostasis (intracellular iron ion homeostasis, erythrocyte homeostasis, heme catabolic process) and stress-related pathways (cadmium response, hypoxia, estrogen response) that commonly feed into apoptosis and autophagy regulation (intrinsic apoptotic signaling in response to DNA damage, apoptotic process, negative regulation of macroautophagy). The plant-specific term likely reflects annotation noise, but the dominant theme is iron/heme metabolism coupled with cellular stress and apoptotic/autophagic responses.","confidence":"Medium","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0006879","count":3},{"id":"GO:0010229","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0034101","count":2},{"id":"GO:0042167","count":2}]},{"hash":"530208740875111957","title":"Autophagy and organelle turnover","description":"The GO terms cluster around various autophagy-related processes, including autophagosome assembly and maturation, nucleophagy, mitophagy, and Cvt pathway\u2013mediated transport to the vacuole. The presence of vesicle trafficking terms (ER-to-Golgi) further ties these into the autophagic machinery that delivers cargo to degradation compartments, indicating a cohesive theme of organelle turnover via autophagy.","confidence":"High","size":24,"edges":130,"triangles":387,"max_degree":20,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034727","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0000045","count":5},{"id":"GO:0044805","count":5},{"id":"GO:0043278","count":5}]},{"hash":"34768384376868042","title":"Post-transcriptional mRNA processing and translation control","description":"The terms cluster around mRNA splicing and polyadenylation, nuclear export, mRNA stability, and translation initiation/reinitiation, plus regulatory ncRNA-mediated silencing, indicating a cohesive module governing RNA processing and translational control after transcription.","confidence":"High","size":24,"edges":64,"triangles":38,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":15},{"id":"GO:0048026","count":15},{"id":"GO:0006378","count":14},{"id":"GO:0045292","count":14},{"id":"GO:0002188","count":13}]},{"hash":"866083743904701831","title":"Nuclear Transport and RNA Processing","description":"The top GO terms are dominated by nuclear-related processes: mRNA export from the nucleus, mRNA stabilization, import of NLS-bearing proteins into the nucleus, and mitotic chromosome condensation. These point to a coherent role in nucleocytoplasmic transport and RNA metabolism during the cell cycle, with other terms like iron-sulfur cluster assembly and GTPase regulation representing broader cellular functions that may accompany these core activities. Confidence: Medium","confidence":"","size":24,"edges":78,"triangles":60,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:0048255","count":2},{"id":"GO:0016226","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0045429","count":2}]},{"hash":"659400401686877846","title":"Osmotic stress response and ion homeostasis","description":"The Top Terms show a prevailing theme of osmotic stress response, water homeostasis, and ion transport, with additional detoxification activity, indicating a cluster of proteins involved in managing osmotic/ionic balance and oxidative stress. Less-relevant terms such as cellulose catabolic process and meiosis-related processes appear only modestly, suggesting they are annotations rather than core functions of this cluster. Therefore, the label reflects the central theme of osmotic stress response and ion homeostasis.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0009992","count":2},{"id":"GO:0071470","count":2},{"id":"GO:0034220","count":2}]},{"hash":"744791809230262845","title":"Cell cycle control and embryonic neural/skeletal development","description":"The top GO terms are dominated by centrosome cycle, DNA replication, mitotic G1 DNA damage checkpoint signaling, and DNA-templated transcription, pointing to core cell cycle regulation and replication machinery. Additionally, embryonic cranial skeleton morphogenesis, nervous system development, and skeletal muscle tissue development indicate involvement in proliferative growth and differentiation of neural and skeletal tissues during development. Potassium ion transport is present but less central, possibly reflecting neural activity. Overall, the cluster seems best described by a combined theme of cell cycle control with embryonic neural/skeletal development.","confidence":"High","size":24,"edges":58,"triangles":59,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007098","count":11},{"id":"GO:0006260","count":11},{"id":"GO:0048701","count":10},{"id":"GO:0010571","count":10},{"id":"GO:0043552","count":9}]},{"hash":"2166789705966709102","title":"Centromere chromatin assembly and mitosis","description":"The top terms point to centromeric chromatin assembly (CENP-A), histone methylation, and DNA-templated transcription, all tied to chromosome segregation during cell division, along with microtubule severing. Although vesicle trafficking terms are present, the strongest signal is centromere-associated chromatin organization and mitotic processes.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0051568","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0034729","count":4}]},{"hash":"1582561781285821392","title":"Plant Hormone Biosynthesis and Stress Signaling","description":"GO terms center on biosynthesis and catabolism of plant hormones (ethylene, gibberellin, auxin, salicylic acid) and related stress responses, plus secondary metabolite production and redox-associated defense. The penicillin biosynthetic term seems unrelated noise. Overall, the cluster reflects growth regulation and defense signaling in plants.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":14},{"id":"GO:0009693","count":8},{"id":"GO:1902835","count":8},{"id":"GO:0042318","count":8},{"id":"GO:0009686","count":8}]},{"hash":"74971636532119627","title":"Bacterial polysaccharide and sugar-nucleotide biosynthesis","description":"This cluster is dominated by GO terms for biosynthesis of polysaccharides and sugar nucleotides, including lipopolysaccharide, colanic acid, rhamnose, GDP-mannose, and ADP-L-glycero-beta-D-manno-heptose, along with poly-hydroxybutyrate biosynthesis. These interconnected pathways point to proteins involved in building bacterial exopolysaccharides and LPS-related structures, with some noise from plant secondary metabolite terms. Overall, the common theme is polysaccharide and sugar-nucleotide production in bacteria.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":19},{"id":"GO:0042619","count":12},{"id":"GO:0009103","count":11},{"id":"GO:0019878","count":10},{"id":"GO:0009242","count":10}]},{"hash":"255446617219818889","title":"Plant hormone biosynthesis and fruit ripening","description":"The top GO terms converge on biosynthesis and catabolism of plant hormones (ethylene, gibberellin, auxin, salicylic acid) and related secondary metabolism, plus a key developmental process (fruit ripening) and stress-related hydrogen peroxide\u2013mediated PCD. This suggests a cohesive cluster of proteins involved in hormone production/regulation and ripening-associated metabolism rather than a single pathway, justifying the label.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":15},{"id":"GO:0009693","count":10},{"id":"GO:0042318","count":10},{"id":"GO:0009686","count":10},{"id":"GO:0045487","count":10}]},{"hash":"1851183610431221435","title":"Plant cell wall biosynthesis and polysaccharide metabolism","description":"The top GO terms point to plant-specific processes: plant-type secondary cell wall biogenesis and modification, along with xylan and xyloglucan biosynthesis/metabolism, which together highlight a cohesive function in plant cell wall construction and remodeling. Additional terms like phytochelatin biosynthesis and freezing response suggest supporting stress-related roles in these proteins. Overall, the cluster appears centered on plant cell wall biosynthesis and associated polysaccharide metabolism, with some ancillary stress-related activities.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043085","count":5},{"id":"GO:1904715","count":5},{"id":"GO:0006508","count":5},{"id":"GO:0046938","count":5},{"id":"GO:0009834","count":5}]},{"hash":"1142031495524182917","title":"Unknown","description":"The GO terms are highly heterogeneous (lipid metabolism, neural development, hormone response, plant seed dormancy, and reproductive assembly) with obsolete terms, offering no clear shared function; thus no coherent label beyond Unknown.","confidence":"","size":24,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016126","count":3},{"id":"GO:0048666","count":2},{"id":"GO:0046855","count":2},{"id":"GO:0071442","count":2},{"id":"GO:0048633","count":2}]},{"hash":"655723635075463320","title":"Cytokinin/Gibberellin Signaling and Chlorophyll Regulation","description":"The prominent GO terms cluster around plant hormone signaling (cytokinin-activated signaling, gibberellin response) with regulation of chlorophyll biosynthesis and leaf senescence, suggesting a hormone-driven growth and photosynthetic regulation module. Osmotic stress response and flavonol biosynthesis fit into stress-related metabolic regulation in plants, while chromatin remodeling and snRNA transcription reflect broader transcriptional control. Overall, this cluster appears to represent plant hormone signaling linked to chlorophyll metabolism and leaf development.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":16},{"id":"GO:1900056","count":14},{"id":"GO:0010380","count":14},{"id":"GO:0009739","count":14},{"id":"GO:0006970","count":14}]},{"hash":"230543963075486396","title":"Plant hormone signaling and stress responses","description":"The top GO terms cluster around plant hormone signaling pathways (gibberellin, ethylene, cytokinin, salicylic acid) and stress responses (osmotic stress) plus regulation of chlorophyll biosynthesis and leaf senescence, suggesting the proteins collectively participate in growth regulation and defense responses in plants. The presence of a viral process term may reflect pathogen-response context, while the meiosis-related term is less directly connected but could be part of broader reproductive regulation. Overall, the cluster seems to represent plant hormone-driven growth and stress signaling rather than a single enzymatic function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0010520","count":6},{"id":"GO:0009739","count":6},{"id":"GO:1901348","count":6},{"id":"GO:0009723","count":6},{"id":"GO:0009751","count":6}]},{"hash":"575931367522127192","title":"RNA processing and transcription regulation","description":"The top GO terms emphasize transcriptional regulation and multiple RNA modification/export processes (tRNA/rRNA methylation, ribosomal export) along with post-transcriptional control (miRNA silencing) and related signaling, suggesting a cluster focused on RNA metabolism and gene expression regulation.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:1900246","count":2},{"id":"GO:2000637","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1020161776734861298","title":"Plant hormone signaling and leaf development","description":"The top GO terms point to cytokinin-activated signaling and gibberellin responses, along with regulation of chlorophyll biosynthesis and leaf senescence, suggesting a hormone-regulated program governing leaf growth and chloroplast function. Additional signals for flavonol biosynthesis, secondary cell wall biogenesis, and chromatin remodeling indicate broader developmental and metabolic control, while osmotic stress and viral process terms reflect associated stress responses. Together they imply a cohesive module linking hormone signaling to leaf development and stress adaptation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":19},{"id":"GO:0043044","count":11},{"id":"GO:1901348","count":11},{"id":"GO:1900056","count":10},{"id":"GO:0010380","count":10}]},{"hash":"1209350514267388062","title":"Membrane Transporters (Ion and Metabolite)","description":"These proteins show a pattern of transmembrane transport functions across diverse substrates (phosphate, nitrate/nitrite, urate, potassium, vitamin), and include a vesicular neurotransmitter loading term, collectively pointing to membrane transporter activity and related vesicular transport roles.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":3},{"id":"GO:0015747","count":2},{"id":"GO:0015707","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0071805","count":2}]},{"hash":"2255915488330077341","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000380","count":3},{"id":"GO:0006334","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000350","count":2},{"id":"GO:0000389","count":2}]},{"hash":"2037377866534070584","title":"Plant cell wall remodeling and pollen tube growth","description":"Top terms are dominated by pectin/mucilage biosynthesis, cellulose/cell wall modification, and pollen tube growth, indicating plant cell wall remodeling and pollen tube development. A few non-plant terms appear, likely annotations from other species, but the core signal is plant-related.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":3},{"id":"GO:0048358","count":3},{"id":"GO:0009860","count":3},{"id":"GO:0043086","count":3},{"id":"GO:0042545","count":3}]},{"hash":"1013396785623600129","title":"Unknown","description":"The top terms span yeast growth responses (invasive growth, pseudohyphal growth), secondary metabolism (L-ascorbic acid and alkaloid metabolism), membrane transport (proton and sodium transport), plus some mammalian-specific processes (sperm capacitation, cardiac conduction) and obsolete terms, indicating a highly heterogeneous set with no clear shared function. Therefore, there is no cohesive theme to name the cluster. ","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001403","count":3},{"id":"GO:0019853","count":3},{"id":"GO:0009820","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0007124","count":2}]},{"hash":"1977807529929488456","title":"Unknown","description":"The terms span plant-specific pollen tube guidance and growth, general intracellular signaling, immune responses, and ubiquitin-mediated protein turnover (including ERAD), with no clear, single cohesive function linking them. The graph shows no edges, suggesting disconnected components, so a unified label isn't supported.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0035556","count":9},{"id":"GO:0010183","count":9},{"id":"GO:0080092","count":9},{"id":"GO:0051092","count":9},{"id":"GO:0032186","count":8}]},{"hash":"1216692773583914537","title":"Hormone-regulated plant development and stress responses","description":"These GO terms cluster around plant hormone signaling pathways (cytokinin-activated signaling, response to gibberellin) and developmental processes (secondary cell wall biogenesis, chlorophyll biosynthetic regulation, flavonol biosynthesis), along with stress-related responses (osmotic stress, leaf senescence) and chromatin remodeling. The combination suggests a coordinated role for hormonal control in growth, metabolism, and stress adaptation, with transcriptional regulation via chromatin changes supporting these processes. ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0000183","count":10},{"id":"GO:1901348","count":10},{"id":"GO:0009736","count":10},{"id":"GO:1900056","count":9},{"id":"GO:0010380","count":9}]},{"hash":"855458418028130473","title":"Yeast sporulation and cell polarity regulation","description":"The top GO terms center on fungal sporulation and polarity: ascospore-type prospore-specific spindle pole body remodeling, regulation of establishment of cell polarity, and regulation of filamentous growth. Additional terms about responses to pH, nutrient, and toxic substances align with development and stress responses during sporulation, with DNA-templated transcription providing a broad regulatory backdrop. Overall, the cluster appears to group proteins involved in yeast/fungal sporulation and cell polarity control.","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:0060548","count":2},{"id":"GO:2000114","count":2},{"id":"GO:0031322","count":2},{"id":"GO:0009268","count":2}]},{"hash":"1357099748272873448","title":"Developmental Gene Regulation and DNA Processing","description":"Contains GO terms for developmental processes (skeletal muscle development, multicellular organism development), transcription regulation (DNA-templated transcription, positive regulation of protein binding) and DNA-related activities (DNA repair, histone H4 acetylation), plus hormone response terms. The cluster appears to group genes involved in regulating development via transcription and chromatin remodeling, though its inclusion of plant ABA signaling and varied terms reduces cohesion; thus a moderate, development/DNA-focus label is appropriate.","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:0030220","count":3},{"id":"GO:0043627","count":3},{"id":"GO:0032092","count":3},{"id":"GO:0007519","count":3}]},{"hash":"2111724257646982110","title":"Unknown","description":"The top GO terms span multiple, unrelated biological contexts (muscle differentiation, organ development in animals and plants, immune cell differentiation, circadian rhythm, cell cycle regulation) with no common process linking them. With 0 edges and highly heterogeneous terms, there isn\u2019t a coherent function tying these proteins together, so a generic label 'Unknown' is most appropriate.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051146","count":2},{"id":"GO:0045497","count":1},{"id":"GO:0072156","count":1},{"id":"GO:2000176","count":1},{"id":"GO:1900477","count":1}]},{"hash":"973456792336979464","title":"Osmotic Stress and Ion Transport","description":"The GO terms cluster around osmoregulation and ion/solute transport (water homeostasis, hyperosmotic response, acetate and potassium transport, endosomal acidification), suggesting a shared theme of maintaining cellular ionic balance, with a few outliers that may reflect annotation noise.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030157","count":4},{"id":"GO:0009992","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0072232","count":3},{"id":"GO:0080029","count":3}]},{"hash":"914051023361793219","title":"Oocyte Meiosis and Neural Development","description":"The cluster is dominated by GO terms tying two clear themes: meiotic regulation in oocytes (oocyte maturation; spindle assembly in female meiosis I; ubiquitin-protein ligase activity in mitotic cell cycle) and neural development (initiation of neural tube closure; third ventricle development; microtubule polymerization). This suggests a module coordinating meiotic spindle dynamics with early neural development processes, with proteolysis and microtubule dynamics as supporting mechanisms. ","confidence":"High","size":24,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":21},{"id":"GO:0001556","count":20},{"id":"GO:0021678","count":20},{"id":"GO:0006516","count":20},{"id":"GO:0051436","count":20}]},{"hash":"1393151503935396633","title":"Unknown","description":"TheTopTerms are highly heterogeneous, including plant reproductive processes (double fertilization, zygote/endosperm, sperm capacitation), immune cell differentiation (T and B cells), DNA repair pathways (SSA and NHEJ), antibiotic biosynthesis, and ER-related maintenance. With no shared function or pathway evident and no interactions among proteins, there isn\u2019t a coherent theme to name the cluster beyond Unknown.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0009567","count":1},{"id":"GO:2000008","count":1},{"id":"GO:0080155","count":1},{"id":"GO:0048240","count":1}]},{"hash":"288143559530190302","title":"Developmental signaling and morphogenesis","description":"The cluster\u2019s prominent GO terms center on developmental signaling and morphological processes, including neurotrophin TRK receptor signaling, Wnt pathway regulation, optic nerve morphogenesis, and face development, with related FGFR apoptotic signaling. These point to roles in vertebrate development and neural patterning; ancillary terms like DNA replication and defense/response likely reflect general cellular states rather than core functions of the cluster. Overall, the dominant theme is developmental signaling and morphogenesis.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":24},{"id":"GO:0048011","count":23},{"id":"GO:0090090","count":23},{"id":"GO:0020021","count":23},{"id":"GO:0071469","count":23}]},{"hash":"1112241047089274818","title":"Osmoregulation and Ion Transport","description":"This cluster centers on water balance and ion transport, with GO terms like intracellular water homeostasis, cellular response to water deprivation, hyperosmotic response, acetate transport, potassium ion transmembrane transport, and endosomal lumen acidification. Kidney development term reinforces the fluid/electrolyte balance theme, suggesting a cohesive function around osmoregulation and membrane transport. Some terms (visual perception, pancreatic juice secretion) appear as outliers, possibly due to broad annotations, but the dominant signal is transport and osmotic homeostasis.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009992","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0072232","count":3},{"id":"GO:0080029","count":3},{"id":"GO:0006846","count":3}]},{"hash":"1294174554783536001","title":"Mitochondrial Translation and Import","description":"The dominant GO terms point to mitochondrial-focused functions: regulation of mitochondrial membrane permeability, protein import into the mitochondrial matrix, and core translation/tRNA charging activities. This suggests the cluster centers on mitochondrial protein synthesis and import machinery, with a few peripheral terms related to lipid metabolism or cell-cycle regulation that are not defining the main theme.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":1},{"id":"GO:0010867","count":1},{"id":"GO:1903740","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0070940","count":1}]},{"hash":"1284794441156801615","title":"Plant organelle RNA editing and processing","description":"Most top GO terms point to RNA modification and processing in plant organelles (chloroplasts and mitochondria), including cytidine-to-uridine editing and chloroplast RNA processing, plus signaling between chloroplasts and the nucleus. A plant developmental term is present but does not override the organelle RNA metabolism theme. Thus the cluster appears to collect proteins involved in plant organelle RNA editing/processing.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0000961","count":2},{"id":"GO:1905639","count":2}]},{"hash":"900372449986766614","title":"Unknown","description":"The top GO terms span neuronal, plant, immune, placental, and muscle development as well as transcription, with no clear, shared function tying the proteins together. The lack of edges or cohesive pathway signal means there isn\u2019t a single interpretable theme to name other than unknown.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048666","count":7},{"id":"GO:0009636","count":7},{"id":"GO:0009738","count":7},{"id":"GO:0007118","count":7},{"id":"GO:0006351","count":7}]},{"hash":"1969309923561330156","title":"Innate Immunity and Endocytosis","description":"The terms show innate immune activation (innate immune response, LPS signaling) alongside endocytic/phagocytic processes and cytoskeletal/cell-polarity dynamics (endocytosis, actin patch localization, establishment of cell polarity) and EGFR signaling, suggesting a cluster of proteins involved in immune signaling linked to membrane trafficking and cytoskeletal remodeling. A few terms like social behavior may be incidental. Overall, the theme is innate immunity coupled with endocytosis and cytoskeletal regulation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031666","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0007173","count":2},{"id":"GO:0035176","count":2},{"id":"GO:0006909","count":2}]},{"hash":"1717545907125785592","title":"Vesicle Trafficking and Signaling in Immune and Neural Cells","description":"The dominant terms center on intracellular transport and vesicle fusion, pointing to vesicle trafficking, while several terms relate to signaling in immune (B cell receptor pathways, phagocytosis regulation) and neural contexts (reelin signaling, radial glia migration). The cluster seems to group proteins involved in vesicle-mediated transport and coordinated signaling that affect cell motility and immune/neural functions, justifying this label.","confidence":"Medium","size":23,"edges":6,"triangles":0,"max_degree":3,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":5},{"id":"GO:0050764","count":4},{"id":"GO:0006906","count":4},{"id":"GO:0050861","count":4},{"id":"GO:0021814","count":4}]},{"hash":"1524784910185492339","title":"TLR-MYD88 Immune Signaling and Neurodevelopmental Functions","description":"The terms center on innate immune signaling through MyD88 and TLR4 (MyD88-dependent path, TLR4 signaling), JNK cascade regulation, and Th1 responses, suggesting a primary immune signaling theme. Additional terms touch on neuronal/Vesicle-related processes (brain development, regulation of synaptic vesicle exocytosis, mechanosensory response, and multivesicular body size), indicating a link between immune pathways and neuronal/synaptic function. This supports naming the cluster around TLR/MyD88 signaling with neurodevelopmental associations.","confidence":"Medium","size":23,"edges":13,"triangles":0,"max_degree":5,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0046330","count":8},{"id":"GO:0032707","count":8},{"id":"GO:0042088","count":8},{"id":"GO:0071260","count":8},{"id":"GO:2000300","count":7}]},{"hash":"950765338891274699","title":"Neuronal synaptic vesicle trafficking and spine development","description":"The proteins cluster around neuronal synaptic functions, including synaptic vesicle budding, neurotransmitter receptor transport to the postsynaptic membrane, and positive regulation of dendritic spine development, suggesting a cohesive role in synapse formation and transmission; additional terms for mitochondrial fission and GTPase activity reflect supporting neuronal signaling and organelle dynamics.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060999","count":3},{"id":"GO:1902307","count":3},{"id":"GO:0055108","count":3},{"id":"GO:0070142","count":3},{"id":"GO:0000266","count":3}]},{"hash":"109956416073724966","title":"Unknown","description":"The top terms span apoptosis regulation, metabolism, erythrocyte development, ubiquitin-proteasome\u2013dependent protein turnover, plant development, and antiviral defense, covering animal and plant processes with no clear shared function. There isn\u2019t a single cohesive theme linking these proteins, so a precise label cannot be inferred from the given terms.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033033","count":2},{"id":"GO:0045721","count":2},{"id":"GO:0048822","count":2},{"id":"GO:0043161","count":2},{"id":"GO:0042787","count":2}]},{"hash":"1905916711554560077","title":"Protein quality control and ER stress response","description":"Many proteins in this cluster are linked to translation and its regulation under endoplasmic reticulum (ER) stress, including positive regulation of translation initiation in response to ER stress, as well as quality-control pathways that handle misfolded proteins via transport, nuclear ubiquitin-proteasome\u2013mediated degradation, and targeted protein trafficking. Collectively, this pattern reflects cellular proteostasis: maintaining proper protein folding, processing, and turnover during stress.","confidence":"High","size":23,"edges":204,"triangles":1108,"max_degree":21,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0036494","count":5},{"id":"GO:0006626","count":5},{"id":"GO:0070843","count":5},{"id":"GO:0071630","count":5}]},{"hash":"1759237047028000604","title":"Photosynthesis Light Harvesting and Photoprotection","description":"These proteins cluster around chloroplast photosynthesis and light-responsive processes: multiple terms relate to photosynthesis (PS I and II, light harvesting) and photoprotection (nonphotochemical quenching), with related light intensity and spectral responses (red light, UV-A). A few outliers (ion transport) exist but the dominant signal points to chloroplast light reactions and protective responses.","confidence":"High","size":23,"edges":217,"triangles":1143,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0010196","count":4},{"id":"GO:0099132","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0009768","count":2},{"id":"GO:0009645","count":2}]},{"hash":"2246264574222167257","title":"Stress-Responsive mRNA Processing and Translation","description":"The top GO terms cluster around post-transcriptional regulation: mRNA stability under stress, alternative and cis-splicing via the spliceosome, mRNA export from the nucleus, and translation reinitiation (including viral-like contexts). This points to a cohesive module of mRNA processing and translational control activated by stress. The emphasis on spliceosome-mediated processing and export, plus translation reinitiation, supports a specific post-transcriptional regulation theme rather than other RNA-level processes.","confidence":"High","size":23,"edges":118,"triangles":388,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":11},{"id":"GO:1900363","count":10},{"id":"GO:0002188","count":10},{"id":"GO:0075525","count":10},{"id":"GO:0006378","count":10}]},{"hash":"1457421188542445813","title":"Bacterial cell envelope biosynthesis and antibiotic production","description":"The highest GO terms cluster around cell wall and envelope construction (cell wall organization, teichoic acid D-alanylation, lipid A biosynthesis) and related fatty acid biosynthesis, suggesting a focus on bacterial cell envelope biogenesis. The presence of antibiotic biosynthetic process and nonribosomal peptide biosynthetic process points to microbial secondary metabolism linked to envelope-associated compounds. Translation and photosynthesis terms appear as broader cellular processes annotated across organisms, but do not define this cluster\u2019s central theme. Taken together, the cluster seems to represent bacteria coordinating cell envelope biosynthesis with secondary metabolite production.","confidence":"Medium","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0009245","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0030150","count":2},{"id":"GO:0015979","count":2}]},{"hash":"298987194725134000","title":"Plant organellar RNA editing and processing","description":"This cluster is dominated by terms related to RNA editing and processing in mitochondria and chloroplasts (cytidine to uridine editing; mitochondrial and chloroplast RNA modification/processing; regulation of mitochondrial RNA catabolic processes), with plant-specific contexts like embryo development ending in seed dormancy, indicating a cohesive theme of organellar RNA metabolism in plants. The presence of both mitochondrial and chloroplast RNA-related terms supports a unified function rather than disparate processes, though one term about spinal cord development may be a distant annotation artifact.","confidence":"High","size":23,"edges":34,"triangles":11,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0021510","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0000961","count":3}]},{"hash":"1313647563052341962","title":"Sulfur-containing amino acid biosynthesis","description":"The cluster\u2019s top GO terms are dominated by biosynthetic processes for sulfur-containing amino acids and related compounds: transsulfuration, hydrogen sulfide biosynthesis, and biosynthesis of cysteine, homocysteine, and serine. This points to a common function centered on synthesis and interconversion of sulfur-containing amino acids, with a few outlier terms (lipopolysaccharide and antibiotic biosynthesis) likely reflecting broader GO annotations rather than a different primary theme. Overall, the proteins likely participate in sulfur amino acid metabolism and related biosynthetic pathways.","confidence":"High","size":23,"edges":178,"triangles":747,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":6},{"id":"GO:0017000","count":6},{"id":"GO:0042853","count":5},{"id":"GO:0019346","count":5},{"id":"GO:0019343","count":5}]},{"hash":"1200563663924609061","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0090617","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0080156","count":2}]},{"hash":"2263088356424268059","title":"Unknown","description":"The GO terms are diverse (carbohydrate metabolism, lipid/choline metabolism, neurotransmitter processing, and development) with minimal network connectivity (1 edge, 0 triangles), giving no clear shared function for the cluster.","confidence":"","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0030245","count":4},{"id":"GO:0051262","count":4},{"id":"GO:0010325","count":3},{"id":"GO:0001507","count":3}]},{"hash":"636924635988548131","title":"Unknown","description":"The top GO terms cover diverse metabolic and structural processes across organisms (uracil catabolism, alkaloid and menaquinone biosynthesis, chlorophyll catabolism, fungal cell wall biosynthesis, division septum assembly), with several terms labeled obsolete. This lack of a cohesive shared function across the cluster prevents a single, representative label beyond Unknown.","confidence":"","size":23,"edges":59,"triangles":42,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006212","count":3},{"id":"GO:0009820","count":3},{"id":"GO:0007568","count":2},{"id":"GO:0043182","count":2}]},{"hash":"1578578655204913820","title":"Plant organellar RNA editing and processing","description":"This cluster is driven by GO terms for RNA modification and editing in mitochondrial and chloroplast RNAs, plus plastid transcription and chloroplast-nucleus signaling. These terms define a common plant-specific theme of organellar gene expression regulation (RNA editing/processing) in chloroplasts and mitochondria, with a developmental cue in seed dormancy linked to plant development. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":8},{"id":"GO:0016554","count":8},{"id":"GO:0080156","count":8},{"id":"GO:0000961","count":8},{"id":"GO:1905639","count":8}]},{"hash":"1088854009962783664","title":"Lipid, Steroid, and Pigment Metabolism","description":"These proteins map to a broad set of metabolic processes including fatty acid elongation, androgen and C21-steroid hormone metabolism, retinal metabolism, phylloquinone biosynthesis/catabolism, and melanin biosynthesis, as well as tetrahydrobiopterin biosynthesis. The convergence on lipid-derived pathways, steroid metabolism, and pigment/cofactor biosynthesis suggests a cohesive metabolic cluster rather than a single, narrow function, justifying the label. ","confidence":"Medium","size":23,"edges":138,"triangles":408,"max_degree":19,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":23},{"id":"GO:0031427","count":22},{"id":"GO:0006710","count":22},{"id":"GO:0006729","count":22},{"id":"GO:0008207","count":22}]},{"hash":"725140523541040133","title":"Developmental transcription and stress-response cluster","description":"Top GO terms indicate a core of DNA-templated transcription and multiple development processes (forebrain, skeletal system, multicellular development) paired with stress-related responses (defense to Gram-positive bacteria, cadmium ion response, ER-stress\u2013induced apoptosis) and cell cycle activity. This suggests a cohesive theme of developmental gene regulation intertwined with cellular stress signaling, rather than a single isolated pathway, hence a label reflecting both developmental transcriptional programs and stress responsiveness. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0007275","count":6},{"id":"GO:0030900","count":5},{"id":"GO:0001501","count":5},{"id":"GO:0050830","count":5}]},{"hash":"987605496852834121","title":"DNA-Templated Transcription Regulation","description":"This cluster is strongly tied to transcription control, as shown by GO terms for DNA-templated transcription, regulation of DNA-templated transcription, and positive regulation of transcription by RNA polymerase II. A few peripheral terms (blastocyst formation, self pollen rejection, antibiotic biosynthetic processes) appear unrelated to core transcription activity, indicating some noise but not altering the dominant theme. Overall, the dominant function is transcription regulation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0001825","count":1},{"id":"GO:0000028","count":1},{"id":"GO:1901766","count":1}]},{"hash":"203785071594892024","title":"Pyrimidine salvage and nucleotide metabolism","description":"Most frequent terms are salvage pathways for cytosine/uracil nucleotides (CMP, UMP, CTP, uracil salvage) and overall pyrimidine nucleobase metabolic process, pointing to a shared role in nucleotide salvage and metabolism. While other terms (protein tetramerization, zinc stress response, antibiotic biosynthesis, CoA biosynthesis) appear, they are less representative of the cluster\u2019s core function; thus the label emphasizes pyrimidine salvage and nucleotide metabolism.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051289","count":4},{"id":"GO:0006206","count":3},{"id":"GO:0006238","count":3},{"id":"GO:0006223","count":3},{"id":"GO:0016310","count":3}]},{"hash":"111576034700374476","title":"ABA-regulated transcription in plant development","description":"Top GO terms indicate DNA-templated transcription and its regulation, coupled with abscisic acid-activated signaling, across multiple plant-development processes (bract, seed, floral meristem growth). The presence of response to chitin and cutin biosynthesis suggests ABA-coordinated defense and cuticle-related development. Overall, the cluster centers on transcriptional control governed by ABA signaling during plant development.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0009738","count":8},{"id":"GO:0006355","count":8},{"id":"GO:0007275","count":8},{"id":"GO:0010200","count":6}]},{"hash":"1772441983279346550","title":"Lipid Catabolism & Endocannabinoid Signaling","description":"The cluster is dominated by lipid breakdown processes (monoacylglycerol, triglyceride, diacylglycerol, phosphatidylserine catabolism) and includes regulation of endocannabinoid signaling, pointing to a cohesive theme of lipid metabolism coupled with lipid-based signaling pathways. A few terms appear ancillary or outdated, but they do not override the central lipid-centric pattern.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0052651","count":10},{"id":"GO:0006660","count":10},{"id":"GO:2000124","count":10},{"id":"GO:0019433","count":10},{"id":"GO:0030245","count":8}]},{"hash":"146011616468651356","title":"Pollen Tube Growth and Floral Development with Transporters","description":"The top terms point to pollen tube growth, floral meristem growth, and seed/bract development, highlighting plant reproductive development and accompanying cell-wall remodeling (e.g., pectin catabolic process and cutin biosynthesis). The xenobiotic transmembrane transport term adds a transporter's role within this developmental context, suggesting membrane-associated functions alongside growth programs. Transcription-related and auxin-signaling terms further support regulation of these developmental processes. Together, they indicate a coherent theme of plant reproductive development with transporter activity.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0045490","count":2},{"id":"GO:0009860","count":2},{"id":"GO:0010200","count":1},{"id":"GO:0010432","count":1}]},{"hash":"669380124359590680","title":"Plant vascular development and organogenesis","description":"The top GO terms cluster around vascular tissue differentiation (protoxylem development, xylem vessel member cell differentiation, sieve element enucleation), secondary cell wall biogenesis, and various plant organ formation processes (root cap development, fruit dehiscence, timing of organ formation, callus formation). Together these terms point to a cohesive theme of plant vascular development and broader organogenesis, supported by multiple related processes across development and differentiation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009834","count":3},{"id":"GO:0048829","count":3},{"id":"GO:0090709","count":3},{"id":"GO:1990110","count":3},{"id":"GO:0090059","count":3}]},{"hash":"1132414273179475315","title":"Plant secondary cell wall biogenesis and transcription regulation","description":"This cluster is dominated by plant-specific processes: strong signals for plant-type secondary cell wall biogenesis and its positive regulation, plus GO terms for DNA-templated transcription and its regulation, suggesting a core role in transcriptional control during cell wall formation and plant development. Additional terms point to organ formation timing and root cap development, with some members involved in phytochelatin biosynthesis and proteolysis, indicating related metabolic and developmental coordination. Overall, the data converge on a theme of plant developmental transcription coordinating cell wall biosynthesis, with secondary metabolic processes accompanying it.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901348","count":6},{"id":"GO:0009834","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0006355","count":5},{"id":"GO:0043085","count":4}]},{"hash":"819996964801623155","title":"Membrane transport and lipid trafficking","description":"The top GO terms cluster around transport across membranes and related lipid processes, including molybdate and cobalt ion transport, teichoic acid transport, vitamin transmembrane transport, phospholipid and ceramide translocation, long-chain fatty acid import into peroxisomes, and cholesterol absorption. This suggests a coherent theme of membrane transport and lipid movement, though some terms (e.g., nodulation, cytochrome complex assembly) are less directly connected and may reflect broader contexts or annotation noise.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015689","count":4},{"id":"GO:0009877","count":4},{"id":"GO:0015777","count":3},{"id":"GO:0015910","count":3},{"id":"GO:0030299","count":3}]},{"hash":"831122550002024138","title":"RNA Transcription and Ribosome Biogenesis","description":"The cluster is dominated by GO terms for DNA- and RNA-templated transcription, including RNA polymerase II transcription, its elongation and termination, as well as tRNA transcription by RNA polymerase III, plus a couple entries for ribosome biogenesis. This points to a core function in transcriptional machinery with a link to ribosome production, hence the label. Some unrelated terms appear (transposon integration, proton transport), but the predominant theme is transcription and ribosome biogenesis.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006354","count":2},{"id":"GO:0001172","count":2},{"id":"GO:0042797","count":2},{"id":"GO:0042254","count":2}]},{"hash":"536018029753577177","title":"RNA Methylation and Protein Methylation","description":"The top GO terms cluster around RNA-level modifications (tRNA wobble uridine modification, tRNA methylation) and methylation of proteins (N-terminal peptidyl-alanine trimethylation, peptidyl-arginine methylation), pointing to a core theme of methyltransferase activity and RNA processing. Other terms hint at ribosome biogenesis and broader plant metabolism, but the dominant signal is methylation/modification processes.","confidence":"Medium","size":23,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":2},{"id":"GO:0002098","count":1},{"id":"GO:0016049","count":1},{"id":"GO:0018012","count":1},{"id":"GO:0019919","count":1}]},{"hash":"595889723655544176","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"The top GO terms are strongly centered on female meiosis, oocyte maturation, and spindle assembly (e.g., oocyte maturation, spindle assembly in female meiosis I, microtubule polymerization), with supporting protein turnover processes (ubiquitin-proteasome pathways) relevant to cell-cycle control. While neural development terms appear, they likely reflect broader developmental context rather than a different function, reinforcing a focus on meiosis-related maturation and spindle dynamics.","confidence":"High","size":23,"edges":61,"triangles":24,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":22},{"id":"GO:0021678","count":22},{"id":"GO:0006516","count":22},{"id":"GO:0051436","count":22},{"id":"GO:0046785","count":22}]},{"hash":"1468525684972706003","title":"DNA replication, transcription, and repair","description":"The top GO terms are dominated by DNA metabolism: transcription (DNA-templated), repair, and replication, which together point to nuclear DNA maintenance. Other terms (vacuolar acidification, amino acid starvation response, signaling pathways) appear less central to the main theme, making DNA replication/repair/transcription the most representative unifying function.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006281","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0007035","count":3},{"id":"GO:0034198","count":3}]},{"hash":"827061116674715915","title":"Plant growth, chlorophyll biosynthesis, and stress response","description":"The top GO terms cluster around plant development and stress physiology, including regulation of leaf senescence, chlorophyll biosynthesis, gibberellin signaling, osmotic stress response, and flavonoid biosynthesis, along with chromatin remodeling and transcription-related processes. This points to a cohesive theme of plant growth regulation and adaptive metabolism under environmental cues, despite some outliers (viral processes, telomere-related activities) that may reflect broader or ancillary roles. ","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:1900056","count":12},{"id":"GO:0010380","count":12},{"id":"GO:0009739","count":12},{"id":"GO:0006970","count":12},{"id":"GO:0016032","count":12}]},{"hash":"704089361978085946","title":"Lipid catabolism and detoxification","description":"This cluster is enriched for several lipid-related catabolic processes (triglyceride, monoacylglycerol, phosphatidylserine catabolism) and includes terms related to endocannabinoid signaling regulation, detoxification (cellular oxidant detoxification, response to toxic substance), and xenobiotic degradation (beta-ketoadipate pathway). While some terms are less directly linked (chlorophyll catabolic, biotin biosynthetic), the shared theme points to lipid metabolism and detox pathways as the core function of these proteins. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":6},{"id":"GO:0019433","count":6},{"id":"GO:0098869","count":5},{"id":"GO:0052651","count":5},{"id":"GO:0006660","count":5}]},{"hash":"589384963532587659","title":"Neural development signaling and morphogenesis","description":"This cluster is dominated by terms related to neural development and morphogenesis, including neurotrophin receptor signaling, optic nerve morphogenesis, and face development, alongside growth-factor\u2013mediated pathways (FGFR signaling and PI3K/AKT). The co-occurrence suggests a cohesive role in neural and craniofacial development, with broader involvement of Wnt regulation. Some terms (e.g., symbiont-mediated transformation) are less directly tied but do not overturn the central theme. ","confidence":"Medium","size":23,"edges":53,"triangles":28,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":22},{"id":"GO:0090090","count":22},{"id":"GO:0020021","count":22},{"id":"GO:0071469","count":22},{"id":"GO:0060324","count":22}]},{"hash":"1139024898143128865","title":"Plant Hormone Signaling and Cell Wall Regulation","description":"The proteins in this cluster are enriched for plant hormone responses (gibberellin, salicylic acid), stress responses (osmotic stress), leaf senescence regulation, and regulation of chlorophyll and flavonol biosynthesis, along with secondary cell wall biogenesis and chromatin remodeling. This combination suggests a cohesive plant growth and defense program centered on hormonal signaling and cell wall remodeling, with connections to viral processes.","confidence":"Medium","size":23,"edges":22,"triangles":3,"max_degree":6,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009739","count":10},{"id":"GO:1901348","count":10},{"id":"GO:0009751","count":10},{"id":"GO:1900056","count":9},{"id":"GO:0010380","count":9}]},{"hash":"2297346034431132666","title":"Plant Hormone Biosynthesis and Defense","description":"This cluster's top GO terms cluster around plant hormone biosynthesis (ethylene, gibberellin) and hormone catabolic processes (auxin, salicylic acid), plus defense-related processes such as cell wall organization and hydrogen peroxide\u2013mediated programmed cell death, indicating a phytohormone signaling/defense hub. An outlier term for penicillin biosynthesis appears among the annotations, but the dominant theme remains hormone production and defense-related remodeling.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009664","count":3},{"id":"GO:0009693","count":3},{"id":"GO:0042318","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0009686","count":3}]},{"hash":"143772228405412657","title":"Wnt-regulated development and regeneration","description":"This cluster centers on developmental signaling and tissue repair, highlighted by negative regulation of canonical Wnt signaling, face development, angiogenesis, and organ regeneration, with associated immune regulation and receptor turnover.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090090","count":23},{"id":"GO:0060324","count":23},{"id":"GO:0009636","count":23},{"id":"GO:0001525","count":23},{"id":"GO:0031100","count":23}]},{"hash":"290482568398719929","title":"Plant Cell Wall Remodeling and Growth Regulation","description":"These proteins show enrichment for plant cell wall biology (xyloglucan metabolism, cell wall biogenesis, plant-type cell wall modification) and growth control (negative regulation of cell growth, extracellular matrix assembly). Some terms hint at reproduction (stamen filament development) and defense against fungi (detection of molecule of fungal origin, fungal-type cell wall organization), suggesting a cluster centered on plant cell wall dynamics with growth regulation and defense-related cues.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0080086","count":1},{"id":"GO:0009831","count":1},{"id":"GO:0031505","count":1},{"id":"GO:0010411","count":1}]},{"hash":"1447739095257708992","title":"Pollen Tube Growth and Cell Wall Remodeling","description":"The supported terms cluster around pollen\u2013pistil interaction and pollen tube growth, together with cell wall/pectin processes (cell wall organization, pectin catabolic and mucilage pectin biosynthetic processes, and cell wall modification). This points to a plant reproductive context where pollen tube growth requires targeted cell wall remodeling and pectin metabolism. Overall, the label captures the tie between pollen tube development and cell wall dynamics.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0045490","count":2},{"id":"GO:0043086","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1662392554175313736","title":"Ubiquitin-Dependent Proteolysis and NF-kB Signaling","description":"The dominant GO terms center on ubiquitin-dependent protein catabolism and polyubiquitination, including SCF-dependent proteasomal degradation, which points to a core ubiquitin-proteasome system. Additional terms connect to NF-kappaB signaling, apoptosis regulation, and immune-related processes (V(D)J recombination), suggesting these proteins collectively modulate protein turnover and signaling in immune pathways. This combination supports a cohesive function in ubiquitin-mediated degradation and NF-kB/immune signaling.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0031146","count":9},{"id":"GO:0000209","count":8},{"id":"GO:1903265","count":7},{"id":"GO:0042981","count":6}]},{"hash":"1762613079491046078","title":"Ubiquitin-Proteasome-Mediated Protein Degradation","description":"This cluster is dominated by GO terms describing ubiquitin-dependent protein catabolic processes, SCF-dependent proteasomal ubiquitination, K48-linked ubiquitination, and general protein ubiquitination and autoubiquitination. Together these indicate a set of proteins responsible for tagging substrates for proteasomal degradation, including components of ubiquitin ligase (SCF) pathways and proteolysis-related regulation; occasional terms about histone turnover and septin ring organization reflect ancillary roles in chromatin remodeling and cytoskeletal dynamics tied to ubiquitination. Thus the common theme is tagging and degradation of proteins via ubiquitin and the proteasome.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":12},{"id":"GO:0031146","count":10},{"id":"GO:0070936","count":8},{"id":"GO:1903265","count":8},{"id":"GO:0036205","count":8}]},{"hash":"875155317309615269","title":"Ubiquitin-Proteasome Regulation in Meiosis","description":"This cluster is dominated by GO terms for ubiquitin-dependent proteolysis (ubiquitin-dependent protein catabolic process, protein polyubiquitination, SCF-dependent proteasomal ubiquitin-dependent protein catabolic process) and meiosis/oocyte-related processes (oocyte maturation, spindle assembly in female meiosis I). Together these suggest a group of proteins governing targeted protein degradation to regulate meiosis progression and cell-cycle events, with circadian regulation and glycoprotein turnover as related aspects of proteostasis.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":12},{"id":"GO:0031146","count":10},{"id":"GO:0000209","count":8},{"id":"GO:0042752","count":7},{"id":"GO:0001556","count":6}]},{"hash":"2011696616633844477","title":"Neural signaling and visual perception","description":"Most enriched GO terms point to neural communication and sensory processing, including regulation of synaptic vesicle fusion, positive regulation of synaptic transmission, detection of light stimulus involved in visual perception, and visual learning. While there are also some unrelated terms (e.g., transcription, cell wall biogenesis, amino acid transport), the dominant theme centers on neural signaling and visual/sensory functions, justifying this label.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:1901348","count":2},{"id":"GO:0010226","count":2},{"id":"GO:0008542","count":2},{"id":"GO:0007476","count":2}]},{"hash":"2235488007858864347","title":"Plant cell wall remodeling and fungal defense","description":"The GO terms cluster around plant-type cell wall modification and biosynthesis (e.g., xyloglucan metabolism, cell wall biogenesis) and defense against fungi, including detection of fungal molecules. Although some terms are plant-specific (stamen development), the dominant theme links cell wall remodeling with antifungal immunity and fungal-origin molecule sensing.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0080086","count":1},{"id":"GO:0009831","count":1},{"id":"GO:0031505","count":1}]},{"hash":"460762334978114007","title":"Unknown","description":"The top GO terms span immune defense (fungal defense, salicylic acid signaling, NOD1 pathway), basic cellular processes (lipid transport, mRNA processing, protein localization), and distinct physiological functions (cardiac action potential depolarization, vasopressin secretion). There is no single cohesive function connecting these terms across the cluster, so a reliable, specific label cannot be assigned.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":4},{"id":"GO:0050832","count":4},{"id":"GO:0006869","count":4},{"id":"GO:2000031","count":2},{"id":"GO:1900827","count":2}]},{"hash":"719577804682875239","title":"Neural development and synaptic assembly","description":"This cluster centers on neuronal development and synapse formation, highlighted by terms like positive regulation of synapse assembly, axonal fasciculation, and branching morphogenesis of a nerve, as well as a node related to response to cocaine, indicating a shared theme of neuronal signaling and connectivity. Some ER-related terms appear as ancillary cellular context but do not define the main function of the cluster.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":1},{"id":"GO:0051965","count":1},{"id":"GO:0007166","count":1},{"id":"GO:0071787","count":1},{"id":"GO:0007413","count":1}]},{"hash":"1651604050575004389","title":"Cell signaling and vesicle trafficking","description":"This cluster is enriched for GO terms tied to signaling and vesicle dynamics: vesicle fusion, regulation of phagocytosis, and multiple regulatory pathways including B cell receptor signaling, reelin-mediated signaling, insulin secretion, and transcriptional control. The mix of immune, neural migration, and secretion-related terms points to a module where signaling events coordinate vesicle trafficking and cross-talk between immune and neural processes.","confidence":"Medium","size":22,"edges":61,"triangles":30,"max_degree":13,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0060304","count":12},{"id":"GO:0050764","count":11},{"id":"GO:0006906","count":11},{"id":"GO:0050861","count":11},{"id":"GO:0021814","count":11}]},{"hash":"1104320577565243267","title":"Multisystem Developmental Transcription Regulation","description":"The GO terms include DNA-templated transcription and diverse developmental processes across tissues (fat cell differentiation, kidney morphogenesis, germinal center formation, pro-T cell differentiation, IgE isotype regulation), suggesting a shared theme of transcriptional control in development across multiple organ systems.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0045600","count":1},{"id":"GO:0032981","count":1},{"id":"GO:0045497","count":1},{"id":"GO:0072156","count":1}]},{"hash":"353592107640434367","title":"Developmental gene regulation and actin remodeling","description":"Top GO terms indicate a developmental program (multicellular organism development, skin development) tightly linked to gene expression (DNA-templated transcription, mRNA transport) and signaling with cytoskeletal remodeling (positive regulation of GTPase activity, Arp2/3 complex\u2013mediated actin nucleation, protein phosphorylation). This combination suggests proteins coordinating transcriptional programs with cytoskeletal changes during tissue development, especially in the epidermis. Hence the chosen name reflects both developmental regulation and actin-driven remodeling as a unifying theme.","confidence":"Medium","size":22,"edges":19,"triangles":5,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":7},{"id":"GO:0043588","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0031954","count":6},{"id":"GO:0071456","count":6}]},{"hash":"485937361573230537","title":"Organellar RNA editing and processing (mitochondria & chloroplasts)","description":"The top GO terms point to RNA modification/editing (e.g., cytidine to uridine), mitochondrial and chloroplast RNA processing/modification, and chloroplast-nucleus signaling, indicating a shared function in organellar gene expression and communication with the nucleus. This supports a cohesive role in organellar RNA maturation and regulation.","confidence":"High","size":22,"edges":228,"triangles":1482,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0000961","count":3}]},{"hash":"368915013629027638","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"This cluster is strongly enriched for processes tied to female meiosis and oocyte development, including oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization, with supporting links to ubiquitin-dependent protein degradation during the cell cycle. A few terms pertain to broader developmental processes, but the dominant signal is meiosis/oocyte maturation. ","confidence":"High","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":22},{"id":"GO:0006516","count":22},{"id":"GO:0008285","count":22},{"id":"GO:0007057","count":22},{"id":"GO:0051436","count":22}]},{"hash":"1963876280115552152","title":"Ribosome Biogenesis and RNA Modification","description":"Most frequent GO terms revolve around ribosome assembly (ribosome biogenesis, LSU biogenesis) and RNA processing/modification (rRNA and tRNA methylation, rRNA maturation). This points to a cluster centered on ribosome production and RNA maturation, with peripheral terms that are less representative of the main function. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0042273","count":4},{"id":"GO:0036265","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0000747","count":3}]},{"hash":"1556507510228855695","title":"Oocyte meiosis I spindle assembly and ubiquitin-dependent proteolysis","description":"The top terms cluster around oocyte maturation, spindle assembly in female meiosis I, and ubiquitin-dependent proteolysis, with microtubule polymerization reinforcing spindle dynamics. This suggests a cohesive program governing meiosis entry and progression in oocytes, coordinated by targeted protein degradation and microtubule remodeling; a few developmental terms appear less central.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":14},{"id":"GO:0001556","count":11},{"id":"GO:0006516","count":11},{"id":"GO:0008285","count":11},{"id":"GO:0007057","count":11}]},{"hash":"356377319398689713","title":"Ribosome assembly and translation machinery","description":"The cluster is dominated by translation-related terms (GO:0006412) and ribosomal large subunit assembly (GO:0000027), with additional terms touching on translation termination and transcription-related regulation that may reflect overlapping cellular processes. Overall, the strongest signal ties to protein synthesis and ribosome assembly, with some stress- or antibiotic-induced responses that can influence translation.","confidence":"High","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":18},{"id":"GO:0046677","count":4},{"id":"GO:0000027","count":4},{"id":"GO:0006415","count":3},{"id":"GO:0006353","count":3}]},{"hash":"739130704312792162","title":"Unknown","description":"The top GO terms span translation, plant hormone (auxin) signaling, DNA repair, immune cytokine production, sterol biosynthesis, and signaling pathway regulation with no single coherent function tying them together. With only a few terms clustered around translation and many disparate processes, the proteins likely do not share a unified biological function, making an intuitive label difficult.","confidence":"","size":22,"edges":229,"triangles":1501,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046620","count":2},{"id":"GO:0009734","count":2},{"id":"GO:0009926","count":2},{"id":"GO:0009733","count":2}]},{"hash":"2291781922495321873","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by protein synthesis processes: translation and cytoplasmic translation, translation termination, and ribosome biogenesis. While there are some peripheral terms (response to immobilization stress, retina vasculature development, methylation, etc.), the strongest and most frequent terms point to ribosomal function and translation machinery, suggesting proteins in this cluster mainly participate in ribosome-based protein production.","confidence":"High","size":22,"edges":18,"triangles":17,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0035902","count":4},{"id":"GO:0032259","count":4},{"id":"GO:0061298","count":4}]},{"hash":"952569952812583513","title":"Development and stress responses","description":"The top GO terms cluster around developmental processes (forebrain development, multicellular organism development, skeletal system development) but also include defense and stress-related responses (defense response to Gram-positive bacterium, cellular response to cadmium, ER-stress\u2013related apoptotic signaling) and general transcription/cell cycle activities. This pattern suggests a group of proteins involved in development that also participate in regulatory and stress-response pathways, hence a label that reflects both developmental roles and stress responses.","confidence":"Medium","size":22,"edges":10,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":8},{"id":"GO:0006351","count":7},{"id":"GO:0030900","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0001501","count":6}]},{"hash":"1835259748055595771","title":"Diverse solute membrane transporters","description":"The GO terms show transmembrane transport across diverse substrates (arabinose, galactose, nitrate/nitrite, sodium/potassium ions, sialic acid, 4-hydroxyphenylacetate) and a vesicle-related process (neurotransmitter loading). This indicates a cluster of membrane transporter proteins with broad substrate specificity rather than a single specific transporter pathway.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":3},{"id":"GO:0042891","count":3},{"id":"GO:0015757","count":3},{"id":"GO:0035725","count":3},{"id":"GO:0042128","count":3}]},{"hash":"1139371247978790548","title":"mRNA Processing and Export Regulation","description":"Based on frequent GO terms related to splicing via the spliceosome, mRNA polyadenylation, mRNA export from the nucleus, and regulation of post-transcriptional processes (including mRNA stability and ncRNA-mediated regulation), this cluster appears to group proteins involved in RNA processing and post-transcriptional gene expression control, with some links to translation reinitiation in stress or viral contexts.","confidence":"High","size":22,"edges":199,"triangles":1120,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":17},{"id":"GO:0006378","count":16},{"id":"GO:0045292","count":16},{"id":"GO:0010610","count":16},{"id":"GO:0048026","count":16}]},{"hash":"2062659263790721558","title":"Calcium-Triggered Transcription and Signaling","description":"The cluster is enriched for calcium ion\u2013related response terms and transcriptional regulation terms (RNA polymerase II\u2013mediated transcription, DNA-templated transcription), along with signaling pathways (SMAD signaling, histone deacetylation regulation) and development-related processes (osteoblast proliferation, eye morphogenesis). This pattern suggests a cohesive theme where calcium signaling modulates transcription and developmental signaling. Some terms (ABA response, arachidonate chemotaxis) appear as peripheral signals but do not overturn the central link between calcium responsiveness and transcriptional regulation.","confidence":"Medium","size":22,"edges":226,"triangles":1450,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071277","count":11},{"id":"GO:0006366","count":9},{"id":"GO:0009737","count":8},{"id":"GO:0006351","count":8},{"id":"GO:0031063","count":7}]},{"hash":"1008918191106758045","title":"Flavonoid and phenylpropanoid metabolism","description":"Most top GO terms point to flavonoid biosynthesis (anthocyanins, kaempferol, cyanidin glucoside) and lignin/phenylpropanoid metabolism, with related glycosylation steps. Some entries reference detoxification (glucuronidation, estrogen catabolism) that may reflect annotation noise, but the dominant signal supports a flavonoid/phenylpropanoid biosynthesis cluster.","confidence":"Medium","size":22,"edges":95,"triangles":151,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0002175","count":20},{"id":"GO:0030259","count":20},{"id":"GO:0009808","count":20},{"id":"GO:0033330","count":20},{"id":"GO:0052696","count":20}]},{"hash":"698629342308405233","title":"Plant secondary cell wall biosynthesis","description":"The cluster is dominated by GO terms related to plant cell wall formation, especially secondary wall processes (e.g., plant-type secondary cell wall biogenesis; glucuronoxylan and homogalacturonan biosynthesis), plus glycosylation steps involved in polysaccharide assembly. A few terms like xenobiotic response and muscle regeneration appear peripheral or noisy, but the core signal points to secondary cell wall polysaccharide biosynthesis.","confidence":"High","size":22,"edges":25,"triangles":8,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":6},{"id":"GO:0009834","count":4},{"id":"GO:0010417","count":4},{"id":"GO:0042493","count":3},{"id":"GO:0035269","count":3}]},{"hash":"1347574341581570375","title":"Ribosome biogenesis and translation regulation","description":"The top GO terms are dominated by translation and ribosome-related processes (translation, regulation of translation, maturation of LSU-rRNA), indicating a cluster centered on ribosome assembly and protein synthesis control. Additional terms hint at nuclear/nucleolar functions and cell cycle-related processes, but the core signal remains ribosome biogenesis and translation. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046656","count":2},{"id":"GO:0000470","count":2},{"id":"GO:0006417","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006281","count":2}]},{"hash":"913050749581888924","title":"Bacterial cell division and peptidoglycan synthesis","description":"Most frequent GO terms cluster around cell division, cell wall organization, and peptidoglycan biosynthesis, indicating a coherent theme of bacterial cell wall biogenesis and cytokinesis. While a few terms (e.g., translation initiation under ER stress, histone methylation, virus defense) are less consistent with bacteria, the dominant signals support a division- and cell-wall-centric group.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":11},{"id":"GO:0071555","count":8},{"id":"GO:0008360","count":7},{"id":"GO:0009252","count":7},{"id":"GO:0055114","count":6}]},{"hash":"1940292825862459932","title":"Plant energy production and oxidative stress response","description":"The top GO terms point to energy generation via photosynthesis and mitochondrial respiration (light reactions, NADH-to-ubiquinone electron transport, ATP synthesis) and to oxidative stress defense (response to oxidative stress, cellular oxidant detoxification). Additional plant-specific terms (plant-type cell wall organization) and lignin catabolic process hint at cell-wall\u2013related remodeling in a plant context. Taken together, these terms describe a coherent theme of energy metabolism balanced with redox homeostasis in plants, with some cell wall activity.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006810","count":2},{"id":"GO:0019684","count":2},{"id":"GO:0042773","count":2},{"id":"GO:0006120","count":2}]},{"hash":"2072347296335134439","title":"ABA-regulated transcription and plant development","description":"The cluster is enriched for transcription-related GO terms (DNA-templated transcription and its regulation) along with plant-specific developmental and hormone signaling terms (abscisic acid-activated signaling, multicellular development, bract development). This suggests proteins functioning in transcriptional control during plant development and ABA-mediated responses, with auxiliary links to stress-related metabolism. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0009738","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0007275","count":4},{"id":"GO:0055114","count":3}]},{"hash":"1287965660382068389","title":"ABA-regulated plant development and transcription","description":"Dominated by transcription-related terms, with ABA signaling and developmental processes (bract, seed, floral meristem) and cuticle biosynthesis, indicating transcriptional regulators coordinating ABA responses with plant development and epidermal lipid production.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0006355","count":7},{"id":"GO:0009738","count":6},{"id":"GO:0010200","count":5},{"id":"GO:0010432","count":5}]},{"hash":"552106653259969997","title":"Plant organelle RNA editing and processing","description":"These proteins show a strong enrichment for organelle RNA editing and processing in plants (mitochondrial and chloroplast), including cytidine-to-uridine editing, mitochondrial/chloroplast RNA modification, and RNA processing. Developmental and defense terms are present but secondary; the core signal points to post-transcriptional regulation in plant organelles.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0009451","count":4},{"id":"GO:0016554","count":4}]},{"hash":"415639949544353013","title":"Unknown","description":"The top GO terms cover a mix of plant-specific developmental processes (stomatal movement/opening, pollen tube growth, endoreduplication, cell size regulation) and unrelated pathways (p53-mediated apoptotic signaling, ribosomal biogenesis/ export, LDL receptor catabolism). This lack of a coherent, single functional theme across the cluster makes a unified label inappropriate.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042771","count":2},{"id":"GO:1902456","count":1},{"id":"GO:0009860","count":1},{"id":"GO:0010118","count":1},{"id":"GO:1904669","count":1}]},{"hash":"39069478583564789","title":"Unknown","description":"The terms collectively span immune signaling, transcription, multiple developmental processes across species, signaling pathways, and apoptosis, with no single cohesive function tying the proteins together.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097011","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0048829","count":3},{"id":"GO:0043491","count":2},{"id":"GO:0008542","count":2}]},{"hash":"2259570148661367761","title":"Plant Hormone Signaling and Chloroplast Regulation","description":"The top GO terms cluster around hormone responses (ethylene, gibberellin), leaf senescence regulation, chlorophyll/chloroplast-related processes, and stress responses (osmotic stress, flavonol biosynthesis), with supporting roles in chromatin remodeling and cell wall regulation. This pattern suggests a cohesive module governing hormone signaling, chloroplast function, and stress adaptation in plants, rather than unrelated processes. There is one outlier term (viral process), but the dominant signal points to plant hormone-driven growth and stress response pathways.","confidence":"High","size":22,"edges":11,"triangles":0,"max_degree":10,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0043044","count":8},{"id":"GO:0009723","count":8},{"id":"GO:0055114","count":7},{"id":"GO:1900056","count":7},{"id":"GO:0010380","count":7}]},{"hash":"2094148069366605447","title":"Cell Cycle and DNA Replication","description":"The top GO terms cluster around cell division, mitotic cell cycle, DNA replication, transcription related to replication, and centrosome cycle, suggesting a core theme of cell-cycle progression and genome duplication. Some terms (defense response, forebrain development, imprinting) appear as outliers or multifunctional annotations, indicating noise rather than a unifying function. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0006260","count":3}]},{"hash":"2275511441791490176","title":"Membrane Transport and Synaptic Function","description":"Top terms point to multiple transmembrane transport activities (xenobiotic, nitrate/nitrite, potassium ion) and a neuronal-specific function (neurotransmitter loading into synaptic vesicles), suggesting a cluster centered on membrane transport with neural/synaptic relevance. While some terms are regulatory or related to learning, the transport-centric terms dominate, supporting this label.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0051534","count":2},{"id":"GO:0034351","count":2},{"id":"GO:0008542","count":2}]},{"hash":"2172695769285025856","title":"Unknown","description":"The GO terms are spread across development (forebrain, neural tube, skeletal system, multicellular development), transcription (DNA-templated transcription), and stress/immune responses (ER-stress\u2013related apoptosis, defense to Gram-positive bacteria, metal ion response), with no single cohesive function tying all proteins. The lack of edges and a unifying process supports labeling it Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":22},{"id":"GO:0006349","count":22},{"id":"GO:0001403","count":22},{"id":"GO:0030900","count":22},{"id":"GO:0006351","count":22}]},{"hash":"1624024424456144957","title":"Neuroinflammatory Innate Immune Signaling","description":"The top GO terms point to strong involvement in innate immune responses to pathogens (dsRNA, LPS, Gram-positive bacteria) and interferon-beta production, indicating a cluster of genes engaged in innate immune signaling, potentially in the CNS. Some neural development/synapse-related terms appear, but the core theme remains innate immune response.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0043330","count":22},{"id":"GO:0071222","count":22},{"id":"GO:0050830","count":22},{"id":"GO:0045087","count":22},{"id":"GO:0014068","count":22}]},{"hash":"1655289531458689212","title":"Plant Abiotic Stress Response and Hormone Biosynthesis","description":"These proteins are enriched for plant abiotic stress and hormone-related GO terms (desiccation response, high light response, cellular oxidant detoxification, ABA biosynthesis, ethylene biosynthesis), and also include plant-type secondary cell wall biogenesis; together they point to a module coordinating stress adaptation and hormone signaling in plants.","confidence":"High","size":22,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009269","count":2},{"id":"GO:0010116","count":2},{"id":"GO:0009644","count":2},{"id":"GO:0098869","count":2}]},{"hash":"1238453310047552891","title":"Germline and neural development","description":"The top GO terms show strong germline/gamete-related processes (piRNA processing, male meiotic division, DNA methylation in gamete generation) alongside neural development terms (optic nerve morphogenesis, axonal fasciculation, equilibrioception, genitalia morphogenesis). This mix suggests a cluster of proteins involved in developmental programs spanning both germline and nervous system tissues, rather than a single, narrow pathway.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034587","count":3},{"id":"GO:0007140","count":3},{"id":"GO:0043046","count":3},{"id":"GO:0048807","count":2},{"id":"GO:0033628","count":2}]},{"hash":"453224903760459032","title":"DNA replication and transcription regulation","description":"The top GO terms cluster around DNA replication, recombination, DNA-templated transcription, and regulation/termination of transcription, along with base-excision repair. This points to a core function in nuclear DNA metabolism and transcription control. A few terms related to immune signaling and cell adhesion appear but are likely peripheral to the main theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0043029","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3}]},{"hash":"709239539183045304","title":"Plant RNAi and miRNA processing under stress","description":"This cluster is enriched in RNA processing and RNAi-related terms (RISC complex assembly, pre-miRNA processing, mRNA processing, RNAi antiviral immunity) alongside plant-stress responses (desiccation, high light, heat) and ABA biosynthesis regulation. The convergence of RNA silencing machinery and stress signaling suggests a plant-specific RNAi/miRNA processing cluster activated during stress.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0009269","count":2},{"id":"GO:0010116","count":2},{"id":"GO:0009644","count":2}]},{"hash":"823083748074921440","title":"Plant Growth and Stress Response Regulation","description":"The proteins appear linked to plant development and metabolism regulated by hormones and stress signals, including gibberellin response, leaf senescence, chlorophyll biosynthesis regulation, flavonol biosynthesis, and secondary cell wall modulation, as well as chromatin remodeling and snRNA transcription. These together suggest a broad regulatory cluster governing growth, photosynthesis-related processes, and stress adaptation, rather than a single, specific pathway. The occasional presence of actin organization and viral process terms likely reflects general cellular processes rather than a distinct functional module in this cluster.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":3},{"id":"GO:0030036","count":2},{"id":"GO:1900056","count":2},{"id":"GO:0010380","count":2},{"id":"GO:0009739","count":2}]},{"hash":"471385533252568955","title":"Plant Growth and Stress Signaling with Chromatin Remodeling","description":"GO terms indicate plant hormone signaling (cytokinin, gibberellin), development (secondary cell wall biogenesis, chlorophyll and flavonol biosynthesis), stress responses (osmotic stress, leaf senescence), and chromatin remodeling, suggesting a regulatory module that coordinates growth and environmental responses via epigenetic mechanisms; the viral process annotation is likely incidental. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:1901348","count":8},{"id":"GO:0009736","count":8},{"id":"GO:0016032","count":7},{"id":"GO:0070933","count":7},{"id":"GO:1900056","count":6}]},{"hash":"1602349876667478305","title":"Unknown","description":"The top terms span diverse contexts (DNA endoreduplication, mRNA stabilization, transcriptional/export regulation, multiple signaling pathway regulations including BMP/TGF-beta and NF-kappaB, vacuole fusion, meristem identity, and dephosphorylation) with no clear single functional theme, so no coherent label can be assigned beyond Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042023","count":2},{"id":"GO:0048255","count":2},{"id":"GO:0030514","count":2},{"id":"GO:0042347","count":2},{"id":"GO:0061191","count":2}]},{"hash":"1082610526480632083","title":"Plant cell wall biosynthesis and plasmodesmata organization","description":"The dominant GO terms indicate plant-specific cell wall processes, including cell wall organization, plasmodesma organization, and regulation of cellulose biosynthesis, suggesting the cluster centers on plant cell wall biosynthesis and intercellular connectivity. Some terms like insulin response and leukocyte adhesion appear present but are likely non-specific annotations rather than core functions of this cluster.","confidence":"Medium","size":22,"edges":20,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":6},{"id":"GO:0006486","count":4},{"id":"GO:0005978","count":3},{"id":"GO:2001009","count":3},{"id":"GO:0009663","count":3}]},{"hash":"9101731626723017","title":"Oocyte meiosis, spindle assembly, and early development","description":"The GO terms point to meiotic processes (oocyte maturation, spindle assembly in female meiosis I) and early development (neural tube closure initiation, third ventricle development), with supporting roles for proteasomal ubiquitin-dependent protein catabolism and microtubule dynamics. This suggests a cluster of proteins coordinating meiosis and early developmental progression.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":18},{"id":"GO:0001556","count":13},{"id":"GO:0021678","count":13},{"id":"GO:0006516","count":13},{"id":"GO:0051436","count":13}]},{"hash":"877524346634269209","title":"Oocyte Maturation and Meiotic Spindle Dynamics","description":"The top terms center on oocyte maturation, spindle assembly in female meiosis I, and SCF-dependent ubiquitin-proteasome\u2013mediated protein degradation, all hallmark features of meiotic progression and spindle dynamics in oocytes. Microtubule polymerization further supports a focus on spindle apparatus, while related terms about cell proliferation regulation fit within meiotic control. Some neural development terms are peripheral, but the core theme is meiosis and oocyte-related processes, making this label representative and specific.","confidence":"High","size":22,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":17},{"id":"GO:0001556","count":15},{"id":"GO:0006516","count":15},{"id":"GO:0008285","count":15},{"id":"GO:0007057","count":15}]},{"hash":"1030592535174260150","title":"Ubiquitin-Dependent Proteolysis and Immune Signaling","description":"The top GO terms cluster around ubiquitin-mediated protein catabolism (ERAD, K48-linked ubiquitination) and regulation of apoptosis, with immune-related pathways (V(D)J recombination, NF-kappaB activation, TNF signaling) and histone ubiquitination also represented. This points to a group of proteins primarily involved in tagging substrates for degradation and modulating immune signaling cascades.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0030433","count":10},{"id":"GO:0070936","count":9},{"id":"GO:0042981","count":9},{"id":"GO:0033151","count":9}]},{"hash":"873585273170331182","title":"Plant Hormone-Responsive Chromatin Regulation","description":"The GO terms cluster around plant hormone signaling (cytokinin, gibberellin, and salicylic acid responses) and chromatin dynamics (chromatin remodeling, histone acetylation regulation, histone H2A deubiquitination, and heterochromatin formation), with a note on leaf senescence regulation. This suggests a cohesive theme where hormone signaling modulates transcription via changes in chromatin state, affecting development and stress responses in plants.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":12},{"id":"GO:0009739","count":11},{"id":"GO:0043044","count":11},{"id":"GO:0010520","count":11},{"id":"GO:0035066","count":11}]},{"hash":"798530800218735727","title":"Unknown","description":"The Top Terms span disparate biological contexts: animal reproduction (sperm capacitation, double fertilization), plant-specific processes (aerenchyma formation, pectin/cellulose catabolic), and signaling/neural processes (endocannabinoid signaling, neuroblast proliferation). There is no single unifying function or pathway linking these terms, so a coherent label cannot be assigned.","confidence":"","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048240","count":5},{"id":"GO:0009567","count":4},{"id":"GO:2000008","count":4},{"id":"GO:0080155","count":4},{"id":"GO:0045490","count":3}]},{"hash":"212655485800531202","title":"Rho/Rac GTPase Signaling Regulation","description":"Top GO terms are dominated by negative regulation of Rac and Rho GTPase signaling and broader GTPase activity control, with related processes like negative regulation of endocytic recycling and ubiquitin deubiquitination activities. Together these suggest a cluster tied to small GTPase\u2013mediated signaling and trafficking regulation, with apoptosis and osteoclast differentiation terms representing downstream effects.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035021","count":4},{"id":"GO:0043547","count":4},{"id":"GO:2001136","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0008625","count":3}]},{"hash":"462747993988224052","title":"Regulatory processes (mixed)","description":"Top GO terms are largely about regulation of enzyme activities (endopeptidase, phosphatase, Ca2+-ATPase), cell proliferation, oxidative stress responses, and apoptosis. A few terms touch on kidney development or defense against fungus, but there is no single cohesive pathway linking the cluster. Therefore, the cluster is best described as regulatory proteins influencing diverse cellular activities rather than a specific process.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":4},{"id":"GO:0001822","count":3},{"id":"GO:0050832","count":3},{"id":"GO:1903629","count":2},{"id":"GO:0007568","count":2}]},{"hash":"731326354607250885","title":"Plant oxidative stress response and cell wall remodeling","description":"The top terms cluster around oxidative stress response, detoxification of reactive oxygen species, and hydrogen peroxide catabolism, plus lignin catabolic process and plant-type cell wall organization, indicating a cohesive plant defense/stress module linking ROS management with cell wall remodeling and lignin metabolism, supported by transcriptional regulation terms. Confidence: High","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006979","count":3},{"id":"GO:0046274","count":3},{"id":"GO:0009664","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0042744","count":3}]},{"hash":"1936187546091357545","title":"Neural and craniofacial development signaling","description":"This cluster is enriched for neural-related signaling terms and developmental processes, including neurotrophin TRK receptor signaling, optic nerve morphogenesis, and face development, along with FGFR-dependent apoptotic signaling and PI3K/AKT signaling, indicating coordination of neural crest\u2013derived tissue and visual system development. A few terms (e.g., symbiont-mediated transformation of host cell) appear less directly related, but the dominant theme centers on neural and craniofacial development and associated growth factor signaling.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":22},{"id":"GO:0090090","count":22},{"id":"GO:0020021","count":22},{"id":"GO:0071469","count":22},{"id":"GO:0060324","count":22}]},{"hash":"1905140883562143433","title":"Plant Metabolism and Stress Response","description":"The GO terms point to plant-specific metabolic processes (chlorophyll catabolic, biotin and menaquinone biosynthesis, nitrogen utilization) alongside detoxification and hormone-related responses (response to toxic substances, strigolactone signaling). This suggests a cluster centered on plant metabolism with associated detox and stress response pathways rather than a single narrow function.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0015996","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0019740","count":2}]},{"hash":"2159071581110839802","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071836","count":2},{"id":"GO:0010930","count":2},{"id":"GO:0015770","count":2},{"id":"GO:1902334","count":2},{"id":"GO:2000344","count":1}]},{"hash":"1770322238064394616","title":"Chromatin regulation and transcription control","description":"The top GO terms cluster around transcriptional control and chromatin-level regulation, including histone deacetylation and chromatin silencing, with links to rDNA and circadian/regulatory regions. This reflects a coherent theme of transcription modulation via chromatin state, with a note of related cell-cycle regulation signals.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000678","count":3},{"id":"GO:0016575","count":2},{"id":"GO:0010971","count":2},{"id":"GO:0042754","count":2},{"id":"GO:0016479","count":2}]},{"hash":"1224867165422446327","title":"RNA polymerase assembly and transcription regulation","description":"The top GO terms center on the assembly of RNA polymerases I, II, and III and on transcription elongation regulation by RNA polymerase II, suggesting a cohesive theme around transcription machinery assembly and control. Other terms point to general cellular assembly processes (tubulin complex assembly, protein folding) and a plant ABA signaling term, which may reflect broader regulatory context rather than a single pathway. Overall, the most representative label is transcription machinery assembly and regulation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":2},{"id":"GO:0043086","count":2},{"id":"GO:0080163","count":2},{"id":"GO:1990113","count":1},{"id":"GO:0007021","count":1}]},{"hash":"1341004475249900970","title":"Mitochondrial Energy Production and Lipid Metabolism","description":"The cluster is dominated by mitochondrial functions: regulation of membrane potential, proton motive force-driven ATP synthesis, and ubiquinone biosynthesis, with supporting signals for ion transport and lipid handling (lipid droplet organization and adipose development). Some terms relate to BMP signaling, abscission, and DNA repair, which are less central to mitochondria, but the core theme centers on energy production and lipid metabolism.","confidence":"Medium","size":21,"edges":22,"triangles":2,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0051881","count":2},{"id":"GO:0042777","count":1},{"id":"GO:0099132","count":1},{"id":"GO:1901006","count":1},{"id":"GO:0000012","count":1}]},{"hash":"844281583936551171","title":"Ubiquitin-Proteasome Regulation and Immune Signaling","description":"This cluster is dominated by proteins involved in protein turnover and ubiquitination (APC-dependent catabolic process, protein deubiquitination, proteasome core complex assembly). Immune signaling terms (Fc-epsilon receptor signaling, negative regulation of inflammatory response) suggest immune pathway involvement, while Wnt-related terms may reflect degradation linking signaling components to the proteostasis machinery. Overall, the theme centers on ubiquitin-proteasome system activity with immune and signaling cross-talk.","confidence":"High","size":21,"edges":47,"triangles":59,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0031145","count":5},{"id":"GO:0016579","count":5},{"id":"GO:0038095","count":4},{"id":"GO:0090090","count":4},{"id":"GO:0061418","count":4}]},{"hash":"1011725346725237420","title":"Ribosome biogenesis and translation initiation","description":"This cluster is dominated by GO terms for ribosome biogenesis, translation initiation complex formation, translation, translation reinitiation, and rRNA processing, all pointing to ribosome assembly and protein synthesis. While a few terms touch on broader processes like DNA repair or chromatin remodeling, the central theme is the production and use of ribosomes. Confidence: High","confidence":"","size":21,"edges":178,"triangles":826,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0001731","count":4},{"id":"GO:0006283","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0001732","count":3}]},{"hash":"976631559478124218","title":"Central carbon metabolism","description":"The top GO terms cluster around glycolysis, the TCA cycle, and glucose metabolism, with related terms for pyruvate decarboxylation to acetyl-CoA, thiamine biosynthesis, menaquinone biosynthesis, and branched-chain amino acid catabolism, pointing to a cohesive energy-generation and central-carbon processing module. Anomalous terms (e.g., olfactory bulb development) likely reflect annotation noise rather than a true cluster theme.","confidence":"High","size":21,"edges":138,"triangles":472,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0006096","count":6},{"id":"GO:0006099","count":6},{"id":"GO:0061732","count":5},{"id":"GO:0006006","count":5}]},{"hash":"463857625740453201","title":"Spliceosome-driven mRNA Processing and Export","description":"The top GO terms strongly point to spliceosome-mediated and alternative mRNA splicing, along with mRNA processing and export from the nucleus, indicating a cohesive group centered on mRNA maturation. Regulatory ncRNA-mediated gene silencing and translation reinitiation appear as related RNA-level regulatory themes, but the core signal is splicing and export. ","confidence":"High","size":21,"edges":63,"triangles":141,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":10},{"id":"GO:0031047","count":8},{"id":"GO:0048026","count":8},{"id":"GO:0045292","count":8},{"id":"GO:1900363","count":7}]},{"hash":"1891893313814384235","title":"Organelle RNA Editing and Plastid Transcription","description":"The top GO terms point to RNA modification and editing activities coupled with plastid/chloroplast functions (plastid transcription, thylakoid membrane organization) and mitochondrial RNA processing (mitochondrial mRNA modification, editing). This suggests a cohesive theme of organelle RNA editing/modification and organelle gene expression, rather than broad cellular processes. Obsolete and outlier terms (e.g., liver regeneration) appear incidental and do not alter the core theme.","confidence":"Medium","size":21,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042793","count":3},{"id":"GO:0010027","count":2},{"id":"GO:0097421","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1621731706660602945","title":"BMP and TGF-beta Signaling Inhibitors","description":"The top GO terms point strongly to negative regulation of BMP signaling and TGF-beta receptor signaling, along with SMAD-related and TGF-beta response processes, suggesting the proteins collectively act to dampen BMP/TGF-beta pathways. A few terms about non-canonical NF-kappaB signaling and nuclear export also fit the theme of broader signaling modulation, but the central theme remains BMP/TGF-beta inhibition.","confidence":"High","size":21,"edges":205,"triangles":1236,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030514","count":12},{"id":"GO:0042347","count":12},{"id":"GO:0061191","count":12},{"id":"GO:0000173","count":12},{"id":"GO:0046827","count":12}]},{"hash":"1831239852884177794","title":"DNA replication and genome maintenance","description":"Most GO terms point to DNA replication, DNA repair, and chromosome maintenance (DNA replication, SOS response, replication-born double-strand break repair via sister chromatid exchange, meiotic chromosome condensation), suggesting a cohesive theme of genome maintenance. A few terms about differentiation and tRNA gene clustering appear incidental given their single-count representation. Therefore the label reflects the core function of this protein cluster.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050873","count":1},{"id":"GO:0048235","count":1},{"id":"GO:0040015","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0060821","count":1}]},{"hash":"1786359295817710348","title":"Developmental Transcription and Stress Responses","description":"The cluster is enriched for DNA-templated transcription and various development terms (forebrain, multicellular organism development, skeletal system development, and general transcription), suggesting a core theme of developmental gene regulation. The presence of stress/immune-related terms (vacuolar acidification, defense against Gram-positive bacterium, cadmium response, ER stress\u2013induced apoptosis) indicates additional regulatory or homeostatic processes that can accompany development in this dataset.","confidence":"Medium","size":21,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007035","count":5},{"id":"GO:0050830","count":5},{"id":"GO:0030900","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0007275","count":4}]},{"hash":"210990580437538029","title":"Metal Ion Transport and Homeostasis","description":"The cluster shows a clear enrichment in metal ion transport and detoxification terms (copper, zinc, mercury, cadmium), including copper ion export, mercury ion transport, and intracellular copper ion homeostasis, alongside detoxification processes. A translation term is also present but likely reflects core ribosomal components carried by many proteins. Overall, these proteins appear to coordinate metal ion handling and detoxification in the cell.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0048515","count":3},{"id":"GO:0070574","count":2},{"id":"GO:0050787","count":2},{"id":"GO:0015680","count":2}]},{"hash":"437817654426866800","title":"TLR-MyD88 NF-\u03baB Innate Immunity","description":"The cluster is enriched for innate immune and antiviral defense terms: I-kappaB phosphorylation (NF-\u03baB activation), defense response to virus, innate immune response, and MyD88-dependent TLR signaling with LPS detection, pointing to coordination of pathogen sensing and inflammatory signaling. The presence of DNA-templated transcription and translation hints at downstream gene expression changes following signaling. Overall, these proteins likely function together in sensing pathogens and triggering inflammatory responses in immune cells, such as macrophage activation.","confidence":"High","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007252","count":4},{"id":"GO:0051607","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0042116","count":3},{"id":"GO:0006351","count":3}]},{"hash":"37381020976228651","title":"Prostaglandin biosynthesis and oxidative stress response","description":"This cluster is dominated by prostaglandin biosynthesis and redox-related terms (cell redox homeostasis, oxidant detoxification), suggesting a core function in eicosanoid signaling and oxidative stress regulation. The presence of related signals (EGF response, zinc ion response, JNK activity regulation, responses to toxic substances, and immune/inflammatory-related processes like neutrophil aggregation regulation and vascular smooth muscle proliferation) indicates a cohesive theme of inflammatory signaling intertwined with redox control and cell signaling pathways. Confidence: High.","confidence":"","size":21,"edges":170,"triangles":757,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":19},{"id":"GO:0045454","count":17},{"id":"GO:0098869","count":17},{"id":"GO:2000429","count":16},{"id":"GO:0071364","count":16}]},{"hash":"168275924961141738","title":"Mitochondrial Fission and Cell Division","description":"The top GO terms cluster around mitochondrial fission (membrane fission and general fission), cell division and cell cycle, with apoptotic processes linked to mitochondrial function, plus related division machinery terms like cell septum assembly. While there are a few RNA-processing terms, the dominant theme centers on mitochondrial dynamics in the context of cell division and growth.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0090149","count":6},{"id":"GO:0000002","count":6},{"id":"GO:0042274","count":4},{"id":"GO:0006915","count":4}]},{"hash":"2039638774209350778","title":"Root development and cell-wall biosynthesis","description":"The cluster shows a coherent emphasis on root-related processes (root hair development, root cap development) and plant-type secondary cell wall biogenesis, with additional signals of plant organ formation timing, suggesting a shared role in root development and cell-wall construction. Some terms are broader or obsolete, but they do not override the central theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0080147","count":2},{"id":"GO:0090502","count":2}]},{"hash":"464309557812218060","title":"RNA Pol III Transcription and Ribosome Biogenesis","description":"The top GO terms cluster around RNA polymerase III\u2013driven transcription (tRNA transcription, elongation, termination) and related RNA transcription processes, plus ribosome biogenesis and RNA-templated transcription, suggesting a nuclear RNA-processing and ribosome assembly theme. A few development-related terms (egg chamber follicle epithelium adhesion, insect visual primordium formation) may reflect tissue-specific expression or annotation noise rather than a core unified function. Overall, the dominant signal points to Pol III transcription activity and ribosome biogenesis as the cluster\u2019s functional center.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000289","count":4},{"id":"GO:0042797","count":3},{"id":"GO:0075015","count":3},{"id":"GO:0007299","count":3},{"id":"GO:0042248","count":3}]},{"hash":"1746846071448391406","title":"DNA Damage Response and Chromatin Ubiquitination","description":"This cluster is dominated by GO terms for DSB repair (NHEJ), meiotic DSB formation, mitosis exit, apoptosis, and ubiquitin-mediated chromatin modification (K48-linked and histone ubiquitination). Together they suggest a cohesive function in DNA damage signaling, repair, and chromatin remodeling during cell-cycle transitions and meiosis.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0070936","count":21},{"id":"GO:0010458","count":21},{"id":"GO:0006303","count":21},{"id":"GO:0006915","count":21},{"id":"GO:0042276","count":21}]},{"hash":"1683340020895495505","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":19,"triangles":7,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006541","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0021756","count":6},{"id":"GO:0006189","count":6},{"id":"GO:0007626","count":5}]},{"hash":"1604663588789395155","title":"Neuronal Transcription and Translational Regulation","description":"The cluster shows strong signals for transcriptional regulation (DNA-templated transcription and its regulation) and multiple terms tied to RNA processing and translation control (splicing, mRNA processing, translation initiation factor assembly). The presence of a term about regulation of presynapse assembly hints at a neuronal context, suggesting these proteins coordinate gene expression at both transcriptional and translational levels in neurons.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:2000507","count":2},{"id":"GO:1905606","count":2},{"id":"GO:0010801","count":2}]},{"hash":"1883113605048499497","title":"Embryonic and neural development","description":"These terms cluster around embryogenesis (primitive streak formation, multicellular organism development) and neural/brain patterning (forebrain/midbrain/hindbrain boundary formation, subpallium neuron fate, visceral motor neuron differentiation), with additional organ development terms (pituitary gland, roof of mouth, uterus, female gonad). The common theme is embryonic development with a strong emphasis on neural development and brain region specification.","confidence":"High","size":21,"edges":96,"triangles":141,"max_degree":16,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0090009","count":8},{"id":"GO:0021983","count":7},{"id":"GO:0060021","count":7},{"id":"GO:0007275","count":7},{"id":"GO:0060065","count":6}]},{"hash":"1141658399249262669","title":"Regulation of erythrocyte and megakaryocyte differentiation","description":"The top GO terms are dominated by regulation and differentiation of erythrocytes and megakaryocytes, including primitive erythrocyte differentiation, indicating hematopoietic lineage specification as the core theme of this cluster. Transcriptional regulation terms also appear, supporting a broader role in gene expression programs that drive blood cell development. Some other terms reflect stress or xenobiotic responses, but they are secondary to the hematopoietic differentiation signal.","confidence":"High","size":21,"edges":19,"triangles":2,"max_degree":8,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0045648","count":8},{"id":"GO:0045654","count":8},{"id":"GO:0010725","count":8},{"id":"GO:0055114","count":7},{"id":"GO:0032496","count":6}]},{"hash":"2191922632766950943","title":"Nuclear import and mitotic cytoskeleton","description":"This cluster is enriched for GO terms related to nuclear import (NLS-bearing proteins), mRNA transport, and microtubule nucleation, which together point to roles in coordinating nuclear trafficking with spindle/cytoskeletal dynamics during cell division. The presence of cell division, regulation of protein kinases, and Golgi-to-lysosome transport further supports a broader role in intracellular transport and signaling relevant to mitosis and development, though some developmental terms (angiogenesis, blastocyst development) suggest additional context in embryogenesis. ","confidence":"Medium","size":21,"edges":10,"triangles":0,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0006607","count":7},{"id":"GO:0051028","count":7},{"id":"GO:0051301","count":5},{"id":"GO:0007020","count":4}]},{"hash":"620265599611067450","title":"Developmental transcription and stress-response pathways","description":"This cluster centers on genes linked to developmental processes (forebrain and skeletal system development, multicellular organism development) and DNA-templated transcription, with additional signals related to cell cycle and apoptosis. The co-occurrence of immune/stress terms (defense response to Gram-positive bacteria, cellular response to cadmium, ER-stress\u2013related apoptotic signaling) suggests that these developmental regulators also participate in stress responses. Since the main theme is developmental regulation with associated stress responses, the proposed label captures the dominant pattern, though the mix of terms indicates functional versatility rather than a single narrow function.","confidence":"Medium","size":21,"edges":12,"triangles":2,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030900","count":19},{"id":"GO:0006351","count":19},{"id":"GO:0007275","count":19},{"id":"GO:0001501","count":19},{"id":"GO:0050830","count":19}]},{"hash":"1985248580831782726","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042273","count":4},{"id":"GO:0006265","count":3},{"id":"GO:0051225","count":3},{"id":"GO:0007131","count":3},{"id":"GO:1902626","count":3}]},{"hash":"1330961107870959656","title":"Unknown","description":"The top GO terms span diverse processes (nitrate assimilation, quinolinate and tetrahydrofolate metabolism, mercury detoxification) along with development (pituitary gland development, neuron maturation, erythrocyte differentiation) and immune response (lipopolysaccharide). The presence of obsolete terms and a lack of a single cohesive function suggests the proteins do not share a clear common role, so a unified label isn\u2019t identifiable.","confidence":"","size":21,"edges":10,"triangles":0,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042128","count":8},{"id":"GO:0055114","count":8},{"id":"GO:0021983","count":6},{"id":"GO:0016575","count":6},{"id":"GO:0045648","count":5}]},{"hash":"624500407317528865","title":"Nucleolar ribosome biogenesis and LSU maturation","description":"The proteins are primarily linked by GO terms for ribosomal large subunit assembly, maturation of 5.8S and LSU rRNA, preribosome assembly, and export of the large subunit from the nucleus, which together define nucleolar ribosome biogenesis and LSU maturation. Some development-related terms (flower, seed development) are present but likely incidental annotations in this context.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0000463","count":1},{"id":"GO:1902626","count":1},{"id":"GO:0000055","count":1}]},{"hash":"2019152098676340325","title":"Plant Hormone Biosynthesis and Fruit Ripening","description":"The GO terms show a clear pattern around synthesis and turnover of plant hormones (ethylene, gibberellin, auxin, salicylic acid) and processes tied to fruit ripening, along with related secondary metabolism and stress-related responses (hydrogen peroxide\u2013mediated PCD). While one term (penicillin biosynthetic process) seems out of place and may reflect annotation noise, the dominant theme points to hormone-driven growth, maturation, and ripening in plants.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":13},{"id":"GO:0009693","count":7},{"id":"GO:0042318","count":7},{"id":"GO:0009686","count":7},{"id":"GO:0045487","count":7}]},{"hash":"1301319403292864967","title":"Cardiac potassium transport and ventricular repolarization","description":"GO terms show dominant involvement in potassium ion export/import across the plasma membrane and cardiac electrophysiology features such as ventricular repolarization, Purkinje cell action potentials, and left ventricular tissue aspects. This points to a cohesive theme of cardiac potassium handling and electrical activity, with a few outliers (e.g., vasopressin/gastric secretion terms) that do not change the central function. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0097623","count":6},{"id":"GO:1990573","count":6},{"id":"GO:0071313","count":5},{"id":"GO:0060453","count":5},{"id":"GO:0060307","count":5}]},{"hash":"1256880844236142483","title":"Sodium and Potassium Ion Transport","description":"This cluster is dominated by GO terms for moving sodium and potassium ions across the plasma membrane, along with related ion homeostasis and proton transport, and cell volume regulation. Together, these indicate a cohesive group of membrane transporters/regulators that maintain ionic balance and cell volume, with some peripheral links to cardiac conduction and neuronal signaling.","confidence":"High","size":21,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0036376","count":5},{"id":"GO:0030007","count":5},{"id":"GO:0097623","count":5},{"id":"GO:1903281","count":4},{"id":"GO:1902600","count":4}]},{"hash":"612083783330573000","title":"GABAergic Synaptic Transmission and Vesicle Trafficking","description":"The cluster is best tied by GO terms centered on neuronal signaling and receptor trafficking, notably GABAergic synaptic transmission, positive regulation of synaptic vesicle recycling, and GPCR internalization. While there are diverse terms present (aging, ribosome biogenesis, peroxisome regulation), the strongest common thread is synaptic signaling and trafficking of vesicles/receptors in neurons.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001300","count":2},{"id":"GO:0033585","count":2},{"id":"GO:1900063","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0051301","count":1}]},{"hash":"859223060650993230","title":"DNA-Templated Transcription Regulators","description":"The cluster is dominated by GO:0006351 and GO:0006355 (DNA-templated transcription and its regulation), indicating proteins that primarily regulate transcription. The remaining terms are sparse and represent diverse processes, so the main theme is transcription control.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0009992","count":1},{"id":"GO:0007601","count":1},{"id":"GO:0072232","count":1}]},{"hash":"156772637234845302","title":"Terpenoid and Isoprenoid Biosynthesis","description":"This cluster shows strong enrichment for terpenoid/isoprenoid biosynthesis terms: cholesterol biosynthesis, farnesyl/diphosphate biosynthesis, geranyl and geranylgeranyl diphosphate biosynthesis, monoterpene biosynthesis, quinone biosynthesis, and cytokinin biosynthesis. These relate to isoprenoid/terpenoid pathways and prenylation steps, suggesting the proteins collectively participate in terpenoid biosynthesis and related lipid modifications; a couple of terms like protein transport and heterotetramerization are broad annotations and less indicative of the core function. Confidence in this labeling is high.","confidence":"High","size":21,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":5},{"id":"GO:0045337","count":5},{"id":"GO:0051290","count":5},{"id":"GO:1901663","count":5},{"id":"GO:0033384","count":5}]},{"hash":"484707373428478535","title":"Plant immune signaling and DNA repair","description":"This cluster combines clear plant defense terms (hypersensitive response, defense against bacteria, innate immune signaling) with DNA repair processes and chromatin-related changes, suggesting proteins that participate in stress responses that link genome maintenance with immunity and growth regulation (meristem activity and symbiont dormancy).","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":1},{"id":"GO:0006307","count":1},{"id":"GO:0006265","count":1},{"id":"GO:0035552","count":1},{"id":"GO:0009626","count":1}]},{"hash":"1658756362149430602","title":"Metal Ion Transport and Detoxification","description":"This cluster centers on proteins with metal ion transport and detoxification activities, including mercury, copper, zinc, and cadmium ion transport and detoxification of mercury, plus copper export. Chromatin remodeling appears but is less frequent, and developmental terms are present only once each, suggesting the dominant theme is metal homeostasis rather than development. Overall, the data point to a cohesive role in metal ion transport and detoxification.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0009790","count":1},{"id":"GO:0048868","count":1},{"id":"GO:0048316","count":1},{"id":"GO:0070574","count":1}]},{"hash":"1787059176312493962","title":"Female reproductive development and retinoid metabolism","description":"The top GO terms cluster around retinoic acid biosynthesis/catabolism and related metabolism (retinoic acid pathways, calcitriol), together with development of female reproductive structures (uterus, female gonad/genitalia). This suggests a coherent module focused on RA signaling and female reproductive tract development, with some incidental metabolic terms.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071615","count":18},{"id":"GO:0042904","count":18},{"id":"GO:0060065","count":18},{"id":"GO:0008585","count":18},{"id":"GO:0034653","count":18}]},{"hash":"2019550613550334859","title":"Immune signaling and cell cycle regulation","description":"The cluster includes GO terms for immune activation (macrophage activation, NOD2 signaling) alongside transcriptional machinery (DNA-templated transcription, mRNA processing), cell cycle control (cell cycle, negative regulation of CDK activity), and development/migration. This suggests proteins involved in coordinating immune signaling with gene expression and proliferation, rather than a single narrow function. The ABA signaling term appears as an outlier, but the core theme centers on immune signaling intertwined with transcriptional and cell cycle processes.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042116","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0006397","count":2}]},{"hash":"1960666837616107392","title":"Antiviral Innate Immune Response","description":"Dominant GO terms are innate immune response and defense against virus, with additional signals for transcriptional regulation and development, implying antiviral signaling proteins with broader regulatory roles.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0051607","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0016525","count":3}]},{"hash":"1269731812442342325","title":"Transmembrane transport of ions and metabolites","description":"This cluster is dominated by GO terms for transporting substrates across membranes (nitrate/nitrite, phosphate, potassium, vitamins, oligopeptides, and other ions), indicating a cohesive theme of membrane transport. A couple of terms relate to signaling, but the prevailing pattern is diverse transport activity across membranes.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":3},{"id":"GO:0015707","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0009734","count":2},{"id":"GO:0071805","count":2}]},{"hash":"1314647861053114161","title":"Plant Hormone Signaling and Growth Regulation","description":"This cluster is dominated by plant hormone-related processes (cytokinin signaling, gibberellin response) and growth regulation (root meristem growth, secondary cell wall biogenesis), with accompanying roles in leaf senescence, chlorophyll biosynthesis, and osmotic stress response. The presence of cellulose catabolic and chromatin remodeling terms suggests coordinated cell wall remodeling and transcriptional control underlying hormone-driven development and stress adaptation. While a viral process term is present, the overall theme centers on hormone-mediated growth and remodeling in plants.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":10},{"id":"GO:1901348","count":6},{"id":"GO:0010082","count":6},{"id":"GO:0030245","count":6},{"id":"GO:1900056","count":5}]},{"hash":"1771460296109182654","title":"Unknown","description":"The terms are scattered across innate immune signaling (TLR/MyD88, LPS detection, defense against virus) and development processes (axon guidance, dendritic cell cytokine regulation, kidney development), with no shared single function and no connecting interactions, so there isn\u2019t a cohesive label beyond Unknown.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045842","count":4},{"id":"GO:0002755","count":3},{"id":"GO:0032497","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0048846","count":3}]},{"hash":"2172838200149622334","title":"ER-to-Golgi Trafficking and ER Targeting","description":"The top GO terms cluster around ER targeting and ER-to-Golgi vesicle transport, indicating proteins involved in the secretory pathway and delivering proteins from the ER to the Golgi. Additional terms touch on related localization processes (protein localization to division sites, cell adhesion), but the strongest signal is ER export and Golgi trafficking, with a few miscellaneous terms likely incidental. This supports a coherent function in ER-Golgi transport and localization.","confidence":"High","size":21,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031987","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0051533","count":2},{"id":"GO:0006465","count":2}]},{"hash":"21343712929080016","title":"Nuclear gene expression regulation and RNA processing","description":"The dominant themes are transcriptional regulation (DNA-templated transcription and its regulation) and RNA processing (spliceosome-mediated splicing), with additional DNA repair and development terms. Together these proteins appear linked to controlling nuclear gene expression and RNA maturation, hence the name.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900056","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0045316","count":1},{"id":"GO:0007469","count":1}]},{"hash":"2149432893298345639","title":"Ribosome biogenesis and rRNA maturation","description":"The cluster is dominated by GO terms tied to ribosomal large subunit assembly, maturation of 5.8S and LSU rRNA, preribosome assembly, and export of the large subunit from the nucleus, indicating a shared role in ribosome biogenesis and rRNA processing. Some other terms (nodulation, embryogenesis) appear but are not the central theme of the cluster.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009877","count":2},{"id":"GO:0046689","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0000463","count":1}]},{"hash":"1436533310707750427","title":"Unknown","description":"Top terms span diverse processes across species (plant hormone signaling, cell wall metabolism, various catabolic processes, transcription regulation, and broad signaling cascades), with no single cohesive function linking them. Therefore a clear, specific label cannot be assigned.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":7},{"id":"GO:0030245","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0090080","count":4}]},{"hash":"2009290942633784650","title":"Endocannabinoid lipid signaling and catabolism","description":"This cluster is enriched with terms tied to lipid metabolism and endocannabinoid signaling, including regulation of endocannabinoid signaling and various lipid catabolic processes (triglyceride, diacylglycerol, monoacylglycerol, phosphatidylserine, and fatty acids). Some outliers like cellulose catabolic process exist, but the dominant theme is lipid signaling and breakdown, making this a concise and representative label for the group.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":7},{"id":"GO:0019433","count":7},{"id":"GO:0030245","count":7},{"id":"GO:0046340","count":7},{"id":"GO:0042136","count":7}]},{"hash":"1417464076325047796","title":"Lipid signaling and detoxification metabolism","description":"The cluster shows notable enrichment for endocannabinoid signaling regulation (lipid signaling) alongside multiple catabolic and detoxification processes (triglyceride catabolism, oxidant detoxification, beta-ketoadipate, glucuronoside, uracil catabolism) and ancillary metabolism (biotin biosynthesis, nitrogen utilization), suggesting a group of proteins involved in lipid-related signaling plus broad metabolic/detox roles.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":9},{"id":"GO:0019433","count":9},{"id":"GO:0098869","count":8},{"id":"GO:0019740","count":8},{"id":"GO:0009102","count":8}]},{"hash":"1647796641016642982","title":"Plant Secondary Cell Wall Biosynthesis","description":"The top GO terms are dominated by plant cell wall carbohydrate biosynthesis and biogenesis: xyloglucan, xylogalacturonan, glucuronoxylan, arabinan, and plant-type secondary cell wall biogenesis, along with associated sugar biosynthesis (fucose) and salicylic acid signaling. These collectively point to proteins involved in constructing and remodeling the plant secondary cell wall, making this a coherent, specific label. Some non-plant terms appear but do not change the overall plant wall biosynthesis theme.","confidence":"High","size":21,"edges":69,"triangles":39,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0009969","count":5},{"id":"GO:0035118","count":4},{"id":"GO:0010398","count":4},{"id":"GO:0009834","count":4},{"id":"GO:0042353","count":4}]},{"hash":"2098499821472409531","title":"Oocyte meiosis and neural development","description":"Top GO terms converge on two themes: ubiquitin-proteasome\u2013mediated protein catabolism and spindle/meiosis-related processes (SCF-dependent degradation, oocyte maturation, spindle assembly in female meiosis I, microtubule polymerization). Alongside, development-related terms (initiation of neural tube closure, third ventricle development) suggest participation in early neural development. Together, they point to a cluster enriched for meiotic cell division machinery with ties to early developmental events.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":21},{"id":"GO:0001556","count":20},{"id":"GO:0021678","count":20},{"id":"GO:0006516","count":20},{"id":"GO:0051436","count":20}]},{"hash":"127825261338994965","title":"Oocyte meiosis and neural development","description":"The cluster is dominated by terms tied to female meiosis (oocyte maturation; spindle assembly in female meiosis I) and proteolysis via SCF-ubiquitin pathways, suggesting regulation of meiosis through targeted protein degradation. Added CNS development terms (initiation of neural tube closure; third ventricle development) indicate a broader developmental context, potentially linking meiotic proteostasis with early neural development. Overall, the common theme centers on meiosis in oocytes with concurrent neural development processes.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":15},{"id":"GO:0001556","count":13},{"id":"GO:0021678","count":13},{"id":"GO:0006516","count":13},{"id":"GO:0051436","count":13}]},{"hash":"255468898522779679","title":"Plant Hormone Signaling and Metabolic Regulation","description":"This cluster is enriched for plant-specific terms such as cytokinin-activated signaling and phytochelatin/glucosinolate metabolic processes, along with regulation of transcription and signaling cascades, suggesting a broad theme around plant hormone signaling and associated metabolic regulation rather than a single precise pathway.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":5},{"id":"GO:0006355","count":4},{"id":"GO:0043085","count":3},{"id":"GO:1904715","count":3},{"id":"GO:0006508","count":3}]},{"hash":"1923157731041886701","title":"Neurodevelopmental Signaling and Angiogenesis","description":"The top GO terms indicate neural development and signaling (neurotrophin TRK receptor signaling, optic nerve morphogenesis) together with growth factor signaling (FGFR, PI3K-Akt) and adhesion/cytoskeleton dynamics (focal adhesion regulation, actin reorganization) and angiogenesis. This suggests a coherent cluster of proteins coordinating neural development with vascular growth through growth factor\u2013mediated signaling and cell-matrix interactions. Some terms appear broader or less cohesive (e.g., symbiont-mediated transformation of host cell), but the dominant theme centers on neurodevelopmental signaling and morphogenesis linked to blood vessel formation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051893","count":20},{"id":"GO:0048011","count":19},{"id":"GO:0020021","count":19},{"id":"GO:0071469","count":19},{"id":"GO:0021631","count":19}]},{"hash":"1706160269030223764","title":"Exocytosis and vesicle trafficking","description":"The top GO terms cluster around exocytosis, exocyst assembly/localization, and Golgi-to-plasma membrane transport, plus general protein transport and vesicle tethering. This points to a cohesive function in vesicle docking/trafficking and secretion, with exocyst components and vesicle tethering as central elements; a bit of Rho signaling supports cytoskeletal involvement in trafficking as well. The terms consistently converge on a vesicle trafficking/exocytosis theme, making this label representative.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0006893","count":1},{"id":"GO:0007266","count":1},{"id":"GO:0006887","count":1},{"id":"GO:0051601","count":1}]},{"hash":"813371115778526321","title":"Diverse biosynthetic pathways","description":"The top GO terms are dominated by biosynthetic processes: lipopolysaccharide and colanic acid biosynthesis, GDP-mannose metabolism (bacterial polysaccharide-related), and plant secondary metabolite biosynthesis (phenylpropanoids, lariciresinol, pinoresinol, anthocyanins). There is also a transcription term and a related catabolic process, but the unifying thread is synthesis of a variety of metabolites across different systems. This makes a label like \u201cDiverse biosynthetic pathways\u201d appropriate and representative, though the cross-kingdom mix lowers precision.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0009242","count":3},{"id":"GO:0019673","count":3},{"id":"GO:1902132","count":3},{"id":"GO:0009699","count":3}]},{"hash":"2245419872578010550","title":"Prostate tissue development and ECM organization","description":"GO terms center on prostate gland development, collagen fibril organization, and cell-cell adhesion, pointing to tissue morphogenesis and extracellular matrix remodeling as a shared function. Additional terms on prolactin secretion and receptor recycling suggest related endocrine signaling and receptor trafficking; overall, the cluster appears to reflect ECM- and adhesion-associated processes in prostate biology.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030850","count":3},{"id":"GO:0009992","count":2},{"id":"GO:0099132","count":2},{"id":"GO:0032804","count":2},{"id":"GO:0070459","count":2}]},{"hash":"1957113827801491501","title":"Diverse Metabolic Biosynthesis and Detoxification","description":"The cluster\u2019s top GO terms center on biosynthetic processes (biotin and antibiotic biosynthesis) alongside multiple catabolic and lipid-related processes (triglyceride, monoacylglycerol, phosphatidylserine catabolism) and detoxification (cellular oxidant detoxification, response to toxic substance) plus nitrogen utilization. This pattern suggests a broad, metabolism-oriented grouping rather than a single cohesive pathway, capturing biosynthetic activity, lipid metabolism, and detox/nutrient processing. Confidence: Medium","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":8},{"id":"GO:0017000","count":8},{"id":"GO:2000124","count":7},{"id":"GO:0019433","count":7},{"id":"GO:0052651","count":6}]},{"hash":"550336219345211111","title":"Plant defense and cell-wall remodeling","description":"The GO terms cluster around plant-specific defense and structural remodeling: defense against fungus, oxidative stress responses, and lignin-related cell-wall processes (lignin catabolism, plant-type cell wall organization), along with abiotic stress like aluminum transport. Pollination appears as a minor plant-process term but the dominant theme is plant defense/stress responses coupled with cell-wall dynamics.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015690","count":4},{"id":"GO:0009856","count":4},{"id":"GO:0050832","count":3},{"id":"GO:0071333","count":2},{"id":"GO:0010951","count":2}]},{"hash":"442586821004000919","title":"Pollen Tube Growth and Cell Wall Remodeling","description":"The terms cluster around pollen tube growth, pollen-pistil interaction, and plant-type cell wall organization, with supporting processes in pectin metabolism and cell wall modification. This points to a coordinated program governing pollen tube development and extracellular matrix remodeling during fertilization, including pectin catabolism/biosynthesis and lignin-related cell wall changes. Overall, they reflect a cohesive function in pollen\u2013pistil interaction and wall dynamics rather than a single pathway.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":2},{"id":"GO:0048358","count":2},{"id":"GO:0009860","count":2},{"id":"GO:0043086","count":2},{"id":"GO:0042545","count":2}]},{"hash":"1825248339567011599","title":"Photoreceptor Differentiation and Visual Perception","description":"The top terms are clearly tied to eye biology, with visual perception and camera-type eye photoreceptor cell differentiation dominating, suggesting the cluster centers on photoreceptor/retina function. The other terms touch on signaling, lysosomal localization, and junction assembly, which can be relevant to photoreceptor cell biology but are less specific. Overall, the cluster appears to group proteins involved in photoreceptor development and vision.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":1},{"id":"GO:0071404","count":1},{"id":"GO:0007166","count":1},{"id":"GO:0060219","count":1},{"id":"GO:1904352","count":1}]},{"hash":"875869635175218553","title":"Innate Immune Signaling and Transcription Regulation","description":"This cluster is dominated by innate immunity terms: defense response to virus, innate immune response, MyD88-dependent toll-like receptor signaling, and detection of lipopolysaccharide, which together point to an antiviral/innate immune activation theme. Added transcription-related terms (DNA-templated transcription and its regulation) suggest concurrent transcriptional regulation in response to these signals. A single odd-term (fruit dehiscence) is likely unrelated noise. Overall, the data best support a cohesive label around innate immune signaling with transcriptional regulation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051607","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0035372","count":2},{"id":"GO:0045345","count":2}]},{"hash":"426745332610303488","title":"Transcription Initiation and Protein Turnover","description":"The cluster\u2019s top terms cluster around RNA polymerase II preinitiation complex assembly and DNA-templated transcription initiation, including a note on Notch-target transcription, pointing to gene expression regulation. The presence of SCF-dependent proteasomal ubiquitin-dependent protein catabolic process suggests coordinated protein turnover, reinforcing a theme of gene expression control and protein quality management. Some GO terms like SRP-dependent cotranslational targeting to membrane are less cohesive with this core, but the dominant signals support this label.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0006616","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0043966","count":1},{"id":"GO:0051123","count":1}]},{"hash":"1746553085846555988","title":"Actin-driven Mitosis and Organelle Inheritance","description":"The top GO terms point to actin-based processes in mitosis (contractile ring assembly, sister chromatid biorientation) and the inheritance/transport of organelles (mitochondria, peroxisomes, vacuoles) via actin filaments, with related polarity and vesicle transport activities. This cohesively links cytoskeletal dynamics during cell division to organelle partitioning and epithelial polarity features such as brush border assembly, suggesting a common actin-dependent functional theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031134","count":2},{"id":"GO:1903477","count":2},{"id":"GO:0000011","count":2},{"id":"GO:0030050","count":2},{"id":"GO:0048496","count":2}]},{"hash":"1490887413931078860","title":"ER-Golgi trafficking and secretion","description":"The top GO terms cluster around vesicle transport from the ER to the Golgi, COPI vesicle budding, ER exit, and Golgi ribbon formation, indicating a coherent theme of the early secretory pathway. A few terms related to development and Wnt secretion are present but appear secondarily linked through secretion processes. Overall, this cluster is best described as ER-Golgi trafficking and secretion.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0006621","count":1},{"id":"GO:0001893","count":1},{"id":"GO:1902003","count":1},{"id":"GO:0070863","count":1}]},{"hash":"364369306535197746","title":"Neural, cardiac, and muscle development","description":"This cluster centers on developmental differentiation across neural lineages (subpallium neuron fate, amacrine cell differentiation) and cardiac/muscle morphogenesis (cardioblast migration, muscle tissue morphogenesis), with supporting roles for cell adhesion and broader transcriptional regulation. The dominant theme is development and morphogenesis in neural and muscular/cardiac tissues.","confidence":"Medium","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":16},{"id":"GO:0031542","count":16},{"id":"GO:0060415","count":14},{"id":"GO:0060163","count":14},{"id":"GO:0033627","count":14}]},{"hash":"36838765660008585","title":"Osmotic stress\u2013associated sugar and ion transport","description":"This cluster is dominated by membrane transport terms across sugars, ions, and metabolites (glucose/fructose transport, nitrite/nitrate/urate transport, sodium-dependent transport, potassium transmembrane transport) plus an osmotic stress response and vesicular transport, suggesting proteins that regulate osmolarity by moving substrates across membranes.","confidence":"High","size":20,"edges":41,"triangles":19,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":3},{"id":"GO:0070715","count":3},{"id":"GO:0044381","count":3},{"id":"GO:0071332","count":3},{"id":"GO:0015707","count":3}]},{"hash":"1103760781650322402","title":"Innate antiviral TLR-NF-\u03baB signaling","description":"This cluster is dominated by terms for defense against viruses, innate immune responses, and the MyD88-dependent TLR signaling pathway, with regulation of NF-kB activity and cytokine production by dendritic cells. Together, these terms point to a coherent module of innate sensing and signaling that activates NF-kB to drive antiviral cytokine responses. The connection is reasonably strong despite zero edges in the observed network, supporting a protective innate immune function.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":12},{"id":"GO:0043123","count":11},{"id":"GO:0051092","count":10},{"id":"GO:0090073","count":9},{"id":"GO:0045087","count":8}]},{"hash":"1840124993353878555","title":"TLR4-MyD88 Innate Immune Signaling","description":"Top terms indicate a cohesive theme of TLR4/MyD88-mediated innate immune activation, including detection of LPS, positive/regulated TLR4 signaling, dendritic cell cytokine production, and defense responses to viruses. The nervous system development term appears peripheral and does not define the main function of the cluster.","confidence":"High","size":20,"edges":15,"triangles":0,"max_degree":5,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0007399","count":6},{"id":"GO:0043086","count":6},{"id":"GO:0051260","count":5},{"id":"GO:0002755","count":5},{"id":"GO:0034145","count":5}]},{"hash":"2083856653421778173","title":"Plant Hormone Signaling and Defense","description":"This cluster centers on plant hormone signaling pathways (ABA, cytokinin, GA) combined with biotic stimulus/defense responses, plus nodulation and related protein transport activities, suggesting a cohesive theme of hormone-driven signaling modulating defense and symbiotic processes in plants.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0009607","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0009877","count":2}]},{"hash":"1652075234692640830","title":"Oocyte meiosis and neural development","description":"The cluster is enriched for oocyte maturation and spindle assembly in female meiosis I, along with neural development terms like initiation of neural tube closure and third ventricle development. Additionally, ubiquitin-proteasome\u2013mediated catabolic processes and microtubule dynamics suggest cell-cycle and cytoskeletal events typical of meiosis and early neural development, justifying a label that ties meiosis/oocyte maturation to neural development.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":15},{"id":"GO:0001556","count":14},{"id":"GO:0021678","count":14},{"id":"GO:0006516","count":14},{"id":"GO:0051436","count":14}]},{"hash":"1633567767772919935","title":"Oocyte Maturation and Spindle Assembly","description":"Top GO terms cluster around oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization, with proteasomal ubiquitin-dependent protein catabolic processes reflecting cell-cycle control during meiosis; a few neural development terms appear as noise, but the dominant signal is meiotic spindle dynamics and oocyte maturation.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0001556","count":12},{"id":"GO:0006516","count":12},{"id":"GO:0008285","count":12},{"id":"GO:0007057","count":12},{"id":"GO:0051436","count":12}]},{"hash":"1575233043487343362","title":"Embryonic Neural and Organ Development","description":"The top GO terms cluster around developmental processes across multiple organ systems (heart, thyroid, forebrain, skeletal muscle, cranial skeleton) with a strong emphasis on neural development and connectivity (axon guidance, synapse assembly, visual perception). This suggests a shared theme of embryonic morphogenesis and neural-organ development, with a minor note that a single term (response to cocaine) reflects neural signaling rather than development. Confidence: High","confidence":"","size":20,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0008045","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0030878","count":3},{"id":"GO:0042220","count":3}]},{"hash":"989881276823002663","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":132,"triangles":422,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":4},{"id":"GO:0080156","count":4},{"id":"GO:1905639","count":4},{"id":"GO:1900865","count":4},{"id":"GO:0031425","count":4}]},{"hash":"395338136305265965","title":"Amino Acid Metabolism and Signaling","description":"The top GO terms are dominated by amino acid metabolism and catabolic/biosynthetic processes (alanine, glutamate, kynurenine, serotonin from tryptophan, isoquinoline alkaloid metabolism), with additional signaling/developmental terms such as Notch signaling, fibroblast migration, thermotaxis, and luteinization. This mix suggests a cluster centered on amino acid metabolism with accompanying signaling and developmental roles, leading to a plausible, if broad, label.","confidence":"Medium","size":20,"edges":183,"triangles":1026,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":9},{"id":"GO:0042853","count":6},{"id":"GO:0097053","count":6},{"id":"GO:0007219","count":6},{"id":"GO:0006538","count":6}]},{"hash":"432143889352125028","title":"Proteostasis and ER Stress Response","description":"The cluster centers on protein quality control and trafficking processes linked to stress responses: ER stress\u2013driven translation regulation, handling of misfolded proteins, ubiquitin-proteasome\u2013mediated nuclear quality control, post-translational targeting, and protein complex assembly. While one term (nonphotochemical quenching) is an odd outlier, the overall pattern points to maintaining proteome integrity under cellular stress and coordinating protein trafficking.","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0010196","count":3},{"id":"GO:0036494","count":2},{"id":"GO:0070843","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0071630","count":2}]},{"hash":"452294532497273737","title":"Microtubule dynamics and motor-driven transport","description":"The terms cluster around microtubule-based processes: dynamic instability and depolymerization at plus-ends, spindle assembly/disassembly, kinetochore interactions, cytokinesis, and plus-end-directed vesicle transport, plus plant-specific chloroplast movement and neuronal dendritic transport. The common thread is microtubule organization and motor-driven cargo movement across diverse cell types.","confidence":"High","size":20,"edges":96,"triangles":237,"max_degree":18,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0009904","count":13},{"id":"GO:0032886","count":13},{"id":"GO:0098971","count":13},{"id":"GO:0070462","count":13},{"id":"GO:0000742","count":13}]},{"hash":"726233232286512951","title":"Plant Hormone Signaling and Growth with RNA Methylation","description":"This cluster shows plant hormone signaling responses (salicylic acid, gibberellin, cytokinin) and growth-related processes (chlorophyll biosynthesis independent of light, secondary cell wall biogenesis), suggesting a developmental/regulatory theme linked to growth. The presence of RNA and protein modification terms (tRNA wobble uridine modification, rRNA modification, peptidyl-lysine dimethylation, N-terminal trimethylation) indicates an accompanying layer of translational and post-translational regulation, possibly coordinating hormone responses with gene expression and protein function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009751","count":4},{"id":"GO:0009739","count":4},{"id":"GO:0002098","count":3},{"id":"GO:1901348","count":3},{"id":"GO:0009736","count":3}]},{"hash":"1689055992112256171","title":"Ribosome Translation and Metal Homeostasis","description":"Top GO terms show a strong ribosome/translation signal (translation, ribosomal large subunit assembly), indicating a core ribosomal/translation theme. The presence of several metal ion transport and detoxification terms (copper, zinc, mercury, cadmium) and related redox processes suggests these proteins may connect protein synthesis with metal homeostasis or stress responses. Because both themes appear, the label reflects a combined ribosome-related function with metal-handling context rather than a single narrow role.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0000027","count":3},{"id":"GO:0097327","count":2},{"id":"GO:0070574","count":1},{"id":"GO:0050787","count":1}]},{"hash":"2055459575464641069","title":"Neuronal signaling and membrane transport","description":"The Top Terms show many transmembrane transport processes (nitrite/nitrate, phosphate, vitamin) and potassium ion transport, along with neurotransmitter loading into synaptic vesicles, indicating a core theme of membrane transport linked to neuronal function; neural crest differentiation is present but not dominant, so the label emphasizes transport and neural signaling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014033","count":2},{"id":"GO:0015707","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0015706","count":2}]},{"hash":"2044717087241178167","title":"Plant Hormone Signaling and Nodulation Defense","description":"The cluster is enriched for plant hormone signaling pathways (gibberellic acid, cytokinin, abscisic acid) and nodulation, along with defense and biotic-stimulus responses, pointing to hormone-regulated plant-microbe interactions and nodulation processes. Photosynthesis terms are minimal and likely background noise. This supports a cohesive theme of hormone signaling coordinating nodulation and defense.","confidence":"High","size":20,"edges":13,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0009740","count":8},{"id":"GO:0009607","count":7},{"id":"GO:0009736","count":7},{"id":"GO:0006952","count":7},{"id":"GO:0009877","count":7}]},{"hash":"2091504481485536208","title":"Membrane transport of lipids, vitamins, and metals","description":"The top GO terms cluster around translocation and import across membranes for lipids (ceramide, phospholipid, long-chain fatty acids), teichoic acid, cobalt ions, vitamins, and heme, plus related processes like cytochrome complex assembly and antibiotic response. This pattern suggests the proteins collectively participate in membrane-associated transport and membrane component assembly, rather than a single, cohesive enzymatic pathway.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046677","count":6},{"id":"GO:0015886","count":6},{"id":"GO:0015777","count":5},{"id":"GO:0015910","count":5},{"id":"GO:0017004","count":5}]},{"hash":"1904238919128235625","title":"Vertebrate developmental transcription regulators","description":"This cluster centers on broad vertebrate development processes (pituitary gland, brain segmentation, rhombomere, primitive streak, heart development) and transcriptional control (RNA polymerase II\u2013mediated transcription, regulation of transcription). The convergence of developmental GO terms with transcription Regulation terms suggests a group of transcription factors and regulators orchestrating embryonic development across tissues.","confidence":"High","size":20,"edges":31,"triangles":11,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0000122","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0035284","count":5}]},{"hash":"214037213045515818","title":"Unknown","description":"GO term diversity spans bacterial secondary metabolism (antibiotic biosynthetic and mycolic acid biosynthetic processes) and broad eukaryotic development and transcription regulation (pituitary gland development, neuron maturation, erythrocyte differentiation, regulation of transcription). The presence of an obsolete term and the lack of a coherent single function across the proteins suggest no unified functional theme for this cluster. ","confidence":"","size":20,"edges":4,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0017000","count":5},{"id":"GO:0042493","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0071768","count":4}]},{"hash":"2077210194035242606","title":"mRNA Splicing and Export Regulation","description":"This cluster is dominated by spliceosome-mediated mRNA splicing terms, plus mRNA export and regulatory ncRNA\u2013mediated gene silencing, with additional signals for mRNA stability in stress and translation reinitiation, all pointing to post-transcriptional RNA processing and control of gene expression.","confidence":"High","size":20,"edges":158,"triangles":699,"max_degree":19,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":14},{"id":"GO:0031047","count":14},{"id":"GO:0006378","count":12},{"id":"GO:0045292","count":12},{"id":"GO:1901407","count":12}]},{"hash":"86505070425930332","title":"DNA transcription and replication regulation","description":"The top GO terms are dominated by DNA-templated transcription, DNA replication, and regulation of transcription, suggesting a nuclear gene-expression and genome-maintenance cluster. The presence of RNA quality-control (nonfunctional rRNA decay) and proteostasis (cellular response to misfolded protein) terms supports a broader link to transcriptional regulation under stress, with some developmental terms appearing incidental. Overall, the cluster centers on nuclear transcription and replication processes.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0070651","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0001824","count":3}]},{"hash":"763360763402575551","title":"Muscle, Heart, and Neural Development","description":"The cluster's top GO terms point to transcriptional regulation by RNA polymerase II and developmental programs across muscle differentiation and morphogenesis (skeletal muscle, cardioblast migration), neural lineage commitment (subpallium neuron fate), and related processes like integrin-mediated adhesion and circadian gene regulation, suggesting a cohesive theme of gene-regulated development of muscle, heart, and neural tissues.","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":17},{"id":"GO:0048712","count":14},{"id":"GO:2000820","count":14},{"id":"GO:2001038","count":14},{"id":"GO:2001016","count":14}]},{"hash":"2296343670527464471","title":"Neural development and growth factor signaling","description":"This cluster is dominated by terms related to neurotrophin TRK receptor signaling, optic nerve morphogenesis, face development, FGFR apoptotic signaling, and PI3K/AKT signaling, all pointing to neural development and growth factor\u2013mediated pathways. The inclusion of Wnt signaling regulation and related developmental processes further supports a coherent theme around neural/craniofacial development and RTK/PI3K signaling networks.","confidence":"High","size":20,"edges":121,"triangles":334,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":19},{"id":"GO:0090090","count":19},{"id":"GO:0020021","count":19},{"id":"GO:0071469","count":19},{"id":"GO:0060324","count":19}]},{"hash":"1722959227988656659","title":"Mitochondrial energy metabolism and transport","description":"This cluster is enriched for GO terms tied to mitochondrial substrate transport (citrate, ornithine, phosphate), energy-generating processes (malate-aspartate shuttle, adaptive thermogenesis), fatty acid response, and iron import into mitochondria, all indicative of mitochondrial energy metabolism and metabolite trafficking.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1990314","count":18},{"id":"GO:0070542","count":18},{"id":"GO:0048250","count":18},{"id":"GO:0034198","count":18},{"id":"GO:0035349","count":18}]},{"hash":"2176619527564171638","title":"Nuclear Transcription Regulation and Chromatin Modification","description":"The top terms point to DNA-templated transcription and its regulation, along with chromatin-related modifications (histone methylation and acetylation) and related deubiquitination processes, all centered in the nucleus. This combination indicates a coherent functional theme of transcription control linked to chromatin state, despite a few peripheral or obsolete terms.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0006355","count":4},{"id":"GO:0051568","count":3},{"id":"GO:0034729","count":3},{"id":"GO:0016579","count":3}]},{"hash":"222195502061472907","title":"Neural development and growth-factor signaling","description":"This cluster centers on neuronal development and growth-factor signaling, with neurotrophin TRK receptor signaling, FGFR/PI3K-AKT pathways, optic nerve morphogenesis, and face development, pointing to neural patterning and craniofacial morphogenesis. Some peripheral terms exist but do not override the main theme.","confidence":"High","size":20,"edges":29,"triangles":8,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":20},{"id":"GO:0090090","count":20},{"id":"GO:0020021","count":20},{"id":"GO:0071469","count":20},{"id":"GO:0060324","count":20}]},{"hash":"421700937695002465","title":"Unknown","description":"The top terms point to several distinct processes: antibiotic biosynthesis, various catabolic pathways (purine/ureide/allantoin and oxalate), retinol metabolism, and intercellular transport, plus transcription regulation. There isn\u2019t a single cohesive biological function linking these terms, so a precise label isn\u2019t justifiable.","confidence":"","size":20,"edges":92,"triangles":171,"max_degree":19,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":13},{"id":"GO:1901766","count":8},{"id":"GO:0000256","count":8},{"id":"GO:0006145","count":8},{"id":"GO:0010136","count":8}]},{"hash":"1810960053602562318","title":"Flavonoid and lignin biosynthesis","description":"The dominant GO terms point to flavonoid production pathways (anthocyanin, kaempferol, cyanidin glucoside biosynthesis) and lignin metabolism, suggesting proteins in the phenylpropanoid pathway. A few unrelated or obsolete terms appear (e.g., paranode localization, xenobiotic/glucuronidation, estrogen catabolic), likely reflecting annotation noise, but they do not outweigh the flavonoid/lignin signal. Overall, this cluster is best described as involvement in flavonoid and lignin biosynthesis.","confidence":"High","size":20,"edges":10,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":16},{"id":"GO:0002175","count":12},{"id":"GO:0030259","count":12},{"id":"GO:0009808","count":12},{"id":"GO:0033330","count":12}]},{"hash":"1680156968694627749","title":"Flavonoid and lignin biosynthesis","description":"Most terms point to production of plant secondary metabolites: anthocyanin, kaempferol, and cyanidin biosynthesis, along with lignin metabolism. This indicates a cluster centered on the flavonoid/phenylpropanoid pathway and related lignin biosynthesis. A few outliers (axon localization, xenobiotic glucuronidation) exist but do not override the main theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":11},{"id":"GO:0002175","count":8},{"id":"GO:0030259","count":8},{"id":"GO:0009808","count":8},{"id":"GO:0033330","count":8}]},{"hash":"1082546838049455188","title":"Detoxification and Redox Metabolism","description":"The top GO terms are dominated by detoxification and redox-related processes (response to toxic substance; cellular oxidant detoxification; oxidation-reduction process), indicating a shared theme around managing toxins and maintaining redox balance. Supporting terms point to broader metabolic functions (lipid catabolism, biotin/menaquinone biosynthesis, nitrogen utilization). The proteins appear to span diverse metabolic activities but coalesce around detoxification and redox/metabolic roles, justifying this label.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":15},{"id":"GO:0098869","count":14},{"id":"GO:0055114","count":14},{"id":"GO:2000124","count":14},{"id":"GO:0019433","count":14}]},{"hash":"2272991013775462739","title":"Cell cycle progression and DNA replication","description":"This cluster centers on cell cycle control and DNA-related processes: multiple GO terms cover G1/S and G2/M transitions, spindle separation, chromosome condensation, and DNA replication, with transcription and proliferation-related terms (angiogenesis, mammary epithelial proliferation) reflecting proliferative contexts.","confidence":"High","size":20,"edges":4,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0001525","count":9},{"id":"GO:0006260","count":8},{"id":"GO:2000775","count":8},{"id":"GO:0033598","count":8}]},{"hash":"628477633711473009","title":"Unknown","description":"The top terms span nuclear transcription and cell-cycle processes, membrane transport, and lipid biosynthesis, with several obsolete terms and no evident unifying function among the 20 proteins. The cluster lacks a cohesive theme to name confidently.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0070940","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0001576","count":2},{"id":"GO:0036210","count":2}]},{"hash":"2214622881935141469","title":"RNA Polymerase III Transcription Machinery","description":"The top GO terms are dominated by RNA polymerase III\u2013related transcription activities\u2014DNA-templated transcription, Pol III transcription, preinitiation complex assembly, and 5S rRNA transcription\u2014indicating these proteins function together in Pol III transcription initiation and activity. A few unrelated terms (nail development, socket cell differentiation) are present but do not define the cluster.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0090437","count":1},{"id":"GO:0001041","count":1},{"id":"GO:0000999","count":1},{"id":"GO:0006359","count":1}]},{"hash":"1035540228412835426","title":"Plant Hormone Response and Chloroplast Regulation","description":"The set is enriched for plant hormone responses (ethylene, gibberellin), leaf senescence, and regulation of chlorophyll biosynthesis, plus osmotic stress and flavonoid pathways, indicating a module tying growth, stress adaptation, and chloroplast function. Chromatin remodeling and snRNA transcription suggest concomitant gene expression regulation, while a viral process term hints broader host-plant interaction. This combination supports labeling as a hormone-stress regulatory cluster with chloroplast involvement.","confidence":"Medium","size":20,"edges":40,"triangles":16,"max_degree":12,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009723","count":9},{"id":"GO:1900056","count":8},{"id":"GO:0010380","count":8},{"id":"GO:0009739","count":8},{"id":"GO:0006970","count":8}]},{"hash":"27832671048383858","title":"Gene Expression and Stress-Response Regulators","description":"This cluster is enriched for terms involving transcriptional regulation and ER-stress\u2013related translation initiation, plus defense and general stress responses, suggesting a set of proteins that regulate gene expression under stress. The presence of development and signaling terms (root cap, gibberellin signaling) alongside cell migration/division hints at broader regulatory roles rather than a single pathway.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0043278","count":2},{"id":"GO:0009938","count":2},{"id":"GO:0048829","count":2},{"id":"GO:0016477","count":2}]},{"hash":"1727073094608355439","title":"Developmental morphogenesis","description":"The Top Terms cluster around morphogenesis and developmental differentiation across tissues (mesoderm, cartilage, hair follicle, trophoblast). While a couple of terms touch on RNA modification, the dominant signal is embryonic development and tissue formation, justifying a Developmental morphogenesis label.","confidence":"Medium","size":20,"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},{"id":"GO:1903026","count":1},{"id":"GO:0060707","count":1}]},{"hash":"2127092416747782496","title":"Plant chromatin remodeling and developmental regulation","description":"Dominated by chromatin-related processes: chromatin remodeling, histone modification (acetylation/deubiquitination), and heterochromatin formation, with links to cytokinin signaling and plant-specific growth traits such as leaf senescence and chlorophyll biosynthesis. Together these terms point to a plant chromatin-regulatory program that coordinates development and aging, rather than a single metabolic pathway.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":8},{"id":"GO:0043044","count":7},{"id":"GO:0010520","count":7},{"id":"GO:1901348","count":7},{"id":"GO:0035066","count":7}]},{"hash":"502226618694391848","title":"RNA processing and neural development regulation","description":"The top GO terms point to RNA-level regulation (positive regulation of mRNA binding, alternative splicing via spliceosome, and miRNA-mediated gene silencing), suggesting a cluster dominated by RNA processing and gene expression control. Added neural-development terms (neural crest fate specification, forebrain-midbrain boundary formation, branching morphogenesis of a nerve) imply a context of neural development. Together, these indicate proteins coordinating RNA processing with neural development processes; the absence of edges reflects that the clustering is GO-term driven rather than known protein interactions. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902416","count":3},{"id":"GO:0000381","count":3},{"id":"GO:2000637","count":3},{"id":"GO:0072711","count":2},{"id":"GO:0048755","count":2}]},{"hash":"1411586978236184660","title":"Cell Growth and Energy Metabolism","description":"The cluster\u2019s top GO terms mainly describe cellular proliferation and growth (stem cell proliferation, cell growth, cell cycle) alongside core metabolic/energy-related processes (rRNA modification, cytochrome complex assembly, long-chain fatty acid import into peroxisome, glycerophospholipid catabolic process, vacuole fusion). This points to a cohesive theme of growth and metabolic capacity, even though a couple of terms (nodulation, teichoic acid transport) are more outlier-like. The lack of edges suggests a broad, not tightly interconnected set, supporting a general growth/metabolism label rather than a specific pathway. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072089","count":3},{"id":"GO:0000154","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0009877","count":2},{"id":"GO:0007049","count":2}]},{"hash":"1443050962258687339","title":"Cell Cycle and Energy Metabolism","description":"This cluster centers on DNA replication, cell division, and energy-related processes (oxidative phosphorylation and ATP biosynthesis), with additional signals like NF-kappaB regulation and viral replication suggesting broader regulatory roles. The dominant themes point to cell cycle progression coupled with cellular energy metabolism, though there are outliers that broaden the functional scope.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0043123","count":2},{"id":"GO:0071650","count":2},{"id":"GO:1903724","count":1}]},{"hash":"1651275250188273245","title":"DNA-Templated Transcription and Cell Cycle Regulation","description":"Most represented terms are DNA-templated transcription regulation, DNA-templated transcription, and cell cycle, pointing to nuclear functions tied to gene expression and cell division. Some terms such as cellulose catabolic process and phytochelatin biosynthetic process appear plant-specific or incidental, suggesting the core signal is transcription control and cell cycle rather than a single cohesive metabolic pathway.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030245","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0043085","count":3}]},{"hash":"1801863166088538517","title":"Plant cell wall biogenesis and glycosylation","description":"The GO terms are dominated by plant-specific cell wall processes (cell wall organization, plant-type secondary cell wall biogenesis, glucuronoxylan and homogalacturonan biosynthesis) and protein glycosylation (O-linked via mannose and via N-acetyl-galactosamine), with related carbohydrate metabolism, indicating a cluster of plant cell wall biosynthesis and glycosylation functions. Some terms (glycogen biosynthesis, ATP generation from poly-ADP-ribose, skeletal muscle regeneration) are less connected to this theme, but the primary signal supports plant cell wall biosynthesis and glycosylation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":4},{"id":"GO:1990966","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0009834","count":2},{"id":"GO:0035269","count":2}]},{"hash":"2189386971124388974","title":"Galactose-Linked Carbohydrate and Lipid Metabolism","description":"This cluster\u2019s GO terms cluster around galactose- and sugar-related metabolism (carbohydrate phosphorylation, glycolytic processing from galactose, D-galacturonate metabolism, GDP-L-fucose salvage) and the mevalonate pathway leading to isoprenoid and cholesterol biosynthesis (IPPs, FPP, cholesterol). A regulatory term for transcriptional activation by galactose reinforces a galactose-responsive metabolic theme. Overall, it points to a coherent module linking sugar metabolism with lipid/sterol biosynthesis, rather than disparate processes.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":4},{"id":"GO:0009088","count":3},{"id":"GO:0000435","count":3},{"id":"GO:0042352","count":3},{"id":"GO:0046396","count":3}]},{"hash":"2272626289345195932","title":"Plant hormone signaling and nitrate/peptide transport","description":"The included terms show strong enrichment for auxin-activated signaling, gibberellic acid homeostasis, nitrate signaling/transport, and dipeptide/oligopeptide transport, indicating a plant-specific network where hormone signaling governs nutrient uptake and transport. The presence of nitrate response and herbicide response supports a plant stress/hormonal context, though a few terms like neurotrophin signaling may be incidental. Overall, the dominant pattern aligns with plant hormone regulation linked to nutrient transport.","confidence":"High","size":20,"edges":17,"triangles":6,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009734","count":10},{"id":"GO:0035672","count":10},{"id":"GO:0042128","count":10},{"id":"GO:0080055","count":10},{"id":"GO:0010167","count":10}]},{"hash":"855393981996040580","title":"Plant lipid and secondary metabolite metabolism","description":"This cluster shows a mix of metabolic processes centered on secondary metabolite biosynthesis (alkaloids, flavonoids, antibiotics) and lipid catabolism (monoacylglycerol, triglyceride, phosphatidylserine). The presence of plant-specific terms (auxin homeostasis, adaxial/abaxial polarity) supports a plant metabolism theme, though some terms like endocannabinoid signaling suggest annotation noise. Overall, the dominant signal is metabolic processes involving lipids and secondary metabolites, making this label representative. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010252","count":6},{"id":"GO:0009820","count":5},{"id":"GO:0017000","count":4},{"id":"GO:0052651","count":3},{"id":"GO:0006660","count":3}]},{"hash":"1365456089584426032","title":"Unknown","description":"The top terms span lipid catabolism (triglyceride and monoacylglycerol breakdown) and signaling regulation, but also include plant-specific cell wall biosynthesis and developmental terms (olfactory bulb, fin morphogenesis), indicating no coherent, unified function across the cluster. Therefore a neutral, Unknown label with no confidence. ","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0019433","count":5},{"id":"GO:0052651","count":4},{"id":"GO:0006660","count":4},{"id":"GO:2000124","count":4},{"id":"GO:0035118","count":3}]},{"hash":"860087813729825858","title":"Lipid Catabolism and Related Metabolic Processes","description":"The top GO terms cluster around lipid breakdown (monoacylglycerol, triglyceride, diacylglycerol, phosphatidylserine catabolism) and lipid-derived signaling (endocannabinoid pathway regulation), with a few outliers like chlorophyll and cellulose catabolism. The dominant pattern is lipid-centric catabolic metabolism, justifying this label.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0052651","count":8},{"id":"GO:0006660","count":8},{"id":"GO:2000124","count":8},{"id":"GO:0019433","count":8},{"id":"GO:0030245","count":5}]},{"hash":"746465069741774275","title":"Plant secondary cell wall biogenesis and organization","description":"The cluster is strongly enriched for plant-type secondary cell wall biogenesis, cell wall organization, and arabinan biosynthesis, pointing to roles in building/remodeling the plant cell wall, with accompanying signals of growth and transcriptional regulation that may reflect broader plant development processes.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901348","count":5},{"id":"GO:0009834","count":4},{"id":"GO:0071555","count":4},{"id":"GO:0008360","count":3},{"id":"GO:0007049","count":3}]},{"hash":"1553322044529229434","title":"Unknown","description":"The top terms mix plant-specific processes (secondary cell wall biogenesis, cytokinin signaling) with animal development and transcription regulation (pituitary gland, heart development, visual perception, DNA-templated transcription), showing no clear shared function across the cluster.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901348","count":5},{"id":"GO:0060021","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0009736","count":4}]},{"hash":"333639483821544829","title":"Membrane Ion Transport and Homeostasis","description":"The cluster is dominated by GO terms for import/export of Na+, K+, Ca2+, Mn2+, and protons, plus intracellular ion homeostasis and antiporter-related activity, pointing to a set of membrane transporters maintaining ion gradients. The inclusion of a cardiac conduction-related term aligns with ion-driven electrical signaling in heart tissue, reinforcing the ion transport/homeostasis theme despite some peripheral signaling terms. ","confidence":"High","size":20,"edges":31,"triangles":17,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":6},{"id":"GO:0097623","count":6},{"id":"GO:0030007","count":4},{"id":"GO:0006828","count":4},{"id":"GO:0098703","count":4}]},{"hash":"1150535635647776935","title":"Meiosis I spindle assembly and ubiquitin-proteasome regulation","description":"The top terms most strongly indicate processes tied to female meiosis and oocyte maturation, including spindle assembly in meiosis I and SCF-dependent ubiquitin-proteasomal protein degradation, i.e., ubiquitin-mediated proteolysis regulating the cell cycle. While a couple of terms hint at broader developmental roles (neural tube development, brain ventricle formation), the dominant signal is meiosis-related control and proteostasis.","confidence":"High","size":20,"edges":67,"triangles":57,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":20},{"id":"GO:0021678","count":20},{"id":"GO:0006516","count":20},{"id":"GO:0051436","count":20},{"id":"GO:0046785","count":20}]},{"hash":"911122000045602542","title":"Oocyte maturation and meiosis spindle assembly","description":"The top GO terms point to oocyte maturation, spindle assembly in female meiosis I, and SCF-dependent ubiquitin-proteasomal degradation, with microtubule polymerization also highlighted. Together these suggest a cluster centered on meiotic progression in oocytes, spindle dynamics, and regulated proteolysis, despite a couple of neural-development terms that may reflect shared cell-cycle components.","confidence":"Medium","size":20,"edges":8,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":14},{"id":"GO:0001556","count":12},{"id":"GO:0006516","count":12},{"id":"GO:0008285","count":12},{"id":"GO:0007057","count":12}]},{"hash":"1964694023114894387","title":"Negative regulation of innate immune signaling and deubiquitination","description":"This cluster is dominated by GO terms that suppress innate immune pathways, including negative regulation of TLR3/5, NOD1/2, and CD40 signaling, as well as terms tied to deubiquitination. The repeated emphasis on deubiquitinases (K11-linked deubiquitination; ubiquitin-dependent catabolic processes) suggests these proteins act to dampen signaling through ubiquitin-modulated regulation, aligning with a cohesive theme of immune signaling repression. A few terms about germinal center formation and hepatocyte proliferation are present but peripheral to the main immune-regulatory signal. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034140","count":2},{"id":"GO:0034148","count":2},{"id":"GO:0070429","count":2},{"id":"GO:0032691","count":2},{"id":"GO:2000347","count":2}]},{"hash":"704277665757087051","title":"Mitochondrial Transport and Metabolism","description":"These proteins appear to be centered on mitochondrial transport and energy metabolism, with GO terms describing transmembrane transport of citrate, ornithine, CoA, and phosphate, plus the malate-aspartate shuttle. Additional terms for responses to insulin-like growth factor, fatty acids, and amino acid starvation, along with adaptive thermogenesis, support a cohesive mitochondria-focused energy-production theme.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990314","count":12},{"id":"GO:0070542","count":12},{"id":"GO:0048250","count":12},{"id":"GO:0034198","count":12},{"id":"GO:0035349","count":12}]},{"hash":"1267164042188128448","title":"Pectin metabolism and cell wall remodeling","description":"This cluster centers on pectin-related processes (catabolic and mucilage/polysaccharide biosynthesis) and cell wall modification/adhesion, suggesting a plant cell wall remodeling theme. The presence of transcription-related terms likely reflects annotation overlap or multifunctional proteins, but the dominant signal is pectin metabolism and cell wall dynamics.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045490","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0048358","count":2},{"id":"GO:0042545","count":2}]},{"hash":"1735444572123885498","title":"Sodium-Potassium Transport and Cardiac Conduction","description":"The dominant GO terms point to ions moving across membranes (sodium import, potassium export, potassium transport, intracellular potassium homeostasis) and processes related to cardiac electrical activity (membrane repolarization, regulation of heart contraction by cardiac conduction). A few other terms (mechanosensory touch, transcription) appear as noise relative to the main theme. Thus, the cluster is best described as ion transport related to cardiac conduction.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0030007","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0098914","count":2}]},{"hash":"1010603023108502001","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031573","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0000480","count":2}]},{"hash":"1367975368996185177","title":"Cell signaling, apoptosis, and adhesion regulation","description":"This cluster contains GO terms tied to modulation of signaling pathways (Rho signaling, adenylate cyclase activity), regulation of cell death and apoptosis (extrinsic apoptotic signaling, negative regulation of cell death), and processes affecting cell adhesion and extracellular interactions (cell-matrix adhesion, osteoclast differentiation). The common thread is broad regulatory control over cellular signaling that influences survival, polarity, secretion, and adhesion, rather than a single, cohesive pathway.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"lysosome organization","top_go_terms":[{"id":"GO:0060548","count":3},{"id":"GO:2001136","count":3},{"id":"GO:0045762","count":3},{"id":"GO:2000114","count":3},{"id":"GO:0046929","count":3}]},{"hash":"1916665429688694644","title":"Intracellular Signaling and Vesicle Trafficking","description":"The top GO terms point to internal signaling pathways (intracellular signal transduction, regulation of GTPase activity) and membrane trafficking (COPII-coated vesicle budding), along with lipid transport. This suggests a cohesive role in coordinating signaling with vesicle formation and cargo movement, rather than a single enzyme activity, with a possible immune/defense context represented by the fungus defense term.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":3},{"id":"GO:0007205","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0035556","count":2}]},{"hash":"492515893987032316","title":"Unknown","description":"This cluster\u2019s top GO terms cover very different biological domains (fungal defense, plant fertilization, animal signaling, capsule biosynthesis) with no single shared function or pathway. The network has no edges, suggesting no cohesive functional linkage, so there isn\u2019t a defensible specific label beyond Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":3},{"id":"GO:0050832","count":3},{"id":"GO:0006869","count":3},{"id":"GO:0009567","count":2},{"id":"GO:2000008","count":2}]},{"hash":"2099386136828032381","title":"Ubiquitin-Proteasome Degradation Pathways","description":"The top terms cluster around ubiquitin-dependent protein catabolism, including SCF-dependent ubiquitin\u2013proteasome degradation and K48-linked ubiquitination, indicating a primary theme of ubiquitin-mediated protein turnover. Some related terms touch on regulatory signaling (TNF, JNK) and histone modification, but the dominant signal is proteolysis via the ubiquitin\u2013proteasome system, justifying a label centered on degradation pathways.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":13},{"id":"GO:0031146","count":12},{"id":"GO:0070936","count":10},{"id":"GO:0070535","count":10},{"id":"GO:1901253","count":10}]},{"hash":"419818076016637196","title":"Pectin metabolism and cell wall remodeling","description":"This cluster centers on pectin turnover and mucilage pectin biosynthesis, plus cell wall modification and pollen tube growth, with a sprinkling of defense and immune-related terms. Together, they suggest a theme of dynamic pectin remodeling in plant cell walls that supports growth processes like pollen tube elongation and may also participate in plant defense signaling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":3},{"id":"GO:0048358","count":3},{"id":"GO:0042545","count":3},{"id":"GO:0009860","count":2},{"id":"GO:0043086","count":2}]},{"hash":"556840893810624439","title":"Telomere maintenance and telomeric localization","description":"This cluster centers on GO terms tied to telomere maintenance, telomere capping, and localization to telomeric regions, with several entries mentioning regulation of telomere length via telomerase. Related processes like PARP-mediated protein modification and mitotic chromosome aspects (spindle assembly) appear, but the dominant theme is telomere biology, suggesting a coherent functional group focused on chromosome end maintenance and telomere regulation.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0070212","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0032212","count":2}]},{"hash":"1791999093489432069","title":"Mitotic spindle assembly and regulation","description":"This cluster is dominated by GO terms related to mitotic spindle organization, spindle assembly, and activation of protein kinase activity, suggesting a focus on cell division machinery. A few terms linked to plant development and morphogenesis are present but appear ancillary to the core spindle-related signals. Overall, the main functional signal is mitotic spindle dynamics, with some annotation breadth contributing secondary signals.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060236","count":2},{"id":"GO:0032147","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0022622","count":1},{"id":"GO:0010088","count":1}]},{"hash":"669174324620850579","title":"Intracellular cholesterol/sterol transport","description":"This cluster shows a clear focus on cholesterol and sterol trafficking within cells, including cholesterol transport, regulation of intracellular cholesterol transport, sterol import, and related lipid distribution processes across ER-Golgi and endosomal compartments, with supporting terms like bile acid metabolism and sterol regulation.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035621","count":2},{"id":"GO:0007032","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0032889","count":2},{"id":"GO:0097036","count":1}]},{"hash":"553149386010013795","title":"RNA Pseudouridylation and Splicing","description":"This cluster is characterized by multiple GO terms for pseudouridine synthesis across tRNA, mRNA, and snRNA, along with RNA splicing, indicating a cohesive function in RNA modification and processing. A few terms related to development or other processes appear incidental noise rather than core cluster biology.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031119","count":2},{"id":"GO:1990481","count":2},{"id":"GO:0031120","count":2},{"id":"GO:0008380","count":2},{"id":"GO:0008585","count":2}]},{"hash":"2254305063735773042","title":"Plant stress response and detoxification","description":"This cluster\u2019s top GO terms are dominated by plant-specific processes, especially phytochelatin biosynthesis (metal detoxification) and regulation of ethylene signaling, plus detection of stimulus and circumnutation (a plant growth movement). While there are more general terms like proteolysis and transcriptional regulation, the emphasis on plant stress and detox pathways suggests a coherent theme around plant environmental response and detoxification mechanisms.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0043085","count":6},{"id":"GO:1904715","count":6},{"id":"GO:0006508","count":6},{"id":"GO:0046938","count":6},{"id":"GO:0006355","count":4}]},{"hash":"359834539258984909","title":"Migration and Signaling Pathways","description":"The cluster includes terms for cell migration (tangential migration, fibroblast migration) and cellular responses to mechanical stimulus, linked with signaling cascades such as Ras and JNK. Immune-related terms (TH1 response, IL-23 regulation) suggest immune signaling involvement, which can intersect with migration and tissue remodeling. A mitochondrion-organization regulation term also aligns with energy-demanding signaling/migration processes. Together, these point to a module of migration coordinated with signal transduction in neural/immune contexts. Confidence: Medium","confidence":"","size":19,"edges":49,"triangles":40,"max_degree":8,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0022028","count":11},{"id":"GO:0032707","count":10},{"id":"GO:0071260","count":10},{"id":"GO:0046330","count":10},{"id":"GO:0042088","count":10}]},{"hash":"1527949940553435533","title":"TLR/MyD88-driven innate immune signaling and cytokine production","description":"The cluster is dominated by GO terms tied to innate immune sensing and signaling (TLR/MyD88 pathway, LPS detection), antiviral defense, and cytokine production, with support from JNK cascade regulation and Th1-type responses. Peripheral terms like brain development and platelet activation may reflect broader signaling roles but do not override the central immune theme.","confidence":"Medium","size":19,"edges":43,"triangles":4,"max_degree":9,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0046330","count":6},{"id":"GO:0032707","count":6},{"id":"GO:0042088","count":6},{"id":"GO:0010572","count":6},{"id":"GO:0071260","count":6}]},{"hash":"1366310694089728546","title":"Dendritic spine morphogenesis and Rac/Ras signaling","description":"The cluster is dominated by GO terms for dendritic spine development and morphogenesis, actin cytoskeleton remodeling (lamellipodium/ruffle assembly) via Rac and Ras signaling, and hippocampus development, pointing to a neuronal spine formation and signaling theme, with membrane trafficking contributing to surface protein delivery.","confidence":"High","size":19,"edges":121,"triangles":395,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060999","count":13},{"id":"GO:0016601","count":13},{"id":"GO:0010592","count":13},{"id":"GO:0097178","count":13},{"id":"GO:0043001","count":13}]},{"hash":"755114699241761012","title":"Developmental signaling and hormone response","description":"Top GO terms point to developmental signaling control (mesoderm formation; Hedgehog pathway regulation) and cellular responses to hormonal stimuli (peptide hormone, parathyroid hormone, follicle-stimulating hormone). While other terms reflect general processes like DNA replication, fatty acid oxidation, and heat response, the dominant theme is signals governing development and endocrine signaling.","confidence":"Medium","size":19,"edges":112,"triangles":341,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0061059","count":5},{"id":"GO:0032781","count":3},{"id":"GO:1901621","count":3},{"id":"GO:0071375","count":3},{"id":"GO:0071374","count":3}]},{"hash":"404750428503799507","title":"Brain development and synaptic signaling","description":"The most represented terms are brain development and long-term synaptic potentiation, pointing to neural differentiation and plasticity, with supporting signals of broader cellular signaling and growth regulation; however, the presence of non-neural terms (xenobiotic response, plant ABA signaling) reduces cohesion, giving a moderate level of confidence in a neural-focused label.","confidence":"Medium","size":19,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0014912","count":3},{"id":"GO:0042493","count":3},{"id":"GO:1900087","count":3}]},{"hash":"577855155266173094","title":"Trafficking and Gene Expression","description":"The GO terms cluster around membrane trafficking (Golgi to plasma membrane transport; endocytic recycling) and core gene expression steps (cytoplasmic translation; DNA-templated transcription and its regulation). A few obsolete or plant-specific terms (bract development, response to chitin) may reflect annotation noise or broader roles, but the dominant signals point to proteins involved in intracellular transport alongside gene expression processes.","confidence":"Medium","size":19,"edges":5,"triangles":0,"max_degree":3,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006893","count":3},{"id":"GO:0032456","count":3},{"id":"GO:0039694","count":3},{"id":"GO:0002181","count":3},{"id":"GO:0006351","count":3}]},{"hash":"392147666256458541","title":"Embryonic Neurodevelopment and Brain Patterning","description":"The top GO terms cluster around early development with a clear focus on neural patterning and brain regionalization, including forebrain-midbrain and midbrain-hindbrain boundary formation and subpallial neuron fate, plus gastrulation-related processes like primitive streak formation. While some terms touch on development of other organs (pituitary, uterus), the dominant signal is embryonic neurodevelopment and brain patterning.","confidence":"High","size":19,"edges":8,"triangles":0,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":9},{"id":"GO:0090009","count":7},{"id":"GO:0007275","count":6},{"id":"GO:0021882","count":6},{"id":"GO:0006355","count":6}]},{"hash":"1274900020482837417","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":9,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0008584","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0008283","count":2}]},{"hash":"77729365508028663","title":"Fertilization and Reproductive Regulation","description":"The top GO terms cluster around fertilization events (double fertilization forming a zygote and endosperm, sperm capacitation) and related regulatory processes (regulation of protein localization to the cell surface, negative regulation of endopeptidase activity), suggesting a cohesive theme of reproductive activation and control across species, with a few outliers like defense response to fungus that do not change the main signal.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":4},{"id":"GO:0009567","count":3},{"id":"GO:2000008","count":3},{"id":"GO:0080155","count":3},{"id":"GO:0048240","count":3}]},{"hash":"187811640452698322","title":"Spliceosome-Mediated mRNA Processing","description":"The major signals are mRNA splicing and processing via the spliceosome (cis and alternative splicing), plus regulation of splicing and mRNA export. There are also terms for mRNA stability regulation and RNA-mediated gene silencing, and even translation reinitiation. This points to a cluster of proteins involved in post-transcriptional mRNA maturation and control.","confidence":"High","size":19,"edges":152,"triangles":784,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":14},{"id":"GO:0045292","count":13},{"id":"GO:0010610","count":13},{"id":"GO:0048026","count":13},{"id":"GO:0031047","count":13}]},{"hash":"1316837586439375436","title":"Plant development and cuticle biosynthesis","description":"The top GO terms cluster around plant developmental processes (bract and floral meristem development, seed development, hormone signaling via auxin and ethylene) and epidermal barrier formation (cutin and wax biosynthesis), suggesting a cohesive theme of developmental regulation linked to cuticle biosynthesis. A secondary defense-related term (response to chitin) is present but not central to the main pattern.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000184","count":2},{"id":"GO:0010200","count":2},{"id":"GO:0010432","count":2},{"id":"GO:0048316","count":2}]},{"hash":"1399449677657775315","title":"ER stress response and protein folding","description":"These proteins cluster around ER-associated processes, with direct terms for ER stress response and protein folding in the ER, suggesting a shared role in managing protein quality under stress. The presence of transcriptional regulation terms (RNA polymerase II\u2013related) and nuclear export regulation hints at coordinated stress-responsive transcription control, while oxidative detoxification aligns with cellular stress responses.","confidence":"Medium","size":19,"edges":77,"triangles":130,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:1903026","count":1},{"id":"GO:0034976","count":1},{"id":"GO:0046826","count":1},{"id":"GO:1903206","count":1}]},{"hash":"415891146641352138","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":101,"triangles":192,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":6},{"id":"GO:0090502","count":6},{"id":"GO:0090617","count":6},{"id":"GO:0009451","count":6},{"id":"GO:0080156","count":6}]},{"hash":"526617440478788830","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0009451","count":3}]},{"hash":"1618354597681928498","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0090502","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0080156","count":3}]},{"hash":"1689218366476022894","title":"Transmembrane ion and sugar transporters","description":"Many top GO terms indicate transmembrane transport, including potassium and sodium ion transport, arabinose and galactose transport, nitrate/nitrite transport, and sialic acid transport. A term about neurotransmitter loading into synaptic vesicles further supports vesicle-associated transport. Overall, the cluster centers on proteins that move substrates across membranes, especially ions and sugars, justifying this label.","confidence":"High","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":5},{"id":"GO:0035725","count":5},{"id":"GO:0071555","count":4},{"id":"GO:0015751","count":3},{"id":"GO:0042891","count":3}]},{"hash":"2112930057387357936","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006189","count":5},{"id":"GO:0006695","count":5},{"id":"GO:0045337","count":5},{"id":"GO:0051290","count":5},{"id":"GO:1901663","count":5}]},{"hash":"1165551779638668411","title":"Ribosome Biogenesis and Translation Machinery","description":"This cluster is dominated by translation- and ribosome-related GO terms, including translation, ribosome biogenesis, ribosomal subunit biogenesis, translation preinitiation complex formation, and translational termination, indicating proteins that form or regulate the protein synthesis machinery. A few secondary terms (e.g., response to antibiotic, mRNA decay) are incidental. Overall, the core theme is ribosome production and cytoplasmic translation.","confidence":"High","size":19,"edges":111,"triangles":347,"max_degree":18,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0042254","count":6},{"id":"GO:0046677","count":3},{"id":"GO:0006407","count":3},{"id":"GO:0042274","count":3}]},{"hash":"1880442178689833505","title":"Osmotic Stress\u2013Linked Solute Transporters","description":"The GO terms show a clear transport/solute movement theme across membranes, including sugars (glucose/fructose import), various ions (potassium, nitrate), and organic cation transport, alongside a cellular response to osmotic stress and vesicle-based neurotransmitter loading. This suggests a cohesive cluster of membrane transport proteins involved in solute uptake and osmotic regulation, with some vesicular transport connections.","confidence":"High","size":19,"edges":22,"triangles":35,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006970","count":7},{"id":"GO:0070715","count":7},{"id":"GO:0044381","count":7},{"id":"GO:0071332","count":7},{"id":"GO:0015707","count":7}]},{"hash":"1828725458383745294","title":"Endosomal-Golgi Trafficking","description":"The cluster is dominated by GO terms for endosome-to-Golgi transport, Golgi-to-endosome transport, multivesicular body sorting, and endocytosis, all pointing to vesicle trafficking within the endomembrane system. While a few terms touch on other processes, the strong, repeated trafficking/sorting signals indicate a cohesive endosomal/ Golgi transport function.","confidence":"High","size":19,"edges":17,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0034498","count":3},{"id":"GO:0006895","count":3},{"id":"GO:0071985","count":3},{"id":"GO:0006897","count":3},{"id":"GO:0045740","count":2}]},{"hash":"479828041904811052","title":"Neuronal signaling and synaptic plasticity","description":"The top GO terms cluster around neuronal signaling and calcium-dependent processes: phosphatidylinositol signaling, neurotransmitter secretion, cellular response to calcium, and long-term synaptic potentiation, pointing to synaptic transmission and plasticity. A few terms are unrelated (plant-specific or meiosis-related), likely noise, but the core theme remains neuronal signaling. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":2},{"id":"GO:0007269","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0071277","count":2},{"id":"GO:0060291","count":2}]},{"hash":"1237173910487560109","title":"Cardiovascular and neural development","description":"The cluster shows strong enrichment for heart development, angiogenesis, Schwann cell development, and axonogenesis, indicating coordinated development of heart, vasculature, and the nervous system. Supporting terms like centrosome cycle and G2/M transition point to cell-cycle control in organogenesis, while positive regulation of apoptotic processes suggests tissue remodeling; one plant-specific term (abscisic acid signaling) is likely noise. Overall, the dominant theme is developmental programs across cardiovascular and neural tissues.","confidence":"Medium","size":19,"edges":32,"triangles":13,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046827","count":17},{"id":"GO:0001525","count":15},{"id":"GO:0009738","count":15},{"id":"GO:0000086","count":15},{"id":"GO:0043065","count":15}]},{"hash":"501383865461955372","title":"Fungal mating, cytoskeleton, and cell cycle","description":"This cluster centers on actin-based movement and GTPase regulation, with terms for nuclear migration during conjugation, ascospore formation, and cell-cycle transitions (G1/S, mitosis), plus regulation of CDK activity and vesicle trafficking. These collectively point to fungal developmental processes involving cytoskeletal rearrangements, mating-related nuclear events, and cell-cycle control. A noise term related to GPCR signaling for defense appears minimal. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0000743","count":2},{"id":"GO:0030437","count":2},{"id":"GO:0030048","count":2},{"id":"GO:0000082","count":2}]},{"hash":"976056793201967538","title":"RNA splicing and translation initiation","description":"The proteins are strongly linked to mRNA processing via the spliceosome (cis/alternative splicing, export, and splicing regulation) and to translation initiation/reinitiation steps (formation of the preinitiation complex and translation reinitiation), suggesting a cohesive role in post-transcriptional RNA processing coupled to translation initiation. ","confidence":"High","size":19,"edges":8,"triangles":1,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":4},{"id":"GO:1900363","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0006378","count":3}]},{"hash":"914799537738031327","title":"Protein acetylation and chromatin modification","description":"Top GO terms show widespread acetylation activities across substrates: spermidine, putrescine, spermine, histone H4, N-terminal methionine, lysine residues, and N-acetylglucosamine-related metabolism, plus mycothiol biosynthesis. The common thread is acetyltransferase-mediated modifications that affect chromatin (histone H4) and various metabolic/structural substrates, with a related cell-cycle/chromosome cohesion term suggesting chromatin regulation during mitosis.","confidence":"High","size":19,"edges":24,"triangles":10,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0032918","count":15},{"id":"GO:0043967","count":15},{"id":"GO:0006526","count":15},{"id":"GO:0032920","count":15},{"id":"GO:0006044","count":15}]},{"hash":"1866463238953250810","title":"Broad developmental regulation","description":"The cluster's top GO terms repeatedly describe regulation of development and differentiation across diverse systems (muscle and cardiac differentiation, endochondral ossification, plant floral/meristem development, germinal center formation, and transcriptional regulation contexts). The common theme is modulation of developmental programs rather than a single pathway, making 'Broad developmental regulation' a concise umbrella label.","confidence":"Medium","size":19,"edges":132,"triangles":526,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001016","count":19},{"id":"GO:0055012","count":17},{"id":"GO:0001958","count":17},{"id":"GO:2000111","count":17},{"id":"GO:0010582","count":17}]},{"hash":"1439711711763439195","title":"Organelle Protein Import (mitochondria and chloroplasts)","description":"The top GO terms emphasize protein import into chloroplast stroma and mitochondrial matrix, plus mitochondrial inner membrane insertion, which together strongly indicate a cluster of proteins involved in importing and integrating proteins into mitochondria and chloroplasts. Other terms about fatty acid metabolism and stress responses are present but secondary; the import-related terms best capture the core function of the cluster.","confidence":"High","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045037","count":2},{"id":"GO:0045039","count":2},{"id":"GO:0000002","count":2},{"id":"GO:0032094","count":2},{"id":"GO:0030150","count":2}]},{"hash":"621167819538685863","title":"Muscle and neural differentiation","description":"The cluster\u2019s top terms center on development and differentiation across muscle and neural lineages (skeletal muscle differentiation, muscle morphogenesis, cardioblast migration, subpallium neuron fate, amacrine cell differentiation), along with supporting processes like integrin-mediated adhesion and circadian regulation of gene expression. This suggests a cohesive module coordinating muscle and neural development, with broader transcriptional regulation. ","confidence":"Medium","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":17},{"id":"GO:2001016","count":10},{"id":"GO:0060415","count":9},{"id":"GO:0060163","count":9},{"id":"GO:0033627","count":9}]},{"hash":"1677674853805688683","title":"Fatty acid oxidation and retinoic acid metabolism in development","description":"Top terms indicate fatty acid omega-oxidation and retinoic acid biosynthesis/catabolism as core metabolic themes, with several development-related processes (uterus, female gonad, digestive tract development) suggesting a link between lipid metabolism and developmental signaling. While some terms are broad or less coherent (e.g., camphor catabolic), the overall pattern supports a cluster centered on lipid metabolism intersecting with retinoid pathways during development.","confidence":"Medium","size":19,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019383","count":4},{"id":"GO:0010430","count":4},{"id":"GO:0060065","count":4},{"id":"GO:0008585","count":4},{"id":"GO:0048565","count":4}]},{"hash":"2174814482038489309","title":"Plant chlorophyll regulation and stress response","description":"These proteins cluster around chlorophyll biosynthesis regulation, leaf senescence control, and growth/stress signaling (gibberellin response, osmotic stress), plus flavonoid biosynthesis and chromatin remodeling. This suggests a coherent theme of coordinating pigment metabolism and environmental responses in plants, likely via transcriptional and chromatin-level regulation. The viral process and telomeric D-loop disassembly terms hint at broader genome regulation roles that may be engaged during stress or defense. ","confidence":"Medium","size":19,"edges":129,"triangles":421,"max_degree":17,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:1900056","count":6},{"id":"GO:0010380","count":6},{"id":"GO:0009739","count":6},{"id":"GO:0006970","count":6},{"id":"GO:0016032","count":6}]},{"hash":"1640762087396363924","title":"Spliceosome-Mediated RNA Processing","description":"Top terms cluster around mRNA processing and splicing via the spliceosome (cis and alternative) and related RNA maturation steps. Although some terms are unrelated or obsolete, the spliceosome-related signals dominate, justifying a label focused on RNA processing.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":4},{"id":"GO:0006378","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0000380","count":3},{"id":"GO:0009089","count":3}]},{"hash":"441139610266701900","title":"Amino acid and lipid metabolism","description":"The cluster prominently features amino acid catabolic and biosynthetic terms (L-alanine, L-serine, kynurenine, glyoxylate, lysine/phenylalanine biosynthesis) and lipid pathways (fatty acid transport, heme, sphinganine biosynthesis). Notch signaling is also present but appears peripheral to the main metabolic theme. Overall, the grouping centers on metabolism of amino acids and lipids.","confidence":"Medium","size":19,"edges":167,"triangles":903,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042853","count":8},{"id":"GO:0097053","count":8},{"id":"GO:0007219","count":8},{"id":"GO:0009436","count":7},{"id":"GO:0006564","count":6}]},{"hash":"2234831568643896080","title":"Actin Cytoskeleton Assembly and Contractile Ring Formation","description":"The cluster\u2019s top GO terms are dominated by actin-related processes: actin filament network formation, actomyosin contractile ring assembly, and formin-mediated actin cable assembly, pointing to coordinated actin cytoskeleton organization and contractile structure formation, especially linked to cell division. Other terms like leaf development or mitochondrial inner membrane insertion are less central, but the dominant theme is actin organization and contractile machinery.","confidence":"High","size":19,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048366","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0032979","count":1},{"id":"GO:0051639","count":1},{"id":"GO:0071519","count":1}]},{"hash":"988125200150781673","title":"Plant cell wall polysaccharide biosynthesis","description":"The cluster is enriched for plant-specific cell wall biosynthesis terms, including secondary cell wall biogenesis, glucuronoxylan and homogalacturonan/mucilage biosynthesis, and related glycosylation and carbohydrate metabolism processes, pointing to a cohesive function in constructing the plant cell wall and its components.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":6},{"id":"GO:0009834","count":4},{"id":"GO:0035269","count":4},{"id":"GO:0010417","count":4},{"id":"GO:0010289","count":4}]},{"hash":"1128558415673357673","title":"Organelle RNA Processing and Membrane Targeting","description":"The top GO terms cluster around RNA metabolism (splicing, modification, editing) in organelles (mitochondria and chloroplasts), suggesting roles in organellar gene expression. The presence of misfolded protein transport and post-translational protein targeting to membranes indicates additional involvement in protein trafficking/import to membranes, which often accompanies organelle biogenesis and function. Together, these point to a cluster of proteins coordinating organellar RNA processing with membrane targeting.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070843","count":3},{"id":"GO:0031204","count":3},{"id":"GO:0008380","count":3},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2}]},{"hash":"1493157251402648731","title":"Neurodevelopment and Innate Immune Signaling","description":"This cluster shows strong neural-development signals (axonogenesis, corpus callosum development, synapse assembly, dopamine-related responses) alongside innate immune responses (LPS signaling, dsRNA response, defense against bacteria, innate immunity). The co-occurrence suggests a theme of neuroimmune coordination or dual-role genes involved in both neural development and immune signaling.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007409","count":10},{"id":"GO:0050830","count":9},{"id":"GO:1903351","count":9},{"id":"GO:0014068","count":9},{"id":"GO:0031663","count":9}]},{"hash":"572964829483499380","title":"Developmental transcription regulators","description":"The cluster\u2019s top GO terms are dominated by DNA-templated transcription and its regulation, with several tissue-development terms (intestinal epithelial cell development, ventricular cardiac muscle cell differentiation, uterus development, Sertoli cell differentiation) appearing as single occurrences. This pattern suggests proteins that regulate transcription to drive developmental differentiation across multiple tissues.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0016267","count":1},{"id":"GO:0060576","count":1},{"id":"GO:0030511","count":1}]},{"hash":"1461503863127841074","title":"Ubiquitin-Dependent Immune Signaling","description":"This cluster centers on ubiquitin-mediated protein turnover and related signaling. The top GO terms include ubiquitin-dependent proteolysis (SCF and ERAD pathways), various ubiquitination types (K6-linked), and immune signaling roles (innate immunity, NF-\u03baB signaling, TNF signaling) with defense against virus. Together they point to proteins that regulate degradation and ubiquitin signaling to modulate antiviral and inflammatory responses.","confidence":"High","size":19,"edges":3,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0090073","count":8},{"id":"GO:0051865","count":8},{"id":"GO:0042787","count":8},{"id":"GO:0051607","count":7},{"id":"GO:0030433","count":7}]},{"hash":"1953894930072182642","title":"ABA-Driven Seed and Floral Development with Cuticle Biosynthesis","description":"This cluster shows strong signals for abscisic acid-activated signaling and transcriptional regulation, along with developmental processes such as seed, bract, and floral meristem growth. Coupled with terms on cutin and wax biosynthesis, the proteins appear linked to ABA-regulated developmental programs and cuticle formation in reproductive and vegetative tissues, with a minor defense-related note (response to chitin) that does not define the main theme.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009738","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0010200","count":4},{"id":"GO:0010432","count":4},{"id":"GO:0048316","count":4}]},{"hash":"855862134094109447","title":"Transcriptional Regulation & Splicing","description":"Top terms are dominated by DNA-templated transcription and its regulation, along with alternative splicing via the spliceosome, suggesting a cluster of proteins involved in transcription control and RNA processing. Some histone modification and development terms appear, but the core signal points to transcriptional regulation and splicing as the main theme.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0021592","count":2},{"id":"GO:0021678","count":2},{"id":"GO:0036123","count":2},{"id":"GO:2000616","count":2}]},{"hash":"377752668863641614","title":"Neural signaling and development","description":"The top GO terms cluster around neural activity (visual perception, excitatory postsynaptic potential, long-term potentiation) and development (Schwann cell development, heart development), with additional links to signaling regulation and cell-cycle processes, suggesting a theme of developmental signaling with neural emphasis rather than a single pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009738","count":19},{"id":"GO:0007601","count":19},{"id":"GO:0060079","count":19},{"id":"GO:0000086","count":19},{"id":"GO:0014044","count":19}]},{"hash":"941010685582857798","title":"Neurodevelopmental signaling and craniofacial formation","description":"The proteins show enrichment for neural development and signaling (neurotrophin TRK signaling, excitatory postsynaptic potential) along with craniofacial and inner-ear development (face development, labyrinthine layer development). While there are broader development and signaling terms (Wnt, NF-kappaB, angiogenesis), the common theme appears to be neurodevelopment with sensory/craniofacial aspects.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010800","count":3},{"id":"GO:0045766","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0060711","count":3}]},{"hash":"54634466227925392","title":"Spliceosome-Driven mRNA Splicing","description":"The cluster's proteins are enriched for GO terms related to spliceosome-dependent processing of pre-mRNA, including snRNP assembly and alternative splicing regulation. A subset of terms references deubiquitination, suggesting some links to nuclear protein regulation, but the dominant signal is RNA splicing in the nucleus.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0035520","count":2}]},{"hash":"365096885857564362","title":"Secretory Pathway and Stress-Response Cluster","description":"The top GO terms are dominated by ER-to-Golgi vesicle transport, vesicle-mediated transport, and protein secretion, indicating a primary linkage to the secretory pathway. Supporting this are terms related to cellular responses to stress and apoptosis (oxidative stress\u2013induced apoptotic signaling and mitochondrial membrane potential regulation), suggesting a module where secretory processes intersect with stress signaling and cell survival decisions, with additional smaller hints from cell adhesion and chemokine production that fit into a broader signaling context.","confidence":"High","size":19,"edges":7,"triangles":1,"max_degree":3,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0010917","count":4},{"id":"GO:0008631","count":4},{"id":"GO:0002037","count":4},{"id":"GO:0007155","count":3}]},{"hash":"1949136678514358169","title":"LPS-Triggered Innate Immune Response","description":"This cluster shows GO terms tied to lipopolysaccharide signaling and cellular responses to LPS, plus innate immune response, indicating an LPS-triggered innate immunity theme. Some polysaccharide metabolism and vacuolar amino acid transport terms are present but do not change the overall LPS-immune emphasis.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0000272","count":3},{"id":"GO:0031663","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0045087","count":2}]},{"hash":"251484741712200000","title":"Unknown","description":"The proteins map to a broad set of GO terms (collagen fibril organization, glucocorticoid response, defense against Gram-positive bacteria, spliceosomal snRNP assembly, water homeostasis, ion transport, LDL receptor regulation, prolactin secretion, and cell\u2013cell adhesion) with little overlap, and the network has no edges. There is no single unifying function that ties the cluster together, so a specific label cannot be justified.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030199","count":4},{"id":"GO:0071385","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0000387","count":2},{"id":"GO:0009992","count":2}]},{"hash":"1489772180452121530","title":"Diverse biosynthesis and detoxification metabolism","description":"The GO terms are spread across detoxification (cellular oxidant detoxification, oxidation-reduction), proteolysis, multiple biosynthetic processes (biotin, antibiotic, plant-type secondary cell wall), and regulatory processes (insulin secretion, cell proliferation). This mix suggests a broad set of metabolic and regulatory activities rather than a single cohesive function, so the label reflects a general metabolic diversity rather than a specific pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0009834","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0017000","count":3}]},{"hash":"2257709506530413421","title":"Plant meristem and organ development transcription regulators","description":"This cluster centers on DNA-templated transcription and regulation of transcription, with strong ties to key plant developmental processes such as longitudinal axis specification, somatic embryogenesis, abaxial cell fate, meristem and flower development, and hormone signaling (auxin and gibberellin). The combination of transcriptional control and multiple developmental pathways suggests these proteins act as regulators coordinating embryogenesis, patterning, and organ formation in plants.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0009942","count":3},{"id":"GO:0010262","count":3},{"id":"GO:0010158","count":3}]},{"hash":"783279399626177904","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"The top GO terms cluster around oocyte maturation and spindle assembly in female meiosis I, with linked processes like microtubule polymerization and SCF-dependent proteasomal protein turnover, pointing to coordinated meiotic progression and spindle dynamics in oocytes. Some terms touch broader developmental processes, but the dominant signal is meiosis-related regulation. ","confidence":"High","size":19,"edges":141,"triangles":555,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":19},{"id":"GO:0006516","count":19},{"id":"GO:0008285","count":19},{"id":"GO:0007057","count":19},{"id":"GO:0051436","count":19}]},{"hash":"258939091507219403","title":"Plant Development and Cuticle Biosynthesis","description":"This cluster centers on plant development and cuticle formation. GO terms include bract development, floral meristem growth, and seed development, plus regulation of DNA-templated transcription, and pathways for cutin and wax biosynthesis. A lipid/metabolism-adjacent term (peroxisome organization) aligns with cuticle component production. Overall, they point to a developmental program in plants tied to surface lipid biosynthesis.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0032581","count":2},{"id":"GO:0010200","count":2},{"id":"GO:0010432","count":2}]},{"hash":"1079523285394282310","title":"Plant Hormone Signaling and Growth Regulation","description":"GO terms cluster around hormonal signaling (cytokinin-activated pathway, gibberellin response), growth-related processes (chlorophyll biosynthesis regulation, leaf senescence regulation, secondary cell wall modulation), and stress/metabolic responses (osmotic stress, flavonoid biosynthesis) with links to chromatin remodeling. This pattern supports a cohesive theme of hormone-mediated growth and stress adaptation in plants, rather than a disparate set of functions.","confidence":"Medium","size":19,"edges":16,"triangles":0,"max_degree":7,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":8},{"id":"GO:0030245","count":5},{"id":"GO:1900056","count":5},{"id":"GO:0010380","count":5},{"id":"GO:0009739","count":5}]},{"hash":"1898398985395347368","title":"Plant phenylpropanoid and cell-wall biosynthesis","description":"Explanation: The dominant GO terms are lignin biosynthesis, cutin biosynthesis, and positive regulation of flavonoid biosynthesis, all central to plant secondary metabolism and cell-wall formation. Although a few terms are generic or unrelated, the main signal points to phenylpropanoid-derived polymers and related cell-wall components, justifying this label.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009963","count":7},{"id":"GO:0080088","count":7},{"id":"GO:0010252","count":7},{"id":"GO:0009809","count":7},{"id":"GO:0010143","count":7}]},{"hash":"8773426310377479","title":"Pollen development and cell wall remodeling","description":"The top GO terms cluster around pollen biology (pollen tube growth, pollen sperm cell differentiation) and plant cell wall/pectin metabolism (pectin biosynthesis/catabolism, cell wall modification), with vesicle transport supporting secretion for wall remodeling. Although a non-plant term appears, the dominant signal is pollen development coupled with cell wall dynamics, justifying this label.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":2},{"id":"GO:0050873","count":1},{"id":"GO:0048235","count":1},{"id":"GO:0040015","count":1},{"id":"GO:0045490","count":1}]},{"hash":"1853517255925579418","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0052889","count":2},{"id":"GO:2000344","count":2},{"id":"GO:0016042","count":2},{"id":"GO:0010039","count":1},{"id":"GO:0055114","count":1}]},{"hash":"2065523152626093114","title":"Actin Dynamics and Spindle Assembly","description":"The cluster is enriched for actin-related processes (actin filament depolymerization; formin-nucleated actin cable assembly) and mitotic spindle assembly, with ties to cell polarity (bipolar polarity) and related fusion processes, indicating a module of actin cytoskeleton remodeling coordinating division and polarity.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030042","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0031915","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0009652","count":1}]},{"hash":"29840298628600764","title":"RNA Processing and Ribosome Biogenesis","description":"This cluster shows a strong representation of RNA metabolism and ribosome assembly: mRNA splicing via spliceosome, formation of translation preinitiation complex, and ribosome biogenesis appear most frequently. Other annotations (DNA repair, ubiquitination, ergosterol regulation, and organelle dynamics) are present but less central, so the core theme remains RNA processing and ribosome production.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0034316","count":2}]},{"hash":"9929476230111754","title":"Ubiquitin-dependent degradation in oocyte meiosis","description":"This cluster is driven by ubiquitin-dependent protein catabolic processes (including SCF-dependent ubiquitination and polyubiquitination) and links to cell-cycle control, notably spindle assembly in female meiosis I and oocyte maturation. The presence of negative regulation of cell proliferation supports a growth-control context, and while circadian rhythm regulation and glycoprotein catabolic process appear, the prominent theme is ubiquitin-mediated proteolysis shaping meiosis and oocyte development.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0031146","count":8},{"id":"GO:0042752","count":6},{"id":"GO:0001556","count":6},{"id":"GO:0006516","count":6}]},{"hash":"666728956579081375","title":"Cell wall biosynthesis and remodeling","description":"The proteins in this cluster are linked by GO terms centered on cell wall biogenesis and structure\u2014peptidoglycan biosynthesis, D-alanine pathways, and cell shape/organization\u2014suggesting a cohesive theme around cell wall synthesis and remodeling. Other terms like defense response to fungus and heme catabolism appear incidental.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0030632","count":1},{"id":"GO:0009252","count":1},{"id":"GO:0071555","count":1}]},{"hash":"839377187081053960","title":"Unknown","description":"Top terms span diverse biology (response to morphine, SCF-dependent proteasomal ubiquitin-dependent protein catabolic process, symbiont-mediated transformation of host cell, positive regulation of glucosylceramide catabolic process, lamellocyte differentiation, positive regulation of Ras signaling, positive regulation of B cell receptor signaling, face development, peptidyl-serine phosphorylation, obsolete protein kinase D signaling). This heterogeneity provides no single cohesive function for the cluster, so a unified label cannot be confidently assigned.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043278","count":4},{"id":"GO:0031146","count":3},{"id":"GO:0020021","count":3},{"id":"GO:2000753","count":3},{"id":"GO:0035171","count":3}]},{"hash":"1196671190983401290","title":"Mitotic Checkpoints and Cell Cycle Regulation","description":"This cluster is driven by mitosis-related processes: mitotic cell cycle, mitotic spindle assembly checkpoint signaling, centrosome cycle, and mitotic G1 DNA damage checkpoint signaling, pointing to a cohesive theme of cell cycle control and spindle surveillance. A few non-mitotic terms (thymus development, branching morphogenesis) and stress responses (cadmium) appear but do not define the group. The presence of negative regulation of cell population proliferation also aligns with growth and division control.","confidence":"High","size":18,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051436","count":10},{"id":"GO:0008285","count":10},{"id":"GO:0000278","count":9},{"id":"GO:0007094","count":9},{"id":"GO:0007098","count":9}]},{"hash":"3988699283895762","title":"Microtubule Dynamics and Transport","description":"The top GO terms cluster around regulation of microtubule-based processes, plus-end depolymerization, and anterograde transport of cargo along microtubules, suggesting proteins involved in cytoskeletal dynamics and intracellular trafficking. Some metabolic/biosynthesis terms are present but appear less central to the core function of microtubule regulation and transport.","confidence":"High","size":18,"edges":105,"triangles":305,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0006635","count":7},{"id":"GO:0009234","count":7},{"id":"GO:0042372","count":7},{"id":"GO:0010124","count":7}]},{"hash":"1485219270945743410","title":"Neuronal Migration and Vesicle Trafficking","description":"The cluster centers on neuronal development and vesicle dynamics, with terms like reelin-mediated signaling, synaptic vesicle maturation, and vesicle fusion, plus radial glia\u2013guided neuronal migration. A few outliers (abscisic acid pathway, B cell signaling, endocytosis regulation) exist, but the dominant theme is neuronal signaling combined with vesicle trafficking.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":2},{"id":"GO:0048260","count":2},{"id":"GO:0016188","count":2},{"id":"GO:0050764","count":1},{"id":"GO:0006906","count":1}]},{"hash":"538700692828483055","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"Based on the prominent GO terms, the cluster centers on oocyte maturation, spindle assembly in female meiosis I, and microtubule dynamics, with a reinforcing role for ubiquitin-proteasome\u2013mediated protein turnover during meiosis. The combination of oocyte maturation (GO:0001556), spindle assembly in female meiosis I (GO:0007057), and microtubule polymerization (GO:0046785) suggests a cohesive theme around meiosis and spindle function in oocytes, while the SCF-dependent proteasomal degradation term (GO:0031146) supports regulated protein turnover during this process. A few terms (nutrient response, glycoprotein catabolic process) appear more general but do not dominate the cluster\u2019s function.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0007584","count":7},{"id":"GO:0001556","count":7},{"id":"GO:0021678","count":7},{"id":"GO:0006516","count":7}]},{"hash":"1468923410159380986","title":"Organelle RNA Editing and Processing (Mitochondria/Chloroplasts)","description":"These proteins are enriched for GO terms related to RNA metabolism in mitochondria and chloroplasts, including mitochondrial mRNA modification/editing (C to U), mitochondrial mRNA processing, chloroplast RNA modification/processing, and plastid transcription, plus polycistronic mRNA processing. This points to a shared function in organellar RNA maturation and regulation, justifying the label. The seed dormancy term appears incidental and does not negate the organelle RNA biology signal.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0080156","count":3},{"id":"GO:0016554","count":3},{"id":"GO:1900865","count":3},{"id":"GO:0031425","count":3},{"id":"GO:0031426","count":3}]},{"hash":"2002844560256442178","title":"Plant organellar RNA editing and processing","description":"The cluster is dominated by GO terms related to RNA modification and cytidine-to-uridine editing in mitochondria and chloroplasts, with several entries on chloroplast RNA processing and mitochondrial RNA processing, plus chloroplast-nucleus signaling. The presence of plant-specific terms like chloroplast functions and seed dormancy\u2013related embryo development supports a cohesive theme of organellar RNA editing/processing in plants, potentially linked to development. ","confidence":"High","size":18,"edges":46,"triangles":22,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":5},{"id":"GO:0016554","count":5},{"id":"GO:0080156","count":5},{"id":"GO:0000961","count":5},{"id":"GO:1905639","count":5}]},{"hash":"1452269864180118998","title":"Unknown","description":"The cluster's top GO terms are highly heterogeneous, spanning photosynthesis (plant energy process) to digestion, blood pressure regulation, midbrain development, endothelial barrier establishment, and immune responses. With only a single edge and no clear shared function, there is no coherent theme to label the cluster. Therefore, Unknown.","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0042127","count":1},{"id":"GO:0003050","count":1},{"id":"GO:0007586","count":1},{"id":"GO:0030901","count":1}]},{"hash":"1586786427876909544","title":"Mitochondrial RNA editing and modification","description":"The cluster is driven by terms tied to mitochondrial RNA metabolism, including mitochondrial mRNA modification, cytidine-to-uridine editing, and regulation of mitochondrial RNA catabolic processes, plus general RNA modification. While a couple of terms touch on cell cycle or antibiotic response, the dominant theme is mitochondrial RNA processing/editing.","confidence":"High","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0046677","count":2}]},{"hash":"284625957582647392","title":"Photosynthesis Light-Harvesting and Light-Response","description":"This cluster shows strong enrichment for photosynthesis and various light-response terms (PS I/II light harvesting, nonphotochemical quenching, and responses to blue, red, and UV light), pointing to proteins involved in light capture and photoprotection.","confidence":"High","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0009768","count":2},{"id":"GO:0009645","count":2},{"id":"GO:0071486","count":2},{"id":"GO:0018298","count":2}]},{"hash":"1041924217499096367","title":"Unknown","description":"The top GO terms are heterogeneous, including transcription regulation and intron splicing (RNA processing) alongside neural signaling, plant-specific processes (aerenchyma formation, cellulose catabolic), and lipid metabolism. There isn't a single dominant function or pathway tying the majority of proteins together, so a cohesive, specific label cannot be assigned beyond Unknown.","confidence":"","size":18,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0000372","count":2},{"id":"GO:0000373","count":2},{"id":"GO:0031954","count":2},{"id":"GO:0098921","count":1}]},{"hash":"432524956366942426","title":"Plant metabolism and development signals","description":"The terms cluster around plant metabolism, including amino acid and cofactor biosynthesis (lysine, leucine, alanine, phenylalanine, biotin, heme/porphyrin), plus fatty acid transport, together with plant development cues (shade avoidance, flower development). This pattern suggests a plant-specific metabolic module tied to growth signaling and development.","confidence":"Medium","size":18,"edges":34,"triangles":36,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":6},{"id":"GO:0009102","count":5},{"id":"GO:0009908","count":4},{"id":"GO:0006782","count":4},{"id":"GO:0009098","count":3}]},{"hash":"840177581619773761","title":"Plant carbohydrate metabolism and cell growth","description":"This cluster highlights carbohydrate biosynthesis (starch, glycogen, glycolipids), cell-wall organization, and growth-related processes (DNA-templated transcription, cell division), with abiotic-stress responses (flooding, mannitol) suggesting a theme of plant growth and cell-wall remodeling linked to carbohydrate metabolism. Some terms (like lactation or obsolete glycosylation) are less coherent but do not override the dominant metabolism/growth signal.","confidence":"Medium","size":18,"edges":100,"triangles":272,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0005978","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0071555","count":4},{"id":"GO:0019252","count":4}]},{"hash":"1627972750287254848","title":"Photosynthetic Pigment and Quinone Biosynthesis","description":"The top GO terms cluster around biosynthesis of photosynthetic cofactors: chlorophyll, phylloquinone, plastoquinone, menaquinone, and related heme biosynthesis. This points to a cohesive role in producing pigments and electron-transport cofactors essential for photosynthesis, with multiple pigment/cofactor biosynthetic pathways enriched. ","confidence":"High","size":18,"edges":31,"triangles":6,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0018298","count":2},{"id":"GO:0006784","count":1},{"id":"GO:0048034","count":1},{"id":"GO:0009234","count":1}]},{"hash":"1645989236784954396","title":"Spliceosome-mediated mRNA splicing regulation and export","description":"Most top GO terms describe regulation of mRNA splicing via the spliceosome (positive/negative, alternative/cis splicing) and mRNA export from the nucleus, with a few related to translation reinitiation; together they indicate a post-transcriptional RNA processing module centered on spliceosome activity.","confidence":"High","size":18,"edges":61,"triangles":113,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048025","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:1900363","count":3},{"id":"GO:0002188","count":3}]},{"hash":"2078958089948316844","title":"Meiosis and Early Neural Development","description":"The terms cluster around female meiosis (oocyte maturation, spindle assembly in meiosis I), ubiquitin-proteasome\u2013dependent protein turnover, and early neural development (initiation of neural tube closure, third ventricle development), with microtubule dynamics supporting spindle formation and developmental proliferation control linking these processes.","confidence":"Medium","size":18,"edges":53,"triangles":62,"max_degree":12,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0031146","count":9},{"id":"GO:0001556","count":8},{"id":"GO:0021678","count":8},{"id":"GO:0006516","count":8},{"id":"GO:0051436","count":8}]},{"hash":"1472178970566831693","title":"Ribosome biogenesis and translation","description":"The cluster is centered on ribosome-related processes, with strong signals for translation (GO:0006412), ribosome biogenesis (GO:0042254), small subunit export and assembly (GO:0000056, GO:0000028), and rRNA processing/maturation (GO:0000448, GO:0000463), indicating roles in ribosome assembly and protein synthesis.","confidence":"High","size":18,"edges":140,"triangles":659,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":15},{"id":"GO:0006407","count":7},{"id":"GO:0042254","count":6},{"id":"GO:0000056","count":3},{"id":"GO:0046677","count":3}]},{"hash":"463983143493731333","title":"Mitochondrial Import and Translation with Transcription Regulation","description":"The dominant terms point to mitochondrial biology: protein import into the mitochondrial matrix, insertion into the outer membrane, and mitochondrial translation, suggesting a shared role in mitochondrial protein handling. The presence of transcription-related GO terms implies these proteins may also affect gene expression, which aligns with dual roles seen for some mitochondrial-associated factors. A couple of development terms may reflect pleiotropy or annotation noise rather than a core function. Overall, the theme is mitochondrial protein processing with associated transcriptional regulation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0045040","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0098779","count":1},{"id":"GO:1903955","count":1}]},{"hash":"516023153321589337","title":"Developmental Transcription and Signaling","description":"This cluster centers on regulation of development via transcription and signaling: transcription machinery (RNA Pol II, DNA-templated transcription), calcium signaling, ERK5 cascade, hormone responses (ABA), and diverse developmental processes (meristem identity, primitive streak formation, cardiac differentiation, ossification). The label Developmental Transcription and Signaling captures this broad, cross-species theme.","confidence":"Medium","size":18,"edges":145,"triangles":698,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090009","count":7},{"id":"GO:0071277","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0010077","count":5},{"id":"GO:0010076","count":5}]},{"hash":"1636180116832677329","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0051301","count":4},{"id":"GO:0000747","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0000480","count":4}]},{"hash":"371019296813255299","title":"Female reproductive development and lipid mediator biosynthesis","description":"The cluster shows strong enrichment for prostaglandin biosynthesis, retinoic acid biosynthesis, calcitriol biosynthesis, and developmental terms like uterus and female gonad development, suggesting a common theme of lipid-mediated signaling in female reproductive development.","confidence":"High","size":18,"edges":32,"triangles":17,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":17},{"id":"GO:0071615","count":16},{"id":"GO:0042904","count":16},{"id":"GO:0060065","count":16},{"id":"GO:0008585","count":16}]},{"hash":"1036918949148272127","title":"Metal ion transport and detoxification","description":"This cluster shows a strong signal for metal ion transport and detoxification, with GO terms for copper, zinc, mercury, and cadmium ion transport/export, and mercury detoxification. A few terms about translation and retina development are likely incidental background associations, so the core theme is metal homeostasis and related redox processes.","confidence":"Medium","size":18,"edges":21,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0061298","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0070574","count":1},{"id":"GO:0050787","count":1}]},{"hash":"2111928057738854903","title":"Plant Cell Wall Biosynthesis and Glycosylation","description":"The cluster is dominated by GO terms for plant cell wall components and assembly, including homogalacturonan and glucuronoxylan biosynthesis and plant-type secondary cell wall biogenesis, along with glycosylation processes (O-linked glycosylation via GalNAc and via mannose) and related galactose metabolism, pointing to coordinated biosynthesis and modification of cell wall polysaccharides. A few terms (e.g., skeletal muscle tissue regeneration) may be unrelated noise.","confidence":"High","size":18,"edges":29,"triangles":9,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":4},{"id":"GO:0016266","count":4},{"id":"GO:0071555","count":4},{"id":"GO:0009636","count":3},{"id":"GO:0009834","count":3}]},{"hash":"1860840187756464112","title":"Plant Development and Transcriptional Regulation","description":"The top GO terms indicate a strong focus on regulation of DNA-templated transcription, alongside plant-specific developmental processes such as bract and seed development and floral meristem growth. Additional terms point to ethylene signaling and regulation of cutin/wax biosynthesis, suggesting a set of proteins coordinating transcriptional control with epidermal development and hormone signaling in plants. A minor association with chitin response is present, but the core theme appears to be transcriptional regulation during plant development.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0006351","count":3},{"id":"GO:0010200","count":2},{"id":"GO:0010432","count":2},{"id":"GO:0048316","count":2}]},{"hash":"1607011973534204865","title":"RNA processing and translation initiation","description":"This cluster is dominated by GO terms related to mRNA splicing (spliceosome-mediated), mRNA maturation (splicing and polyadenylation), export from the nucleus, and importantly, processes governing translation initiation and reinitiation (including preinitiation complex formation and translational initiation regulation). This suggests a functional module linking RNA biogenesis with control of translation, hence a concise label that captures both RNA processing and translational initiation control.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000380","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006446","count":3},{"id":"GO:1900363","count":2},{"id":"GO:0002188","count":2}]},{"hash":"471891478827007072","title":"Stress Granule Dynamics and Protein Homeostasis","description":"These proteins are enriched for stress-related processes, notably stress granule disassembly and RNA metabolism (mRNA export) as well as chaperone functions and protein complex assembly. While there are additional signals (DNA replication, vesicle transport, cytoskeletal regulation), the dominant theme is cellular stress response coordinating RNA handling and protein folding/assembly, justifying this label.","confidence":"Medium","size":18,"edges":5,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035617","count":10},{"id":"GO:0006260","count":9},{"id":"GO:0070389","count":9},{"id":"GO:0006406","count":8},{"id":"GO:1990171","count":8}]},{"hash":"1497583760828401940","title":"Muscle differentiation and transcriptional regulation","description":"This cluster is strongest in terms related to transcriptional control (RNA polymerase II\u2013mediated and DNA-templated transcription) and skeletal muscle development (positive regulation of skeletal muscle cell differentiation, muscle morphogenesis), suggesting a core theme of transcription-driven muscle differentiation. Additional signals like calcium response, integrin-mediated adhesion, and certain neural/circadian terms indicate broader regulatory contexts, but the dominant theme points to muscle differentiation governed by transcriptional regulation.","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":10},{"id":"GO:0071277","count":7},{"id":"GO:2001016","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0031542","count":6}]},{"hash":"780278492741924628","title":"Chloroplast and mitochondrial RNA editing and processing","description":"These proteins cluster around RNA modification and processing in organelles, with strong representation of chloroplast RNA processing/modification, plastid transcription, and mitochondrial mRNA processing, including cytidine-to-uridine editing and regulation of mitochondrial RNA catabolism. There is also a tie to chloroplast-nucleus signaling, supporting a shared organellar RNA metabolism role across chloroplasts and mitochondria.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":4},{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0000961","count":3}]},{"hash":"825392704108633258","title":"Organ development and differentiation","description":"These proteins map to diverse organ-specific morphogenesis and differentiation terms (heart, uterus, inner ear, pancreas, gonads, forebrain), plus a general transcription regulation term, indicating a broad developmental/organogenesis program rather than a single pathway.","confidence":"High","size":18,"edges":131,"triangles":536,"max_degree":17,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060947","count":8},{"id":"GO:0060065","count":6},{"id":"GO:0042472","count":6},{"id":"GO:0003309","count":6},{"id":"GO:0008584","count":6}]},{"hash":"1819775895617757292","title":"Cross-tissue Development and Differentiation","description":"The top GO terms point to broad developmental and differentiation processes across multiple tissues and species\u2014calcium signaling and transcription underpin general development, with vertebrate (cardiac differentiation, ossification) and plant (floral development, fertilization) examples, as well as immune and germinal center formation. This suggests a cohesive theme of development and differentiation rather than a single specific pathway, hence the cross-tissue development label.","confidence":"Medium","size":18,"edges":134,"triangles":570,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071277","count":10},{"id":"GO:0006351","count":10},{"id":"GO:0090009","count":8},{"id":"GO:0055012","count":7},{"id":"GO:0001958","count":7}]},{"hash":"1282650432943211283","title":"Multisystem Development and Differentiation","description":"This cluster aggregates terms spanning transcriptional regulation, circadian control, and several tissue-specific differentiation processes (neuronal, amacrine cells, subpallium, astrocyte regulation, and cardioblast/muscle morphogenesis) plus cell adhesion and signaling pathways. The common thread is a broad developmental regulatory program guiding diverse tissue differentiation, rather than a single pathway, so a multisystem development label fits best.","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":12},{"id":"GO:0048712","count":9},{"id":"GO:2001038","count":9},{"id":"GO:0060415","count":8},{"id":"GO:0060163","count":8}]},{"hash":"90493822622846229","title":"Bone Formation and Remodeling","description":"The cluster shows strong enrichment for bone-related processes: intramembranous ossification and bone resorption directly point to skeletal remodeling, while Wnt signaling regulation is a central driver of osteogenesis. Additional terms like thyroid hormone response and regulation of catalytic activity can modulate bone metabolism, supporting a cohesive theme around bone development and remodeling. Some terms (e.g., decidualization, T cell cytotoxicity) are more peripheral but do not outweigh the dominant bone biology signal.","confidence":"High","size":18,"edges":133,"triangles":570,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0046697","count":18},{"id":"GO:0035593","count":18},{"id":"GO:0050790","count":18},{"id":"GO:0001913","count":18},{"id":"GO:0097067","count":18}]},{"hash":"715216901136264627","title":"Ubiquitination and Protein Degradation","description":"The cluster is dominated by GO terms tied to ubiquitination and ubiquitin-dependent degradation (ERAD, autoubiquitination, proteolytic catabolic processes, and various ubiquitin linkages). This suggests proteins function primarily in tagging substrates for destruction and in ubiquitin-regulated signaling, with auxiliary connections to TNF signaling and chromatin-associated ubiquitination. A few peripheral terms (viral transport regulation, channel activity) likely reflect broader ubiquitin-regulated processes.","confidence":"High","size":18,"edges":6,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0070535","count":4}]},{"hash":"981252869200499821","title":"RNA Modification and Translation in Cell Cycle","description":"This cluster centers on RNA processing/modification (mRNA cap-related methylation, rRNA and tRNA modifications) and components of translation initiation/reinitiation, alongside transcription regulation and cell division processes. The GO terms collectively point to the RNA processing and translation machinery active during cell proliferation and mitosis, making a cohesive label that highlights both RNA modification and translation within the context of the cell cycle.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0036265","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0002188","count":2}]},{"hash":"521688265109744709","title":"Chromosome localization and septin ring organization in cell division","description":"This cluster combines GO terms about chromosome localization/cohesion (meiotic sister chromatid cohesion, centromeric; establishment of protein localization to chromosome) with septin ring organization/disassembly at the bud neck, suggesting a common theme of chromosome segregation and cytokinesis. A few terms (P granule assembly, neurotrophin signaling) seem less connected and may reflect annotation noise.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051754","count":7},{"id":"GO:0090005","count":6},{"id":"GO:0006470","count":6},{"id":"GO:0031107","count":6},{"id":"GO:0070199","count":6}]},{"hash":"572827744350822785","title":"Phytohormone and secondary metabolite biosynthesis","description":"The top GO terms are centered on biosynthetic processes, notably plant hormones (ethylene, gibberellin, auxin-related) and secondary metabolites (proanthocyanidin), with additional antibiotic/PHB biosynthesis terms. The unifying theme is production of diverse metabolites across hormone and secondary metabolite pathways, rather than a single specific function, justifying a label focused on biosynthesis of phytohormones and plant secondary metabolites.","confidence":"Medium","size":18,"edges":4,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":12},{"id":"GO:0042619","count":7},{"id":"GO:0017000","count":6},{"id":"GO:0009693","count":5},{"id":"GO:1902835","count":5}]},{"hash":"1709950020176997393","title":"Flavonoid and lignin biosynthesis","description":"Most top GO terms correspond to biosynthesis or metabolism of flavonoids and related phenylpropanoid products (kaempferol O-glucoside, cyanidin glucoside, anthocyanin-containing compounds) and lignin, suggesting a plant secondary metabolite biosynthesis theme. A few terms (paranode localization, xenobiotic glucuronidation) are outliers, but the core pattern points to flavonoid/lignin production.","confidence":"Medium","size":18,"edges":132,"triangles":527,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0002175","count":11},{"id":"GO:0030259","count":11},{"id":"GO:0009808","count":11},{"id":"GO:0033330","count":11},{"id":"GO:0052696","count":11}]},{"hash":"1952827057759871710","title":"Transcription Regulation and Chromatin Maintenance","description":"The cluster's top GO terms cluster around DNA-templated transcription and its regulation, plus several chromatin-related processes (heterochromatin formation, histone modifications, sister chromatid cohesion), indicating a nuclear role centered on transcription control and chromatin architecture; some minor terms like calcium signaling and Rho regulation appear as secondary associations.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0019722","count":1},{"id":"GO:0070481","count":1},{"id":"GO:0033128","count":1}]},{"hash":"716121524285966220","title":"Cell Wall Biogenesis and Cell Division","description":"The top GO terms center on cell wall biosynthesis and organization (including Gram-negative bacterial wall and plant-type walls) alongside cell cycle and cell division, with a plausible link to regulation of cell shape. This points to a theme of cell growth involving wall construction/remodeling in coordination with division, despite some cross-species terms and obsolete annotations. ","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0043164","count":4},{"id":"GO:0019408","count":4}]},{"hash":"2219597276529798672","title":"Embryogenesis and Cell Cycle Regulation","description":"These terms point to embryogenesis and developmental patterning (in utero development, mesoderm formation, dorsal/ventral neural tube patterning) along with core cell-cycle activities (DNA replication, kinetochore localization, regulation of protein kinases and CDKs). The presence of ER-stress\u2013related translation and macroautophagy suggests integrated growth and stress management during development, supporting a cohesive developmental/proliferative role. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071374","count":3},{"id":"GO:1901621","count":3},{"id":"GO:0001707","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006469","count":3}]},{"hash":"351262732849443444","title":"Regulated LDL receptor endocytosis and cholesterol transport","description":"The cluster\u2019s top GO terms center on LDL receptor biology and related endocytic and catabolic processes, including positive/negative regulation of LDL receptor catabolic process, receptor recycling, and receptor-mediated endocytosis involved in cholesterol transport. Although a couple of terms seem unrelated (e.g., stomatal morphogenesis), the dominant theme ties to LDL receptor trafficking and cholesterol handling, justifying a label around regulated LDL receptor endocytosis.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032805","count":3},{"id":"GO:0032804","count":3},{"id":"GO:0010103","count":3},{"id":"GO:1905598","count":3},{"id":"GO:0007039","count":3}]},{"hash":"411153087604189289","title":"Plant development and RNA processing","description":"This cluster centers on plant development (flower and multicellular organism development) but also heavily features core RNA biology processes (ribosome biogenesis, mRNA splicing/export, translation initiation). The combination suggests proteins that coordinate gene expression during development, linking developmental programs with the machinery of transcriptional and post-transcriptional regulation. The presence of both developmental and RNA-processing terms indicates a broad, integrative function rather than a single enzyme pathway.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009908","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0007275","count":1},{"id":"GO:0030154","count":1},{"id":"GO:1900363","count":1}]},{"hash":"1761033608363358575","title":"Transcription Regulation and Immune Development Signaling","description":"The cluster is centered on transcriptional regulation (DNA-templated) but also includes diverse signaling roles (innate immunity, development, insulin/Rho/cytokinin pathways), making a broad regulatory theme rather than a single pathway.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0051607","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0045087","count":2}]},{"hash":"214452586362875029","title":"Developmental transcriptional regulation and embryogenesis","description":"The cluster shows a strong enrichment for DNA-templated transcription and its regulation, plus terms related to oogenesis, gametogenesis, embryo development, and axis specification, suggesting a coherent program of developmental gene regulation. A few metabolic/autophagy terms are present but are likely secondary or context-specific.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0043046","count":2},{"id":"GO:0010216","count":2},{"id":"GO:0035278","count":2}]},{"hash":"912975537057153993","title":"Neural Development and Morphogenesis","description":"This cluster is dominated by GO terms for forebrain and nervous system development, neural tube closure, and dendrite morphogenesis, indicating a cohesive neural development and neuronal morphogenesis program. The accompanying DNA replication/repair and cell cycle terms likely reflect proliferative neural progenitors and routine genomic maintenance during development, with ER stress\u2013related apoptosis as a quality-control filter. Together, these terms suggest proteins functioning in neural development and neuron morphogenesis.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030900","count":17},{"id":"GO:0007399","count":17},{"id":"GO:0006351","count":17},{"id":"GO:0070059","count":17},{"id":"GO:0001843","count":17}]},{"hash":"1228864908583723693","title":"Developmental signaling and transcription regulation","description":"The cluster combines regulatory signaling activities (positive regulation of GTPase activity, serine/threonine kinase activity, autophosphorylation) with transcriptional control (DNA-templated transcription) and development (multicellular organism development), suggesting proteins that coordinate signal transduction with gene expression during development. Additional terms like hypoxia response, mRNA transport, and cell cycle support a broader regulatory theme, but the central link is signaling-driven transcriptional regulation in development.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0031954","count":4},{"id":"GO:0071456","count":4}]},{"hash":"118570586290063376","title":"Cellular stress response and secretory trafficking","description":"The GO terms point to engagement in ER-to-Golgi vesicle transport, oxidative stress\u2013related apoptotic signaling, and cellular detoxification, all, together with regulation of transcriptional activity and nuclear-cytoplasmic trafficking. This pattern suggests a coordinated response to cellular stress that involves both secretory pathway dynamics and stress-induced gene regulation. Prolyl hydroxylation also hints at stress-related post-translational modification activities. Overall, the cluster seems centered on stress response with links to trafficking and protein regulation rather than a single pathway, hence the name.","confidence":"Medium","size":18,"edges":32,"triangles":8,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0010917","count":2},{"id":"GO:0008631","count":2},{"id":"GO:0002037","count":2},{"id":"GO:1903026","count":2}]},{"hash":"1878035160953946491","title":"Developmental Morphogenesis and Signaling","description":"This cluster links a mix of GO terms involved in development and morphogenesis across tissues and species (eye, ear, petal, somitogenesis, axonal development) and their regulatory signaling pathways, with ubiquitination as a general regulatory process. The shared theme is developmental morphogenesis and its signaling regulation, despite cross-species terms making a single narrow function unlikely.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0010199","count":1},{"id":"GO:0048441","count":1},{"id":"GO:0010161","count":1},{"id":"GO:0048668","count":1}]},{"hash":"1442170795083079636","title":"Unknown","description":"The top GO terms are highly diverse and span actin cytoskeleton regulation, sperm capacitation, cell-matrix adhesion, plant-type cell wall organization, neurotrophin signaling, Wnt pathway regulation, symbiont-host transformation, alkaline pH response, and developmental processes like face and optic nerve morphogenesis. There is no clear, shared function or pathway linking all proteins, and the lack of edges supports a heterogeneous group. Therefore this cluster is best labeled Unknown with no confidence.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000251","count":3},{"id":"GO:0048240","count":3},{"id":"GO:0007160","count":3},{"id":"GO:0009664","count":3},{"id":"GO:0048011","count":2}]},{"hash":"515621436031996614","title":"Plant Development and Cell Proliferation","description":"This cluster shows enrichment in plant-specific developmental processes (seed and bract development) and ethylene signaling, along with DNA-templated transcription regulation and cell cycle/mitotic growth terms. The combination suggests proteins coordinating plant development with controlled cell proliferation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0048316","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0051301","count":2}]},{"hash":"412093804853636815","title":"Neuro-immune signaling and axon development","description":"The set centers on neural development terms like axonogenesis and axonal fasciculation, but also includes innate immune signaling components (TLR signaling, NF-kB/I-kappaB phosphorylation) and defense responses, suggesting a theme of cross-talk between neural development and immune signaling pathways.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007409","count":5},{"id":"GO:0006469","count":5},{"id":"GO:0051607","count":4},{"id":"GO:0007413","count":4},{"id":"GO:0036303","count":4}]},{"hash":"1302987832837639178","title":"ER Stress Response and Nuclear Transport Regulation","description":"The cluster centers on ER proteostasis (protein folding, ER stress response) and transcriptional/nuclear transport regulation (negative regulation of RNAP II transcription, import/export from the nucleus), suggesting a link between ER stress signaling and nuclear processes, though some terms are obsolete and the connection is not perfectly cohesive.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033158","count":2},{"id":"GO:1903026","count":1},{"id":"GO:0034976","count":1},{"id":"GO:0046826","count":1},{"id":"GO:1903206","count":1}]},{"hash":"1540936341062714172","title":"Plant lipid catabolism and UV-B response","description":"The cluster centers on lipid degradation/remodeling (triglyceride, monoacylglycerol, phosphatidylserine, acylglycerol remodeling) and includes plant-specific stress-related terms (camalexin biosynthesis, UV-B response) plus vacuolar processing, suggesting a cohesive theme around lipid metabolism linked to plant defense and stress signaling.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":7},{"id":"GO:0052651","count":7},{"id":"GO:0006660","count":7},{"id":"GO:2000124","count":7},{"id":"GO:0030245","count":6}]},{"hash":"1491619082523012538","title":"Plant organelle RNA editing and processing","description":"These proteins cluster around RNA modification and processing in plant organelles, especially cytidine-to-uridine editing and mitochondrial/chloroplast RNA maturation, plus chloroplast-nucleus signaling. This common theme supports a function in organellar RNA editing/processing in plants; the additional embryo development term may reflect broader plant development context rather than core function.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0000961","count":3},{"id":"GO:1905639","count":3}]},{"hash":"1914209607298588869","title":"Cardiac development and electrophysiology","description":"The cluster shows cardiac-related terms, including left ventricular morphogenesis, regulation of SA node action potential, and clustering of voltage-gated potassium channels, plus positive regulation of heart contraction and mitochondrial calcium regulation, pointing to coordinated cardiac development and electrophysiological function. Some ubiquitination and self-proteolysis terms may reflect protein turnover relevant to cardiac remodeling.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0098907","count":3},{"id":"GO:0097264","count":2},{"id":"GO:0071313","count":2},{"id":"GO:0003220","count":2}]},{"hash":"943374001106248390","title":"Plant and fungal cell wall biosynthesis and remodeling","description":"The top GO terms cluster around plant and fungal cell wall biology\u2014xyloglucan metabolism, cell wall biogenesis, plant growth-related wall modification, and fungal-type wall organization\u2014indicating a cohesive theme of cell wall formation and remodeling across plant and fungal contexts. A few terms (e.g., B cell chemotaxis) appear as outliers and do not fit the main theme.","confidence":"High","size":18,"edges":9,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0080086","count":9},{"id":"GO:0009831","count":9},{"id":"GO:0031505","count":9},{"id":"GO:0010411","count":9},{"id":"GO:0032491","count":9}]},{"hash":"1271913461437311792","title":"Neural development and craniofacial morphogenesis signaling","description":"Several top GO terms center on neural development and craniofacial formation, including neurotrophin TRK receptor signaling, optic nerve morphogenesis, and face development. Additional terms involve signaling pathways commonly active in development (Wnt regulation, PI3K/AKT, FGFR apoptotic signaling), supporting a developmental theme. Some terms appear peripheral (e.g., symbiont-mediated host transformation, alkaline pH response), but they do not counter the dominant neural/craniofacial pattern. Overall, the cluster is best described as neural and craniofacial morphogenesis signaling.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":18},{"id":"GO:0090090","count":18},{"id":"GO:0020021","count":18},{"id":"GO:0071469","count":18},{"id":"GO:0060324","count":18}]},{"hash":"874548984604817407","title":"Plant chloroplast/mitochondrial RNA editing and processing","description":"The cluster\u2019s top GO terms center on RNA modification and editing in mitochondria and chloroplasts, plus chloroplast RNA processing and chloroplast\u2013nucleus signaling, indicating a plant-specific module for organelle RNA maturation/editing and inter-organellar communication, with some developmental context reflected by embryo dormancy terms.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0000961","count":3},{"id":"GO:1905639","count":3}]},{"hash":"307208028567076250","title":"Plant cell wall polysaccharide biosynthesis and glycosylation","description":"The top GO terms are dominated by plant-related cell wall processes: secondary cell wall biogenesis, glucuronoxylan and homogalacturonan biosynthesis, mucilage biosynthetic process, and general cell wall organization, with added signals of protein O-linked glycosylation (via mannose and via N-acetyl-galactosamine). This suggests the cluster centers on synthesis and modification of plant cell wall polysaccharides and their glycosylation, rather than cytoskeletal or signaling roles. Some terms may be incidental noise (e.g., glycogen or skeletal muscle regeneration), but they do not override the core plant cell wall theme.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035269","count":3},{"id":"GO:0009834","count":2},{"id":"GO:0010417","count":2},{"id":"GO:0010289","count":2},{"id":"GO:0043403","count":2}]},{"hash":"492402005933708298","title":"Ubiquitin-Proteasome Proteolysis and Immune Signaling","description":"This cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes, including SCF-dependent proteasomal degradation and K48-linked ubiquitination, pointing to the ubiquitin-proteasome system. Additional terms link to immune signaling (defense response to virus, TNF signaling) and cell-cycle related processes (mitotic spindle checkpoint, V(D)J recombination), suggesting the cluster centers on ubiquitin-mediated regulation of protein turnover with roles in immune responses and apoptosis.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:1903265","count":8},{"id":"GO:0030433","count":8},{"id":"GO:0090073","count":8},{"id":"GO:0031146","count":8}]},{"hash":"548325654423378142","title":"Plant development and cell wall biosynthesis","description":"The proteins show enrichment for plant-specific developmental processes (root cap development, callus formation, regulation of timing of plant organ formation) and plant-type secondary cell wall biogenesis, along with phytochelatin biosynthesis. This combination suggests a cluster focused on plant development and cell-wall\u2013related biosynthetic/metabolic activities, rather than a general cellular process.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0043085","count":3},{"id":"GO:1904715","count":3},{"id":"GO:0006508","count":3}]},{"hash":"414435506101556614","title":"Plant cell wall remodeling and fungal defense","description":"The top GO terms cluster around plant-specific processes: pectin catabolic process and cell wall modification point to remodeling of the plant cell wall, commonly linked to defense against pathogens, supported by cellular response to hydrogen peroxide and defense response to fungus. Additionally, terms like petal development and organ boundary specification hint at a developmental plant context, suggesting the proteins participate in both remodeling and development. A few terms (translation, mitochondrial initiation) are general cellular processes, but the dominant plant wall modification/defense theme stands out.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":2},{"id":"GO:0042545","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0050832","count":2},{"id":"GO:1901001","count":1}]},{"hash":"1971915437295703603","title":"Unknown","description":"The cluster includes varied terms from transcriptional regulation, actin cytoskeleton dynamics, peroxisome targeting, multiple developmental processes (forebrain, retina), fertilization, nuclear pore localization, and lipid signaling (SREBP). This broad mix lacks a single cohesive function or pathway, so a confident, representative label cannot be assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0034316","count":3},{"id":"GO:2001162","count":2},{"id":"GO:0006625","count":2},{"id":"GO:0030900","count":2}]},{"hash":"1745049148776670421","title":"Pollen Tube Growth and Cell Wall Remodeling","description":"This cluster centers on plant-specific cell wall dynamics and pollen tube growth, highlighted by GO terms for pectin catabolic and mucilage pectin biosynthetic processes, and cell wall modification, all key to pollen tube expansion. The zinc/cadmium transport terms suggest membrane transport activities co-occurring in the group, but the dominant theme ties to pectin remodeling and tube growth rather than metal transport alone.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":2},{"id":"GO:0048358","count":2},{"id":"GO:0009860","count":2},{"id":"GO:0043086","count":2},{"id":"GO:0042545","count":2}]},{"hash":"1490539212220222965","title":"Mitosis and Cytokinesis Machinery","description":"This cluster's GO terms cluster around mitotic spindle assembly and organization, contractile ring actin filament bundle assembly, membrane addition at the cytokinesis site, and nuclear migration, with additional terms for organelle inheritance (mitochondrion and vacuole). Together they point to proteins involved in cell division and related membrane remodeling and organelle partitioning, justifying a label focused on mitosis/cytokinesis machinery.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0007107","count":2},{"id":"GO:0051489","count":2},{"id":"GO:0006904","count":2}]},{"hash":"1803950166641334613","title":"Plant Floral Development and Hormone Signaling","description":"The terms cluster around floral meristem growth, bract and seed development, and hormone pathways (ethylene and ABA), with related transcription and cuticle biosynthesis processes, suggesting a cohesive theme of plant floral development tied to hormone signaling and cuticle formation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010200","count":1},{"id":"GO:0010432","count":1},{"id":"GO:0048316","count":1},{"id":"GO:0060774","count":1},{"id":"GO:0010451","count":1}]},{"hash":"752903980255208152","title":"Unknown","description":"The terms cover sporulation, DNA-templated transcription, transcription regulation, LDL receptor-related regulation, stomatal morphogenesis, vacuolar protein catabolism, and renin secretion, with no single shared function or pathway evident across the cluster. The diversity across species and processes suggests no coherent theme for a confident label.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030435","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0032805","count":2},{"id":"GO:0032804","count":2}]},{"hash":"1816751371076449745","title":"Fungal cell wall synthesis and septum assembly","description":"The dominant GO terms are fungal-type cell wall biosynthetic processes and division septum assembly, indicating the proteins cluster around fungal cell wall formation and cytokinesis. A few terms related to neuronal processes and ROS regulation seem incidental rather than central to the cluster\u2019s main function.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000917","count":2},{"id":"GO:0071970","count":2},{"id":"GO:0071940","count":2},{"id":"GO:0001662","count":1},{"id":"GO:2000378","count":1}]},{"hash":"201246282245296518","title":"Plant development and floral meristem patterning","description":"This cluster centers on plant development: transcriptional regulation, meristem and flower development, axis specification, abaxial leaf fate, somatic embryogenesis, auxin signaling, and related morphogenetic processes. The presence of fruit dehiscence and actin filament formation further supports roles in developmental patterning and tissue remodeling in plants.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0010047","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0051639","count":2},{"id":"GO:0009942","count":1}]},{"hash":"1620699875161902346","title":"Meiosis I spindle assembly and proteolysis in oocytes","description":"The cluster\u2019s top GO terms converge on meiotic regulation in oocytes, especially spindle assembly in female meiosis I, oocyte maturation, and SCF-dependent ubiquitin-proteasome\u2013mediated proteolysis, along with microtubule polymerization, indicating coordinated proteolysis and spindle dynamics during meiosis.","confidence":"High","size":17,"edges":113,"triangles":442,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":16},{"id":"GO:0001556","count":15},{"id":"GO:0006516","count":15},{"id":"GO:0008285","count":15},{"id":"GO:0007057","count":15}]},{"hash":"820721687205181019","title":"Unknown","description":"The GO terms span diverse and largely unrelated functions (transcription, brain development, cell division, ubiquitin-mediated pathways, signaling, stimulus detection, and nitrogen regulation) with no clear unifying biological theme. The lack of a cohesive function and no network connectivity suggests this cluster does not reflect a single shared process.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007420","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0000209","count":3}]},{"hash":"551946613161995867","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046620","count":2},{"id":"GO:0009734","count":2},{"id":"GO:0009926","count":2},{"id":"GO:0009733","count":2},{"id":"GO:0043086","count":2}]},{"hash":"937187894653951194","title":"Neural development and glial apoptosis","description":"This cluster is enriched for terms tied to CNS formation and forebrain development, dendrite morphogenesis, and glial cell apoptotic processes, including an intrinsic apoptotic pathway triggered by ER stress. These together suggest a core theme of neural development with glial cells regulating apoptosis. A metabolism term (L-methionine cycle) is present but less central to the main theme.","confidence":"High","size":17,"edges":4,"triangles":0,"max_degree":3,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0007568","count":11},{"id":"GO:0070059","count":11},{"id":"GO:0033353","count":11},{"id":"GO:0048813","count":11},{"id":"GO:0034352","count":11}]},{"hash":"767825162067227719","title":"Developmental transcriptional regulation","description":"The cluster is enriched for transcription by RNA polymerase II and circadian regulation of gene expression, with several differentiation-related terms spanning muscle, heart, and neural lineages (e.g., muscle tissue morphogenesis, cardioblast migration, amacrine cell differentiation, subpallium neuron fate commitment). This suggests a cohesive theme of transcription-driven control of tissue development across multiple lineages.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":14},{"id":"GO:0060415","count":13},{"id":"GO:0060163","count":13},{"id":"GO:0033627","count":13},{"id":"GO:0032922","count":13}]},{"hash":"1411425155715248367","title":"ER stress\u2013linked protein quality control","description":"This cluster centers on proteostasis under stress, with GO terms highlighting ER stress\u2013driven translation initiation, misfolded protein transport, ubiquitin-proteasome\u2013mediated quality control, and post-translational targeting. Together these suggest a coordinated set of proteins involved in maintaining protein homeostasis and quality control across organelles during stress.","confidence":"High","size":17,"edges":120,"triangles":560,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0036494","count":13},{"id":"GO:0070843","count":13},{"id":"GO:0006626","count":13},{"id":"GO:0071630","count":13},{"id":"GO:0097428","count":13}]},{"hash":"1568446839908471740","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":131,"triangles":611,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0009240","count":2},{"id":"GO:0034656","count":2},{"id":"GO:0015967","count":2},{"id":"GO:0015938","count":2},{"id":"GO:1901907","count":2}]},{"hash":"114880535702599357","title":"Central carbon metabolism and stress responses","description":"The top GO terms cluster around glycolytic and TCA cycle activities (glycolytic process, tricarboxylic acid cycle, oxaloacetate metabolism), pointing to central carbon metabolism. Additional terms related to responses to xenobiotics, nutrients, cAMP signaling, and hypoxia suggest this module adapts energy production under environmental stresses. ","confidence":"High","size":17,"edges":122,"triangles":501,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":6},{"id":"GO:0006099","count":5},{"id":"GO:0006107","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0042493","count":4}]},{"hash":"1049123833372032008","title":"Developmental gene expression and signaling","description":"The cluster centers on embryonic development and tissue morphogenesis (embryonic cranial skeleton morphogenesis; multicellular organism development) and combines that with core transcriptional and DNA replication control (DNA-templated transcription; DNA replication; centrosome cycle; positive regulation of nuclear DNA replication). Signaling pathways tied to development (neurotrophin TRK signaling; Wnt pathway regulation) further support a theme of developmentally coordinated gene expression and cell-cycle\u2013related signaling. A minor outlier term related to symbiont-mediated host interactions is present but does not dominate. ","confidence":"Medium","size":17,"edges":19,"triangles":5,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006349","count":15},{"id":"GO:0007098","count":15},{"id":"GO:0006351","count":15},{"id":"GO:0048701","count":15},{"id":"GO:0010571","count":15}]},{"hash":"1752397746112016830","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0000961","count":3},{"id":"GO:0070129","count":3},{"id":"GO:0042793","count":3},{"id":"GO:0031425","count":3}]},{"hash":"152380105806764748","title":"Redox Homeostasis and Detoxification","description":"The top GO terms are dominated by cellular oxidant detoxification and redox homeostasis (oxidation-reduction processes, deglutathionylation), suggesting a cluster centered on managing oxidative stress. Additional terms point to ion stress responses and transporter regulation, which can be linked to maintaining cellular redox balance under varying ionic conditions. Some other terms (like methylamine metabolism or nucleotide biosynthesis) may reflect peripheral or broader metabolic connections, but the core theme appears to be redox regulation and detoxification.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":15},{"id":"GO:0045454","count":15},{"id":"GO:0055114","count":15},{"id":"GO:0030416","count":14},{"id":"GO:0003147","count":13}]},{"hash":"710130939571755515","title":"Neurodevelopmental signaling and morphogenesis","description":"This cluster is dominated by terms related to neural development and tissue morphogenesis, including optic nerve morphogenesis, face development, and neurotrophin receptor signaling (TRK). The presence of negative regulation of Wnt signaling further supports developmental signaling roles, while cell-cycle terms reflect growth and proliferation typical of developing tissues. Some terms (like potassium ion transport) are more general, and a couple of outliers exist, but the core signal points to neural development and morphogenesis. ","confidence":"Medium","size":17,"edges":6,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006813","count":12},{"id":"GO:0046827","count":11},{"id":"GO:0051321","count":11},{"id":"GO:0000278","count":11},{"id":"GO:0048011","count":10}]},{"hash":"1838342733090535169","title":"Organelle metabolism and protein transport","description":"The top GO terms point to chloroplast/plastid metabolism (photosynthesis, one-carbon metabolism) and protein localization/trafficking (protein transport and insertion into the mitochondrial inner membrane), suggesting a core theme of organelle-related metabolism and protein targeting. Some developmental terms appear among the annotations, which may reflect cross-species or incidental annotations rather than a shared function, but the dominant signals support organelle metabolism and trafficking as the cluster's core. Confidence: Medium","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0006730","count":2},{"id":"GO:0015031","count":2}]},{"hash":"544798491332372166","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006620","count":1},{"id":"GO:0051083","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0070843","count":1},{"id":"GO:0006626","count":1}]},{"hash":"859886429658027366","title":"Ubiquitin-Proteasome Regulators","description":"This cluster is dominated by GO terms tied to ubiquitin-dependent ERAD, protein autoubiquitination, and regulation of proteasomal degradation, indicating a core theme of controlling protein turnover via the ubiquitin-proteasome system; additional terms hint at broader stress responses and signaling regulation, but the ubiquitin\u2013proteasome pathway appears central.","confidence":"High","size":17,"edges":133,"triangles":638,"max_degree":16,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0030433","count":16},{"id":"GO:0051865","count":16},{"id":"GO:0070911","count":15},{"id":"GO:0034140","count":12},{"id":"GO:1904049","count":12}]},{"hash":"167183772594276434","title":"Ribosome biogenesis and translation initiation","description":"The proteins are enriched in GO terms related to ribosome biogenesis, maturation of LSU rRNA, and multiple facets of translation initiation and reinitiation (including preinitiation complex formation and IRES-dependent initiation), as well as translation in general. This points to a cohesive role in ribosome assembly and control of protein synthesis, with some viral translation initiation terms reflecting broader translation mechanisms.","confidence":"High","size":17,"edges":128,"triangles":571,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0001825","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0075525","count":3}]},{"hash":"1767289372627800919","title":"Spliceosome-Mediated RNA Splicing","description":"The top GO terms are dominated by spliceosome-driven RNA processing (mRNA splicing, exon ligation, splicing regulation) and related RNA-processing events (snoRNA release). A few terms touch on DNA repair or viral replication, but they are minority. Thus the cluster most likely represents spliceosome-driven RNA processing proteins.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":11},{"id":"GO:0006369","count":7},{"id":"GO:0048026","count":7},{"id":"GO:0031047","count":7},{"id":"GO:0000378","count":6}]},{"hash":"1144769080548901196","title":"Ribosome Biogenesis and Translation","description":"Based on the top GO terms, the cluster is centered on ribosome assembly (ribosomal large subunit biogenesis), general translation, and the formation of translation initiation complexes, with additional terms touching DNA-templated transcription and transcription termination. While there are some cell-cycle related terms (centrosome cycle, spindle assembly) that suggest broader coordination, the strongest and most frequent signals are tied to protein synthesis machinery, justifying a label focused on ribosome biogenesis and translation.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042273","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0031564","count":2}]},{"hash":"1398847572236548140","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0090615","count":2},{"id":"GO:0090502","count":2}]},{"hash":"2086569465907246699","title":"Heavy metal transport and detoxification","description":"The top GO terms cluster around transport and handling of metal ions (cadmium, mercury, copper, zinc) and mercury detoxification, copper homeostasis, and metal-induced stress responses, indicating a cohesive function in moving metal ions across membranes and detoxifying toxic metals.","confidence":"High","size":17,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":2},{"id":"GO:0050787","count":2},{"id":"GO:0015680","count":2},{"id":"GO:0015694","count":2},{"id":"GO:0060003","count":2}]},{"hash":"943726846318396184","title":"Retinoic acid and vitamin D metabolism with prostaglandin biosynthesis","description":"The cluster is dominated by GO terms for prostaglandin biosynthesis, retinoic acid biosynthesis and catabolism, calcitriol biosynthesis, and vitamin D response, along with female reproductive development terms (uterus and gonad development). This pattern suggests a cohesive theme around metabolism and signaling of lipid-derived hormones (retinoic acid and calcitriol) and prostaglandins, with relevance to reproductive development, rather than disparate processes. ","confidence":"High","size":17,"edges":53,"triangles":75,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":13},{"id":"GO:0033280","count":13},{"id":"GO:0071615","count":12},{"id":"GO:0042904","count":12},{"id":"GO:0060065","count":12}]},{"hash":"1782382030587746379","title":"TLR-Mediated Innate Immune Signaling","description":"Based on GO terms, the cluster centers on Toll-like receptor signaling pathways (TLR4, TLR9) and the broader Toll signaling axis, along with macrophage activation and IL-18-related responses, pointing to innate immune recognition of pathogens and initiation of inflammatory responses. Some plant-specific terms appear but do not override the dominant mammalian immune theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":12},{"id":"GO:0050830","count":12},{"id":"GO:0034162","count":12},{"id":"GO:0034142","count":12},{"id":"GO:0008063","count":12}]},{"hash":"1851538451011476003","title":"Developmental apoptosis and cell cycle regulation","description":"This cluster centers on regulation of cell fate and proliferation, highlighted by negative regulation of apoptotic processes and the G0 to G1 transition, with supporting roles in ubiquitin-mediated protein turnover, RNA splicing, and metabolic regulation. The inclusion of morphogenesis terms (endocardial cushion, otic vesicle) suggests a developmental context where coordinated survival, growth, and gene regulation shape tissue formation.","confidence":"Medium","size":17,"edges":16,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043066","count":2},{"id":"GO:0071600","count":1},{"id":"GO:0045023","count":1},{"id":"GO:1904404","count":1},{"id":"GO:0071301","count":1}]},{"hash":"335184755470404557","title":"Neural and Muscle Development via Transcriptional Regulation","description":"This cluster centers on transcriptional control and differentiation in neural and muscle lineages: RNA polymerase II\u2013mediated transcription, muscle morphogenesis, neuron/fate commitment, amacrine cell differentiation, and astrocyte differentiation regulation, with supporting roles for integrin-mediated adhesion and circadian regulation of gene expression. Together these terms point to a cohesive developmental program coordinating gene expression and cell interactions in muscle and brain tissues.","confidence":"Medium","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":14},{"id":"GO:0060415","count":13},{"id":"GO:0060163","count":13},{"id":"GO:0033627","count":13},{"id":"GO:0032922","count":13}]},{"hash":"425962342654889321","title":"Developmental transcriptional regulation cluster","description":"This cluster is dominated by the GO term for regulation of DNA-templated transcription, with many proteins linked to developmental processes such as heart, uterus, inner ear morphogenesis, and various differentiation pathways. Together these suggest a group centered on controlling gene expression during development and organ formation, hence a Developmental transcriptional regulation label.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":15},{"id":"GO:2000032","count":15},{"id":"GO:0060065","count":1},{"id":"GO:0003290","count":1},{"id":"GO:0003281","count":1}]},{"hash":"792078763196302719","title":"Cell Migration and Lamellipodium Assembly","description":"Based on the GO terms, the proteins are enriched for motility-related processes: cell migration, lamellipodium assembly, and regulation of GTPase activity, all hallmark features of actin cytoskeleton remodeling driving movement. While developmental terms (spermatid nucleus differentiation, female gonad development) appear, they do not dominate the cluster's functional theme, so \"cell migration and lamellipodium assembly\" captures the central motif.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007289","count":4},{"id":"GO:0061087","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0008585","count":3}]},{"hash":"253924474154171603","title":"RNA splicing and ribosome biogenesis","description":"This cluster is enriched for spliceosome-mediated mRNA processing (mRNA splicing via spliceosome, regulatory ncRNA-mediated gene silencing, positive regulation of splicing) alongside ribosome biogenesis and rRNA maturation (large and small subunit rRNA maturation, preinitiation complex formation). The mix suggests proteins involved in RNA processing and ribosome assembly/translation readiness, rather than a single, narrow function.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":7},{"id":"GO:0045292","count":7},{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0031047","count":4}]},{"hash":"1765350359058095555","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0071038","count":3},{"id":"GO:0000467","count":3},{"id":"GO:0071035","count":3},{"id":"GO:0034475","count":3},{"id":"GO:0071042","count":3}]},{"hash":"2290432515931198836","title":"Flavonoid and lignin biosynthesis","description":"Most terms point to biosynthesis of flavonoids (anthocyanin, kaempferol, cyanidin derivatives) and lignin, i.e., phenylpropanoid metabolism common in plants. A few unrelated or obsolete terms are present but don\u2019t define the cluster. High","confidence":"","size":17,"edges":57,"triangles":78,"max_degree":16,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009718","count":9},{"id":"GO:0055114","count":7},{"id":"GO:0002175","count":6},{"id":"GO:0030259","count":6},{"id":"GO:0009808","count":6}]},{"hash":"303746780918262117","title":"Flavonoid and phenylpropanoid biosynthesis","description":"The cluster shows strong representation of flavonoid biosynthesis terms (anthocyanin, kaempferol, cyanidin glucoside) and lignin metabolic processes, which are all part of the plant phenylpropanoid pathway. An outlier term about paranode localization to axons likely reflects annotation noise rather than a shared function. Overall, the proteins seem tied to plant secondary metabolite production and cell wall biosynthesis.","confidence":"Medium","size":17,"edges":32,"triangles":11,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":14},{"id":"GO:0002175","count":12},{"id":"GO:0030259","count":12},{"id":"GO:0009808","count":12},{"id":"GO:0033330","count":12}]},{"hash":"1694917382988920642","title":"DNA Metabolism and Development Signaling","description":"The top GO terms cluster around nuclear DNA processes (transcription, replication, repair, mitotic cell cycle) and developmental programs (face and retina vasculature development), with associated signaling pathways (neurotrophin TRK signaling, Wnt regulation). This suggests a cluster of proteins involved in DNA metabolism that also participate in developmental signaling. Some terms are less cohesive (symbiont-host transformation, alkaline pH response) but do not override the main theme.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0006260","count":9},{"id":"GO:0061298","count":9},{"id":"GO:0000278","count":8},{"id":"GO:0006281","count":8}]},{"hash":"2167571200911306466","title":"Retinoic acid signaling in female reproductive development","description":"The cluster centers on retinoic acid metabolism (biosynthesis and catabolic) and reproductive development (uterus and female gonad development), with Wnt signaling regulation supporting a developmental context. Vitamin D metabolism terms (calcitriol biosynthesis) extend this to broader vitamin signaling, while triglyceride and xenobiotic metabolism appear as more peripheral, non-conflicting associations. ","confidence":"Medium","size":17,"edges":24,"triangles":12,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006641","count":5},{"id":"GO:0090090","count":5},{"id":"GO:0071615","count":4},{"id":"GO:0042904","count":4},{"id":"GO:0060065","count":4}]},{"hash":"154171853777161190","title":"Iron acquisition and vitamin biosynthesis","description":"This cluster centers on siderophore biosynthesis and iron-starvation response (catechol-containing siderophores, cellular response to iron ion starvation) alongside several aromatic/vitamin biosynthetic pathways (folic acid, p-aminobenzoate, tryptophan, salicylic acid), suggesting a theme of metal-related metabolism and metabolite biosynthesis. The absence of network edges among members adds some uncertainty, yielding a Medium confidence.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046656","count":2},{"id":"GO:0042407","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0009697","count":1},{"id":"GO:0008153","count":1}]},{"hash":"573484627917736489","title":"NF-kB Signaling and Neurodevelopment","description":"The GO terms point to NF-kappaB pathway activity and signaling, including positive regulation of NF-kappaB transcription factor activity and canonical NF-kappaB signaling, alongside proteasomal ubiquitin-dependent protein catabolic processes that regulate NF-kB. There is also defense response to virus and neural development terms (forebrain and nervous system development), suggesting a theme where NF-kB\u2013mediated signaling intersects with neuronal development. Protein homooligomerization reinforces a transcription factor\u2013dimerization theme common to NF-kB. Overall, a coherent label is NF-kB signaling tied to neurodevelopment, though some terms are broader or less specific.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0090073","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0051607","count":7},{"id":"GO:0051092","count":7},{"id":"GO:0043123","count":7}]},{"hash":"1332012106591163828","title":"Transmembrane Transport of Ions and Metabolites","description":"The dominant GO terms point to diverse transmembrane transport activities (nitrate/nitrite, phosphate, potassium, vitamin, xenobiotic) and vesicular neurotransmitter loading, supporting a cohesive function in moving small molecules across membranes.","confidence":"High","size":17,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":4},{"id":"GO:0035461","count":4},{"id":"GO:0042891","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0015707","count":3}]},{"hash":"1749839250277284913","title":"Neural and craniofacial development signaling","description":"This cluster centers on signaling pathways tied to neural and facial morphogenesis, reflected by neurotrophin TRK signaling, optic nerve morphogenesis, face development, Wnt regulation, FGFR apoptotic signaling, and PI3K-Akt signaling. These terms suggest a cohesive theme of developmental signaling affecting neural and craniofacial tissues, with a few outliers (stress/toxic response, symbiont-related transformation) that are less representative. The sparse connectivity supports a role in shared signaling programs rather than tight protein complexes.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":7},{"id":"GO:0090090","count":7},{"id":"GO:0020021","count":7},{"id":"GO:0071469","count":7},{"id":"GO:0060324","count":7}]},{"hash":"1044017239602523079","title":"Developmental pathways in neurons and reproductive organs","description":"The terms include clear neuronal development signals (motor neuron differentiation, axon guidance, lateral motor column migration) alongside reproductive tissue development (female gonad development, uterine epithelium development, cervix development). While there are a few hormonal or immune terms and one plant term, the dominant theme is development across disparate tissues, so this label reflects a broad developmental focus rather than a single specific process.","confidence":"Medium","size":17,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:2000324","count":2},{"id":"GO:2000691","count":1},{"id":"GO:0097477","count":1},{"id":"GO:0008585","count":1},{"id":"GO:0048482","count":1}]},{"hash":"1669355702510704439","title":"TLR-Myd88 innate immune signaling","description":"The terms cluster around MyD88-dependent Toll-like receptor signaling, innate immune defense, and cytokine regulation (including dsRNA and LPS responses), suggesting a group of proteins coordinating TLR-driven innate immunity and cytokine production.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002755","count":10},{"id":"GO:0051607","count":10},{"id":"GO:0002730","count":10},{"id":"GO:0050707","count":10},{"id":"GO:0045416","count":10}]},{"hash":"1242936856775318465","title":"Neurodevelopmental Growth Factor Signaling","description":"This cluster is enriched in neural development and growth-factor signaling terms, including neurotrophin TRK receptor signaling, FGFR apoptotic signaling, PI3K/AKT pathway, and Wnt signaling, along with optic nerve morphogenesis and face development, suggesting a cohesive role in neural/craniofacial development and related signaling networks.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":17},{"id":"GO:0090090","count":17},{"id":"GO:0020021","count":17},{"id":"GO:0071469","count":17},{"id":"GO:0060324","count":17}]},{"hash":"103530655001318188","title":"Skin barrier lipids and defense signaling","description":"The terms point to epidermal barrier biology: lipid transport and keratinocyte differentiation reflect skin\u2019s lipid-rich barrier formation, while defense response to fungus indicates cutaneous innate immunity; negative regulation of endopeptidase activity may support barrier integrity by moderating protease activity in the epidermis. Other terms like Wnt and neurotrophin signaling or pH response are broader or less specific, but the dominant theme is skin barrier maintenance coupled with antifungal defense.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":5},{"id":"GO:0050832","count":3},{"id":"GO:0006869","count":3},{"id":"GO:0009636","count":2},{"id":"GO:0030216","count":2}]},{"hash":"1780365690092221634","title":"Neural development and apoptotic regulation","description":"The top GO terms cluster around developmental processes (forebrain development, multicellular organism development, neuron apoptotic process) and apoptosis regulation (positive regulation of apoptotic signaling, regulation of apoptotic DNA fragmentation), with supporting signals from TGF-beta response and DNA damage checkpoint signaling. This suggests a cohesive theme of neural development intertwined with apoptotic regulation, potentially reflecting roles in tissue remodeling or developmental neurobiology (and some cardiac-associated apoptosis). ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030900","count":5},{"id":"GO:0072432","count":5},{"id":"GO:0010659","count":5},{"id":"GO:0071560","count":5},{"id":"GO:1902510","count":5}]},{"hash":"1384723856265598328","title":"Protein quality control and ubiquitin\u2013proteasome pathway","description":"The cluster is dominated by GO terms related to ubiquitin-mediated protein turnover, including the obsolete ERAD pathway, proteasome assembly, and autoubiquitination, pointing to ubiquitin\u2013proteasome\u2013ERAD\u2013protein quality control mechanisms. Peroxisome matrix protein import also ties into cellular protein handling, while additional terms like DNA replication, cell division, and oxidative phosphorylation may reflect broader cellular processes involving protein remodeling, making the core theme protein degradation and homeostasis rather than a single, narrow pathway. Confidence: Medium","confidence":"","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:0016558","count":6},{"id":"GO:0006260","count":5},{"id":"GO:0070682","count":5},{"id":"GO:0051865","count":4}]},{"hash":"567009554762256093","title":"Heavy Metal Transport and Detoxification","description":"The top GO terms converge on transport and detoxification of metal ions (cadmium, mercury, copper, zinc) and related transport processes, indicating a functional cluster focused on metal ion homeostasis and detox pathways. A few terms (like dephosphorylation or nitric oxide response) are peripheral, but the dominant theme is metal ion handling through transport and detoxification mechanisms.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":3},{"id":"GO:0071732","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0070574","count":2},{"id":"GO:0050787","count":2}]},{"hash":"1117606218323870667","title":"Metal Ion Transport and Detoxification","description":"This cluster centers on transport and detoxification of various metal ions (cadmium, mercury, copper, zinc) across membranes, plus copper homeostasis and metal ion regulation, with a side note on oxidative stress responses. The grouping suggests a cohesive theme of metal ion transport/export and detoxification, rather than disparate functions.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":1},{"id":"GO:0050787","count":1},{"id":"GO:0015680","count":1},{"id":"GO:0015694","count":1},{"id":"GO:0060003","count":1}]},{"hash":"358104938947626841","title":"Chromatin Modification and Nucleosome Assembly","description":"These proteins show enrichment for chromatin-related processes, especially histone methylation regulation (H3-K4, K9, K27) and nucleosome assembly. The cluster therefore appears to reflect chromatin remodeling/modification activities that influence gene expression. Several terms are marked obsolete, indicating historical annotations, but the common theme of chromatin regulation remains clear.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051573","count":2},{"id":"GO:2000791","count":2},{"id":"GO:0044648","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0002458","count":2}]},{"hash":"331426345836118947","title":"Ubiquitin-Dependent Proteolysis and NF-\u03baB Signaling","description":"The cluster\u2019s top GO terms cluster around ubiquitin-mediated protein degradation (autoubiquitination, ubiquitin-dependent catabolic process, K48-linked ubiquitination) and signaling events such as NF-\u03baB activation and Wnt receptor turnover, with immune-related context like V(D)J recombination. This suggests a cohesive function in tagging proteins for degradation and modulating key signaling pathways, especially inflammatory/immune signaling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0090073","count":11},{"id":"GO:0051865","count":11},{"id":"GO:0042787","count":11},{"id":"GO:0070936","count":10},{"id":"GO:0042981","count":10}]},{"hash":"1771858503305919632","title":"Unknown","description":"These proteins show a scattered mix of GO terms: chemotaxis, glucose metabolism, responses to drugs (cocaine, dopamine), axonogenesis, transcription, placenta development, immune defense, and even obsolete protein import regulation. The lack of a unifying biological process or pathway across the top terms suggests there is no coherent functional theme for this cluster, so a simple 'Unknown' label with no clear confidence is most appropriate.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006935","count":6},{"id":"GO:0006006","count":5},{"id":"GO:0042220","count":5},{"id":"GO:0045793","count":5},{"id":"GO:0001890","count":5}]},{"hash":"807645010275540718","title":"Root development and cell wall remodeling","description":"The dominant signals are pectin metabolism and cell wall modification, together with lateral root branching and invasive growth in response to glucose limitation, indicating a theme of root growth tied to cell wall remodeling, reinforced by nitrogen/ammonium transport terms. Confidence: Medium","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":2},{"id":"GO:0048358","count":2},{"id":"GO:0042545","count":2},{"id":"GO:0001403","count":1},{"id":"GO:0070634","count":1}]},{"hash":"228675288271185999","title":"Broad signal transduction and host interaction","description":"The cluster centers on signal transduction themes, including intracellular signaling, Ras pathway regulation, and immune-related signaling (B cell receptor pathways), with additional terms touching host interactions (symbiont-mediated transformation) and broad regulatory processes. Although a few terms pertain to plant-specific processes or cell wall organization, the common thread appears to be regulation and execution of signaling pathways, including immune and host-interaction contexts.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":3},{"id":"GO:0010183","count":3},{"id":"GO:0080092","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0071555","count":2}]},{"hash":"638761238369868636","title":"Detoxification and aromatic compound metabolism","description":"This cluster shows a cohesive theme around processing and detoxifying toxic substances and degrading aromatic/complex organic molecules, as evidenced by GO terms like cellular oxidant detoxification, response to toxic substance, and the beta-ketoadipate pathway. Additional terms related to antibiotic biosynthesis, chlorophyll catabolic process, and monoacylglycerol catabolism support a broader metabolism and breakdown of varied organic substrates. Overall, a moderate level of confidence that these proteins share a detox/organic metabolism role. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0098869","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0015996","count":4},{"id":"GO:0019740","count":4}]},{"hash":"1653623957247130346","title":"Female reproductive development and retinoic acid metabolism","description":"This cluster is dominated by terms tied to female reproductive development (uterus, female gonad, female genitalia) and retinoic acid metabolic processes (biosynthesis and catabolism), suggesting a theme where retinoic acid signaling intersects with female reproductive development. Additional terms (e.g., calcitriol biosynthesis) appear ancillary or broad, but the core connection remains reproductive development linked with RA metabolism.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071615","count":16},{"id":"GO:0042904","count":16},{"id":"GO:0060065","count":16},{"id":"GO:0008585","count":16},{"id":"GO:0034653","count":16}]},{"hash":"1538675850362803565","title":"Neural development signaling and cell cycle control","description":"This cluster combines neural-development related terms (neurotrophin TRK signaling, optic nerve morphogenesis, face development) with cell-cycle regulation (negative regulation of CDK activity, kinetochore localization), suggesting proteins involved in coordinating neural development with cell division. Additional pathways like Wnt and FGF signaling and some stress/response terms appear, reflecting broader regulatory networks but with a central tilt toward development and mitotic control.","confidence":"Medium","size":17,"edges":106,"triangles":331,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045736","count":17},{"id":"GO:0034501","count":17},{"id":"GO:0048011","count":16},{"id":"GO:0090090","count":16},{"id":"GO:0020021","count":16}]},{"hash":"1152153030486139624","title":"Stress-Responsive RNA Modification and Growth Regulation","description":"Most abundant GO terms point to RNA modification (rRNA and tRNA modifications, RNA guanine-N7 methylation) and transcription, alongside growth-related processes (cell growth, G1/S transition) and chlorophyll biosynthesis, all in the context of stress (response to immobilization stress). This combination suggests a module of proteins that link RNA processing and transcription to growth and stress responses, typical of plant cells adjusting gene expression under stress. Therefore a label emphasizing RNA modification coupled with growth regulation under stress is appropriate.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035902","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0006351","count":3},{"id":"GO:1900087","count":2},{"id":"GO:0019509","count":2}]},{"hash":"872449215767714693","title":"TLR/MyD88-Mediated Innate Immunity","description":"The cluster is dominated by GO terms related to MyD88-dependent TLR signaling, detection of LPS, and defense responses, indicating innate immune activation in dendritic cells. Some axon guidance terms appear, but the core theme centers on Toll-like receptor\u2013driven immune signaling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002755","count":5},{"id":"GO:0032497","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0048846","count":5},{"id":"GO:0007169","count":5}]},{"hash":"2103786242515257565","title":"Neural development and RTK signaling","description":"The cluster is enriched in neural development and growth-factor signaling terms, notably neurotrophin TRK receptor signaling, FGFR apoptotic signaling, and the PI3K/AKT pathway, as well as optic nerve morphogenesis and face development. This combination points to neural development processes guided by receptor tyrosine kinases (TRK/FGFR) and downstream signaling. Minor terms related to alkaline pH or toxin response are present but do not define the main function of the cluster.","confidence":"High","size":17,"edges":126,"triangles":543,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":17},{"id":"GO:0090090","count":17},{"id":"GO:0020021","count":17},{"id":"GO:0071469","count":17},{"id":"GO:0060324","count":17}]},{"hash":"385289626893692698","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":6},{"id":"GO:0090502","count":6},{"id":"GO:0090617","count":6},{"id":"GO:0009451","count":6},{"id":"GO:0080156","count":6}]},{"hash":"110826490044361532","title":"Auxin-regulated plant development and patterning","description":"The cluster repeatedly features auxin-related GO terms (response to auxin, auxin-activated signaling pathway) alongside transcriptional regulation and developmental processes such as meristem development, leaf vascular tissue patterning, axis specification, endosperm cellularization, and fruit dehiscence. The inclusion of SCF-dependent proteasomal ubiquitin-mediated protein catabolic process aligns with the auxin signaling mechanism that governs degradation of transcriptional repressors, coordinating growth and tissue organization. This points to a cohesive role in auxin-mediated development and patterning.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0010342","count":2},{"id":"GO:0009942","count":1},{"id":"GO:0048507","count":1},{"id":"GO:0010305","count":1}]},{"hash":"143765868969132938","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901001","count":1},{"id":"GO:0051245","count":1},{"id":"GO:0000480","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0000472","count":1}]},{"hash":"1027908051613200099","title":"Tissue development and morphogenesis","description":"This cluster\u2019s GO terms are largely about developmental processes and tissue formation, including face development, smooth muscle tissue development, fibroblast migration, trophoblast giant cell differentiation, and respiratory system development. These point to a common theme of differentiation and organization of tissues. A few terms (misfolded protein response, SRP-dependent targeting to membrane, transcription regulation) seem ancillary and may reflect supporting cellular processes that accompany development. Overall, the proteins appear to be involved in tissue development and morphogenesis, with some secondary stress- or translation-related roles.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0071243","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0003016","count":1},{"id":"GO:0071218","count":1}]},{"hash":"1064563944328953358","title":"Ubiquitin-Proteasome Degradation in Oocyte Meiosis","description":"This cluster is strongly enriched for ubiquitin-dependent proteolysis terms (SCF-dependent and ubiquitin-tagged protein degradation) and meiosis-related processes like oocyte maturation and spindle assembly in female meiosis I, suggesting a coherent theme of proteolysis coordinating meiotic progression and spindle dynamics in oocytes. Some terms appear less directly related (e.g., certain developmental terms), but the dominant signal is ubiquitin-proteasome\u2013driven regulation of meiosis.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":9},{"id":"GO:0042787","count":7},{"id":"GO:0001556","count":6},{"id":"GO:0021678","count":6},{"id":"GO:0006516","count":6}]},{"hash":"230353826515894678","title":"SCF ubiquitin ligase in mitosis","description":"The cluster shows strong enrichment for SCF complex\u2013related ubiquitin-dependent proteolysis and mitotic control terms (G2/M transition, exit from mitosis, chromosome segregation), suggesting a cohesive role of SCF-mediated protein degradation in regulating mitosis. Additional signals for ubiquitin-dependent catabolism and DNA repair point to a broader genome maintenance theme, but the dominant pattern centers on SCF-driven regulation of mitotic progression.","confidence":"High","size":16,"edges":110,"triangles":444,"max_degree":15,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0031146","count":14},{"id":"GO:0016032","count":13},{"id":"GO:0070911","count":13},{"id":"GO:0042787","count":12},{"id":"GO:0000086","count":11}]},{"hash":"185912950083702694","title":"Oocyte maturation and meiosis I spindle assembly","description":"This cluster is dominated by GO terms about oocyte maturation and spindle assembly during female meiosis I, plus related microtubule dynamics and ubiquitin-proteasome\u2013mediated protein turnover that regulate meiotic progression. While neural development terms appear, the strongest, most cohesive signal centers on meiosis/oocyte maturation and spindle formation.","confidence":"High","size":16,"edges":118,"triangles":533,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":16},{"id":"GO:0021678","count":16},{"id":"GO:0006516","count":16},{"id":"GO:0051436","count":16},{"id":"GO:0046785","count":16}]},{"hash":"1625683899159446136","title":"ER Stress and Viral Replication Regulation","description":"The top GO terms cluster around endoplasmic reticulum stress responses (UPR), ER localization, and COPII vesicle budding, coupled with host-mediated regulation of viral genome replication, indicating a group of proteins involved in ER-based stress responses and host\u2013virus interaction. A noise term for leaf development is present but does not dominate the functional theme; overall, the cluster reflects ER stress/trafficking and viral replication modulation pathways.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044791","count":2},{"id":"GO:0030968","count":2},{"id":"GO:0044829","count":2},{"id":"GO:0006987","count":2},{"id":"GO:0090114","count":2}]},{"hash":"502273733800462605","title":"Organelle RNA Editing and Processing","description":"The GO terms point to RNA modification and processing in mitochondria and chloroplasts (including C-to-U editing) and associated organelle-nucleus signaling, indicating a role in organellar RNA maturation and communication.","confidence":"High","size":16,"edges":69,"triangles":170,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":12},{"id":"GO:1905639","count":12},{"id":"GO:0080156","count":12},{"id":"GO:0000961","count":12},{"id":"GO:0016554","count":12}]},{"hash":"250107226491965335","title":"Organelle RNA Editing and Processing","description":"The cluster is dominated by GO terms for RNA modification and editing, particularly in mitochondria and chloroplasts, including mitochondrial mRNA processing/modification and chloroplast RNA processing/modification, plus cytidine-to-uridine editing and chloroplast-nucleus signaling. This points to a cohesive function in organellar RNA metabolism rather than a single nuclear pathway, though an outlier seed dormancy term is present. Overall, the terms consistently indicate organelle-specific RNA editing and processing.","confidence":"High","size":16,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":10},{"id":"GO:1905639","count":10},{"id":"GO:0080156","count":10},{"id":"GO:0000961","count":10},{"id":"GO:0016554","count":10}]},{"hash":"248831465012822841","title":"ER stress proteostasis and protein quality control","description":"The cluster is driven by GO terms related to unfolded protein response, ER stress, and quality-control mechanisms for misfolded proteins, including regulation of translation during stress and ubiquitin-proteasome\u2013mediated quality control, suggesting a cohesive proteostasis/ER-associated quality-control theme. Some terms appear peripheral or obsolete, but the dominant signal aligns with protein folding homeostasis and ER stress responses.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0017000","count":2}]},{"hash":"2196305464864455253","title":"Stress-Activated Signaling and Protein Homeostasis","description":"The cluster\u2019s frequent terms cluster around cellular stress responses: stress-activated MAPK cascade, heat response regulation, and protein stabilization, alongside negative regulation of intracellular transport and ROS metabolism, all pointing to proteostasis and stress signaling. Some terms (lens morphogenesis, estradiol response) are peripheral, but the dominant theme supports stress response and protein homeostasis.","confidence":"Medium","size":16,"edges":25,"triangles":11,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0032387","count":3},{"id":"GO:0030308","count":3},{"id":"GO:0050821","count":3},{"id":"GO:0051403","count":3}]},{"hash":"1113173013216106558","title":"mRNA Deadenylation and P-Body Decay","description":"The cluster centers on post-transcriptional control of mRNA stability, with multiple terms for deadenylation (shortening of poly(A) tail), deadenylation-dependent decay and decapping, and P-body assembly, plus miRNA-mediated post-transcriptional gene silencing. These themes together point to a cohesive role in mRNA turnover and regulation of gene expression at the RNA level. A glycogen biosynthesis term appears as noise rather than a core function. Overall, the proteins likely participate in mRNA decay pathways and P-body\u2013associated regulation. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000289","count":6},{"id":"GO:0033962","count":4},{"id":"GO:0090503","count":4},{"id":"GO:0045944","count":4},{"id":"GO:0061014","count":4}]},{"hash":"1854239576656337397","title":"Antiviral RNAi and Interferon Response","description":"The cluster is enriched for antiviral and RNA silencing functions: response to interferon-alpha, negative regulation of viral genome replication and transcription, RISC complex assembly, pre-miRNA processing, and mRNA processing, along with broader translation control and response to virus. This combination suggests a cohesive module where RNA interference machinery and interferon signaling cooperate to limit viral gene expression, with some associated stress-related apoptosis in neurons.","confidence":"High","size":16,"edges":42,"triangles":59,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045071","count":5},{"id":"GO:0035455","count":5},{"id":"GO:0006412","count":4},{"id":"GO:0035280","count":3},{"id":"GO:0031054","count":3}]},{"hash":"153135926730521092","title":"Anti-inflammatory regulation and growth control","description":"The top GO terms are dominated by negative regulation of inflammatory processes (acute inflammatory response, neutrophil aggregation, IL-1\u03b2 production), suggesting these proteins collectively modulate immune response. Additional terms point to growth regulation and signaling (EGF response, linoleic acid metabolism, cellular oxidant detoxification), indicating a broader role in growth and redox-associated pathways alongside inflammation. Overall, the anti-inflammatory theme best ties the cluster\u2019s functions, with some supporting but less central terms.","confidence":"Medium","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0002674","count":15},{"id":"GO:2000429","count":15},{"id":"GO:0014003","count":15},{"id":"GO:0032691","count":15},{"id":"GO:0071364","count":15}]},{"hash":"623629077966279345","title":"Bacterial cell wall biosynthesis and shape regulation","description":"The cluster is enriched for GO terms related to cell envelope construction and morphology, notably peptidoglycan and lipopolysaccharide biosynthesis, plus regulation of cell shape and cell morphogenesis. The presence of response to antibiotic further supports a link to envelope-associated functions and antibiotic susceptibility. Some basic transcription-related terms are present, but the strongest signal centers on cell wall/envelope biogenesis and shape control.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":5},{"id":"GO:0008360","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0019877","count":4},{"id":"GO:0009089","count":4}]},{"hash":"2123113265737534494","title":"Cellular Stress Signaling and Apoptosis","description":"The proteins in this cluster show enrichment for stress-related responses across biotic and abiotic cues (lipopolysaccharide response, TNF signaling, NF-kappaB regulation, ABA response, cold acclimation, water deprivation) and an intrinsic apoptotic pathway in response to DNA damage, along with a spliceosomal RNA processing term. This combination supports a cohesive theme of stress-response signaling with an apoptotic component, with a minor RNA processing association. ","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071222","count":2},{"id":"GO:0090502","count":1},{"id":"GO:0009737","count":1},{"id":"GO:0009631","count":1},{"id":"GO:0009414","count":1}]},{"hash":"1874610145888396203","title":"Unknown","description":"The top GO terms across the 16 proteins cover viral processes, stress response, translation, RNA silencing and transcription regulation, developmental axis specification, and signaling, with no single coherent biological function uniting them. This dispersion suggests the cluster does not reflect a single, well-defined pathway or process, so a specific label is not confidently assignable.","confidence":"","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":3},{"id":"GO:0070301","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0031047","count":2},{"id":"GO:1903026","count":2}]},{"hash":"973351427551835263","title":"ERAD and Protein Quality Control","description":"This cluster centers on ubiquitin-proteasome\u2013mediated handling of misfolded proteins and related quality-control processes, including ER-associated degradation, chaperone-assisted refolding, and protein targeting during ER stress. The presence of terms like ERAD, misfolded protein transport, nuclear quality control, and translation regulation under ER stress points to a cohesive theme of maintaining proteome integrity across compartments under stress.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0006260","count":5},{"id":"GO:0070389","count":5},{"id":"GO:0036494","count":4},{"id":"GO:0070843","count":4}]},{"hash":"121768410814875605","title":"Oxidative stress response and detoxification","description":"The top GO terms cluster around redox balance and antioxidant pathways (cellular redox homeostasis, cellular oxidant detoxification, glutathione metabolic process), with additional signaling related to inflammation and stress (prostaglandin biosynthesis, EGF response, JNK regulation). Together they point to a coherent theme of managing oxidative stress and associated inflammatory signaling, with downstream effects on cell cycle and vascular signaling.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":12},{"id":"GO:0098869","count":12},{"id":"GO:0001516","count":8},{"id":"GO:2000429","count":7},{"id":"GO:0071364","count":7}]},{"hash":"1178151325271686360","title":"Spliceosome-mediated mRNA processing and export","description":"The top GO terms are dominated by spliceosome-related processes: positive regulation of mRNA splicing via spliceosome, alternative splicing via spliceosome, cis splicing via spliceosome, and mRNA export from the nucleus, all pointing to post-transcriptional mRNA maturation. Additional terms about mRNA polyadenylation regulation and ncRNA-mediated gene silencing further support a broader RNA-processing/regulation theme. While there are a few translation reinitiation terms, the central signal is spliceosome-driven RNA processing and export, justifying this label.","confidence":"High","size":16,"edges":92,"triangles":292,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":16},{"id":"GO:0031047","count":16},{"id":"GO:1900363","count":15},{"id":"GO:0002188","count":15},{"id":"GO:0075525","count":15}]},{"hash":"220138636124995011","title":"Lipid biosynthesis and cuticular wax production","description":"The top GO terms cluster around lipid metabolism, including fatty acid responses, monounsaturated fatty acid biosynthesis, sphinganine/sphingolipid metabolism, and cholesterol esterification, plus tarsal gland development\u2014which points to production of cuticular/wax lipids in insects. This combination suggests a cohesive theme of lipid biosynthesis and specialized lipid-containing structures, rather than general metabolism or signaling. ","confidence":"High","size":16,"edges":17,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0050872","count":5},{"id":"GO:0070542","count":5},{"id":"GO:0033561","count":5},{"id":"GO:0044130","count":5},{"id":"GO:0010873","count":5}]},{"hash":"1483564775840089602","title":"Plant membrane transport and immunity","description":"The Top Terms include several transmembrane transport processes (potassium, vitamin, chloride, xenobiotic) along with plant-specific defense and immunity terms (hypersensitive response, defense response to bacterium, innate immune signaling). This suggests a cluster of proteins involved in membrane transport with roles in plant immune signaling or detoxification during defense, hence a combined theme of transport and plant immunity.","confidence":"High","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0035461","count":2},{"id":"GO:1902476","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0009626","count":2}]},{"hash":"38981304560844149","title":"Neural differentiation and muscle morphogenesis","description":"The proteins are enriched for neural development terms such as subpallium neuron fate commitment, spinal cord motor neuron and GABAergic interneuron differentiation, and also muscle-related terms like skeletal muscle cell differentiation and muscle tissue morphogenesis, plus integrin-mediated cell adhesion. Together these indicate coupled neural specification and muscle formation processes.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":11},{"id":"GO:0060163","count":9},{"id":"GO:0021520","count":9},{"id":"GO:0021530","count":9},{"id":"GO:0031018","count":9}]},{"hash":"347813281269748615","title":"Small-molecule metabolism and stress responses","description":"This cluster is enriched for several small-molecule metabolic processes (furaldehyde, sorbitol, xylitol catabolic; pyruvate fermentation to ethanol; prostaglandin and retinoic acid metabolism) and also includes stress-related responses (nitrosative stress, lipopolysaccharide response) plus a physiological term (positive regulation of blood pressure). The combination suggests proteins involved in diverse carbon-source and signaling molecule metabolism with concurrent stress-response roles, indicating a coherent theme around metabolism of small molecules linked to stress signaling.","confidence":"Medium","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0033859","count":16},{"id":"GO:0006062","count":16},{"id":"GO:0043458","count":16},{"id":"GO:0051409","count":16},{"id":"GO:0045777","count":16}]},{"hash":"674735832952506175","title":"Neural and cardiovascular development","description":"Based on the top GO terms, the cluster centers on developmental programs in neural and cardiac lineages, with entries for angiogenesis, heart development, axonogenesis, Schwann cell development, and visual perception, complemented by general growth-related processes like cell cycle and apoptosis. This cohesive theme explains the enrichment across diverse but related developmental processes.","confidence":"High","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001525","count":14},{"id":"GO:0009738","count":14},{"id":"GO:0000086","count":14},{"id":"GO:0043065","count":14},{"id":"GO:0014850","count":14}]},{"hash":"2195762029599702374","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":45,"triangles":9,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0000464","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0000388","count":3},{"id":"GO:0071031","count":3}]},{"hash":"66481355062324393","title":"Developmental transcriptional regulation","description":"The cluster's proteins are enriched for DNA-templated transcription and multiple development-related GO terms (forebrain development, neural tube closure, skeletal system development, multicellular organism development). While there are some stress/immune terms present, the dominant signal is regulation of gene expression during development, suggesting these proteins act in developmental transcriptional control.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0050830","count":5},{"id":"GO:0006349","count":5},{"id":"GO:0001403","count":5},{"id":"GO:0030900","count":5}]},{"hash":"1301059844396912716","title":"Plant secondary cell wall biogenesis and xylem development","description":"This cluster is dominated by GO terms related to plant-type secondary cell wall formation and vascular differentiation, including positive regulation of secondary cell wall biogenesis, protoxylem development, and xylem vessel differentiation. Additional terms cover root cap development, callus formation, and transcription, suggesting a broader plant developmental program centered on cell wall synthesis and vascular tissue maturation. The label captures the main themes without overreaching to unrelated processes.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901348","count":5},{"id":"GO:0009834","count":3},{"id":"GO:0048829","count":3},{"id":"GO:0090709","count":3},{"id":"GO:1990110","count":3}]},{"hash":"516449381318083366","title":"Developmental Apoptosis and Mitochondrial Signaling","description":"The cluster centers on apoptosis-related processes (neuron and cardiac muscle apoptotic activity, regulation of apoptotic signaling, apoptotic DNA fragmentation) and broad developmental contexts (forebrain/multicellular development), with links to mitochondrial-nucleus signaling and TGF-beta\u2013mediated responses, suggesting a cohesive module of programmed cell death intertwined with development.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031930","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0072432","count":3},{"id":"GO:0010659","count":3},{"id":"GO:0071560","count":3}]},{"hash":"1092017964604049283","title":"Unknown","description":"This cluster shows a highly diverse set of GO terms, spanning lipid and secondary metabolite biosynthesis (lipopolysaccharide, anthocyanin, stilbene), metal ion transport (cadmium, copper), hormone response (testosterone), P450 epoxygenase pathways, calcium homeostasis, and several obsolete terms. There isn\u2019t a single coherent biological process or function that ties these proteins together, suggesting the cluster reflects multiple unrelated functions or annotation noise.","confidence":"","size":16,"edges":32,"triangles":33,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0009103","count":5},{"id":"GO:0009718","count":5},{"id":"GO:0070574","count":4},{"id":"GO:0006825","count":4}]},{"hash":"1704496061384407565","title":"Diverse Plant Metabolic Processes","description":"The top GO terms cover a range of metabolic activities (carbohydrate/fructose metabolism; chlorophyll catabolism; cellulose catabolism; biotin biosynthesis; nitrogen utilization; menaquinone biosynthesis) along with detoxification and a plant-specific signaling/response term (strigolactone). There is no single dominant pathway, so a broad label reflecting varied plant metabolism best fits this cluster.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006002","count":2},{"id":"GO:0006000","count":2},{"id":"GO:0015996","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0098869","count":1}]},{"hash":"1414757911587225879","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0045947","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0051260","count":2}]},{"hash":"1769534728448243555","title":"Auxin signaling and transport","description":"The top GO terms are dominated by auxin-related processes: auxin-activated signaling pathway, auxin polar transport, and response to auxin, plus regulation of organ growth. Other transport terms (sodium-dependent organic anion transport, antimonite/arsenite transport) and membrane transport (pyruvate transport) may reflect shared transporter functions in this protein set, suggesting a cluster centered on auxin-mediated growth regulation and transport.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0043251","count":2},{"id":"GO:0015699","count":2},{"id":"GO:0015700","count":2},{"id":"GO:0006849","count":2}]},{"hash":"1281112194374892949","title":"DNA Damage Response and Apoptosis","description":"The top terms point to genome maintenance and cell fate decisions (base-excision repair, DNA catabolic process, apoptotic process) as core processes, with additional signals of stress (response to xenobiotic stimulus) and broader stress signaling (peptide hormone stimuli). Despite some obsoletes, the strongest common theme is DNA damage response coupled with apoptosis, justifying this label.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0007568","count":7},{"id":"GO:2000466","count":7},{"id":"GO:0006915","count":7},{"id":"GO:0090502","count":7},{"id":"GO:0006284","count":7}]},{"hash":"1331141155675779827","title":"Plant defense signaling and cell wall remodeling","description":"This cluster is dominated by plant-specific terms: defense response to fungus, response to chitin, cytokinin-activated signaling pathway, and plant-type cell wall loosening, with additional transcriptional regulation terms. Together they point to a cohesive theme of plant immune signaling coupled with cell wall remodeling, with transcriptional control as a supporting layer. Some terms like apoptosis or sexual reproduction are less central but may reflect broader stress or developmental links.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009409","count":2},{"id":"GO:0010200","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1077078510771390652","title":"Unknown","description":"There is no single dominant function among the top GO terms; they cover transcription, cell cycle, development, stress and redox responses. As a result, a confident, specific label for this cluster cannot be determined.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0046826","count":7},{"id":"GO:0009636","count":6},{"id":"GO:0030900","count":5},{"id":"GO:0000278","count":5}]},{"hash":"1633731362990329253","title":"Gene Expression and Protein Trafficking","description":"This cluster centers on core gene expression steps\u2014transcription, RNA splicing, and translation initiation\u2014and on intracellular protein trafficking like ER-to-Golgi transport and peroxisome targeting. The presence of mitotic spindle assembly adds a cell-cycle dimension, while auxin signaling and development terms are more context-specific regulatory outcomes. Overall, the common thread is cellular machinery for expressing genes and routing proteins.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0001731","count":3}]},{"hash":"1496244814984144738","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0090161","count":2},{"id":"GO:0006621","count":2},{"id":"GO:0006438","count":1}]},{"hash":"410090369114396580","title":"Neural development and growth factor signaling","description":"The cluster is dominated by GO terms related to neural development and signaling by growth factors. Neurotrophin TRK receptor signaling, optic nerve morphogenesis, and face development point to neural/craniofacial patterning, while PI3K-AKT and FGFR apoptotic signaling indicate growth-factor\u2013mediated survival and differentiation. Negative regulation of Wnt signaling also fits into developmental patterning, supporting a coherent neurodevelopmental theme.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":16},{"id":"GO:0090090","count":16},{"id":"GO:0020021","count":16},{"id":"GO:0071469","count":16},{"id":"GO:0060324","count":16}]},{"hash":"1874513917733674572","title":"Floral development and hormone signaling","description":"The terms cluster around plant reproductive development (bract/seed development, floral meristem growth) and transcriptional regulation, with multiple hormone pathways (ethylene, ABA, auxin) implicated. There are also signals related to epidermal lipid biosynthesis (cutin/ wax regulation). Together, these point to a module governing floral development coordinated by hormonal signaling and transcriptional control, with some epidermal surface biosynthesis activity.","confidence":"High","size":16,"edges":17,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010200","count":2},{"id":"GO:0010432","count":2},{"id":"GO:0048316","count":2},{"id":"GO:0060774","count":2},{"id":"GO:0010451","count":2}]},{"hash":"1650150081555311113","title":"Plant Floral Development and Cuticle Biosynthesis","description":"The terms cluster around floral meristem growth, bract and seed development, wax and cutin biosynthesis regulation, and ethylene signaling, indicating a plant developmental program governing reproductive structure formation and the plant cuticle, with transcriptional regulation guiding these processes.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0006355","count":10},{"id":"GO:0010200","count":9},{"id":"GO:0010432","count":9},{"id":"GO:0048316","count":9}]},{"hash":"1898992276938434524","title":"Ion Transport and pH Homeostasis","description":"This cluster is driven by transmembrane ion transport terms (potassium, sodium, bicarbonate) and related processes like fluid transport and regulation of intracellular pH, pointing to a shared function in moving ions across membranes and maintaining pH/volume balance. The neuron development and brain morphogenesis terms, as well as nitrate assimilation and boron response, appear as ancillary annotations and are less central to the main theme. Overall, the dominant signal is membrane ion transport and homeostasis.","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0048854","count":1},{"id":"GO:0010036","count":1}]},{"hash":"512329039890870251","title":"ER proteostasis and mRNA export","description":"The top GO terms are centered on endoplasmic reticulum protein folding and ER-associated degradation (ERAD), with supporting redox-related terms, pointing to ER proteostasis and oxidative folding as the core theme. Some nuclear RNA processing/translation terms appear, but they are weaker signals. Overall, the clearest link is ER protein quality control, with a possible peripheral association to RNA processing/ export. ","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0000122","count":2}]},{"hash":"2133229731437919818","title":"Plant development and stress responses with chromatin remodeling","description":"This cluster combines chromatin-level regulation (chromatin remodeling, nucleosome assembly) with plant-specific processes such as chlorophyll biosynthesis regulation, leaf senescence, gibberellin response, osmotic stress, and flavonol production, pointing to coordinated transcriptional control of growth, development, and stress/hormone signaling in plants. Some terms appear less directly related (e.g., viral process, roof of mouth development), but the dominant theme is plant development coupled with hormone- and stress-responsive regulation.","confidence":"Medium","size":16,"edges":27,"triangles":9,"max_degree":7,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0043044","count":6},{"id":"GO:0006334","count":6},{"id":"GO:0060021","count":6},{"id":"GO:1900056","count":5},{"id":"GO:0010380","count":5}]},{"hash":"1288684883118606504","title":"Developmental transcriptional regulation","description":"Most frequent terms point to transcriptional control (DNA-templated transcription and regulation of transcription) with signals of developmental differentiation (mesenchymal stem cell differentiation, mesoderm/endoderm fate specification, organ development). A few terms indicate signaling pathways (Wnt, TLR4) that modulate these processes, suggesting a set of transcriptional regulators coordinating developmental programs. Therefore, Developmental transcriptional regulation","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:2000741","count":1},{"id":"GO:0034145","count":1},{"id":"GO:0003290","count":1}]},{"hash":"2048012257345162941","title":"Craniofacial and optic nerve development","description":"The top GO terms point to craniofacial morphogenesis (face development) and optic nerve morphogenesis, with strong signals from neural development such as neurotrophin signaling, cell migration, and axon guidance. The inclusion of Wnt pathway and apoptosis/proliferation regulation fits broader developmental patterning common in craniofacial neural crest and optic system formation, suggesting a coherent cluster of proteins involved in craniofacial/neural development rather than a single linear function.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090090","count":16},{"id":"GO:0043065","count":16},{"id":"GO:0008285","count":16},{"id":"GO:0016477","count":16},{"id":"GO:0030517","count":16}]},{"hash":"1285781360627062306","title":"Mitochondrial Lipid Remodeling and Energy Production","description":"The top GO terms cluster around lipid remodeling and biosynthesis linked to mitochondria, including cardiolipin and phosphatidylcholine remodeling, CDP-diacylglycerol biosynthesis, triglyceride biosynthesis, and mitochondrial ATP synthesis. While other terms touch on amino acid metabolism or unrelated processes, the dominant theme is mitochondrial lipid remodeling driving energy production.","confidence":"Medium","size":16,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":2},{"id":"GO:0019509","count":2},{"id":"GO:2001246","count":2},{"id":"GO:0002071","count":2},{"id":"GO:0070970","count":2}]},{"hash":"1542469403158730180","title":"Organellar RNA Editing and Processing","description":"The cluster is dominated by organelle-focused RNA metabolism terms (mitochondrial and chloroplast RNA modification/processing and cytidine-to-uridine editing) and chloroplast-nucleus signaling, indicating proteins involved in RNA editing and processing within organelles; a plant-specific seed dormancy term is present but overall the theme is organellar RNA metabolism.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":14},{"id":"GO:0016554","count":14},{"id":"GO:0080156","count":14},{"id":"GO:0000961","count":14},{"id":"GO:1905639","count":14}]},{"hash":"1678229243240649492","title":"Neural development and proteostasis","description":"This cluster centers on neural development (Purkinje cell maturation; branching morphogenesis of a nerve) and cellular proteostasis (ER\u2013Golgi and Golgi-to-plasma membrane transport; ubiquitin-dependent degradation; deubiquitination; aggresome assembly). While some terms relate to transcription and pigmentation, the dominant themes point to neuronal differentiation with active secretory pathways and protein quality control rather than a single cohesive process.","confidence":"Low","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021691","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0048755","count":2},{"id":"GO:0010216","count":2},{"id":"GO:0035520","count":2}]},{"hash":"1120765824617283882","title":"Metal Ion Transport and Detoxification","description":"This cluster is dominated by GO terms for transporting various metal ions (cadmium, mercury, copper, zinc) and detoxifying metals, indicating a cohesive role in metal homeostasis. Additional terms on protein degradation and transcription are present but less central, so the primary theme centers on metal ion transport and detoxification.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070574","count":1},{"id":"GO:0050787","count":1}]},{"hash":"679197662740460970","title":"Plant pectin metabolism and cell wall remodeling","description":"The top GO terms are dominated by pectin catabolic and mucilage pectin biosynthetic processes, along with cell wall modification, pointing to a cohesive theme of pectin metabolism and cell wall remodeling in plants. Some developmental terms like pollen tube growth and somatic embryogenesis suggest this remodeling occurs in growth and embryogenic contexts, reinforcing a unit focused on plant cell wall\u2013associated metabolism.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":4},{"id":"GO:0048358","count":4},{"id":"GO:0042545","count":4},{"id":"GO:0008654","count":3},{"id":"GO:0006021","count":3}]},{"hash":"829972094154197403","title":"Chromatin Remodeling and Histone Modification","description":"The cluster is dominated by GO terms related to chromatin dynamics: chromatin remodeling, nucleosome disassembly, and histone H3-K14 acetylation, indicating a cohesive chromatin-regulatory function. Other terms (developmental and metabolic processes) are less consistently represented and may reflect broader or noise annotations. Overall, the strongest signal is chromatin modification machinery.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0006337","count":2},{"id":"GO:1903699","count":2},{"id":"GO:0035948","count":2},{"id":"GO:0051039","count":2}]},{"hash":"301319335861855745","title":"Oocyte maturation and meiotic spindle assembly","description":"Based on the top GO terms, the cluster is strongly enriched for processes tied to oocyte maturation, spindle assembly in female meiosis I, and microtubule dynamics, with supporting roles from SCF-dependent ubiquitin-proteasome\u2013mediated protein catabolism. While a few other developmental terms appear, the dominant theme is meiotic progression and spindle formation in oocytes.","confidence":"High","size":16,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":15},{"id":"GO:0006516","count":15},{"id":"GO:0008285","count":15},{"id":"GO:0007057","count":15},{"id":"GO:0051436","count":15}]},{"hash":"1449587971590651397","title":"Oocyte Maturation and Early Embryonic Development","description":"The top GO terms cluster around oocyte maturation, spindle assembly in female meiosis I, and initiation of neural tube closure, pointing to meiotic progression and early embryogenesis as the core theme. Supporting terms on microtubule dynamics and ubiquitin-proteasome\u2013mediated protein turnover reinforce cellular machinery needed for meiosis and early development.","confidence":"Medium","size":16,"edges":13,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":14},{"id":"GO:0021678","count":14},{"id":"GO:0006516","count":14},{"id":"GO:0051436","count":14},{"id":"GO:0046785","count":14}]},{"hash":"1628026716074960358","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"This cluster is dominated by terms for oocyte maturation and spindle assembly in female meiosis I, with supporting connections to microtubule polymerization and the ubiquitin-proteasome\u2013mediated protein catabolic process, suggesting a core role in meiotic progression and cell-cycle control during oogenesis. Some annotations (e.g., development-related or obsolete terms) are peripheral and do not override the central meiosis-focused signal.","confidence":"High","size":16,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":13},{"id":"GO:0006516","count":13},{"id":"GO:0008285","count":13},{"id":"GO:0007057","count":13},{"id":"GO:0051436","count":13}]},{"hash":"502167360155334407","title":"Ubiquitin-Proteasome Proteolysis and Meiosis Regulation","description":"The top GO terms are dominated by ubiquitin-dependent proteolysis (SCF-dependent proteasomal ubiquitin-dependent protein catabolic process; ubiquitin-dependent protein catabolic process), indicating a proteostasis/core protein degradation theme. The presence of oocyte maturation and spindle assembly in female meiosis I points to meiotic regulatory roles. Some terms like nervous system development and glycoprotein catabolic process appear less central but could reflect broader involvement of ubiquitin pathways in development. Overall, the cluster seems to center on ubiquitin-mediated proteolysis with meiosis regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":7},{"id":"GO:0042787","count":6},{"id":"GO:0007399","count":5},{"id":"GO:0051260","count":5},{"id":"GO:0001556","count":5}]},{"hash":"1446927665401603386","title":"Oxidative and Heavy Metal Stress Response","description":"This cluster is dominated by GO terms for oxidative stress (cellular response to hydrogen peroxide) and metal ion stress (response to cadmium and lead), with additional signals of defense against fungus. While some terms are peripheral (e.g., lipid transport, prostate gland development) and a few are obsolete, the clearest common theme is a general stress/defense response, particularly to oxidative and heavy metal stresses.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":5},{"id":"GO:0050832","count":4},{"id":"GO:0006869","count":4},{"id":"GO:0070301","count":3},{"id":"GO:2000531","count":2}]},{"hash":"1828641618978719988","title":"Pollen Tube Growth and Guidance","description":"The top GO terms are strongly dominated by pollen tube growth regulation and pollen tube guidance, each represented by 9 proteins, suggesting a cohesive plant reproductive signaling cluster centered on pollen tube development and directional growth. Other terms (intracellular signal transduction, transcription, and a few niche processes) appear at much lower counts and may reflect broader annotations or cross-species data rather than a unifying function. Overall, the cluster most plausibly reflects proteins involved in pollen tube growth and guidance.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080092","count":9},{"id":"GO:0035556","count":9},{"id":"GO:0010183","count":9},{"id":"GO:0006351","count":2},{"id":"GO:0020021","count":2}]},{"hash":"1661658325621598621","title":"Developmental and Neural Signaling","description":"The top GO terms point to development and neural signaling: multicellular organism development, face development, sensory perception of pain, neurotrophin TRK receptor signaling, and DNA-templated transcription, with negative regulation of Wnt signaling also aligning with developmental patterning. While some terms like sperm capacitation and symbiont-mediated transformation are outliers, the overall signal is dominated by developmental and neural/sensory pathways.","confidence":"High","size":16,"edges":11,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":6},{"id":"GO:0019233","count":6},{"id":"GO:0046827","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0048240","count":4}]},{"hash":"909177211540099466","title":"Unknown","description":"The top GO terms span distinct biological themes: cell migration and mechanical-stimulus response suggest mechanotransduction; telomere maintenance/capping hints at genome stability; adipocyte differentiation and insulin-response-related terms point to metabolic context; and mRNA processing plus CDK activity regulation add general cellular regulation. The mix of divergent processes and a couple obsolete terms indicates there isn\u2019t a single cohesive function uniting this cluster. ","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016477","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0032212","count":4},{"id":"GO:0045736","count":4},{"id":"GO:1904355","count":4}]},{"hash":"43346386464783979","title":"Carbohydrate and amino acid metabolism","description":"This cluster is annotated by multiple metabolic GO terms, especially carbohydrate phosphorylation and carbohydrate metabolic process, along with several amino acid biosynthetic/catabolic processes (methionine, L-threonine, L-glutamate). While a few terms are miscellaneous (serotonin biosynthesis, isoquinoline alkaloid metabolism, triglyceride catabolism) and there is an unrelated fibroblast migration term, the dominant signals point to carbohydrate and amino acid metabolism as the cohesive theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":2},{"id":"GO:0005975","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009086","count":2},{"id":"GO:0019433","count":2}]},{"hash":"841386350891734908","title":"Plant Organellar RNA Editing and Processing","description":"The cluster is dominated by GO terms for RNA modification and processing in mitochondria and chloroplasts (including cytidine-to-uridine editing and chloroplast RNA processing), along with chloroplast\u2013nucleus signaling. This points to a cohesive function in organellar RNA editing/processing in plants, despite one broader plant development term also appearing. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":8},{"id":"GO:0016554","count":8},{"id":"GO:0080156","count":8},{"id":"GO:0000961","count":8},{"id":"GO:1905639","count":8}]},{"hash":"45609874213143731","title":"Regulated signaling and ECM remodeling","description":"Based on the GO terms, the cluster centers on regulation of signaling pathways (autocrine signaling, stress-activated MAPK cascade) and extracellular matrix (ECM) assembly/remodeling, with associations to growth inhibition and cardiac muscle development. This suggests a cohesive theme of signaling control coupled with ECM dynamics rather than a single, isolated process, justifying a label focused on regulated signaling and ECM remodeling.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901201","count":1},{"id":"GO:0030308","count":1},{"id":"GO:0051055","count":1},{"id":"GO:0051966","count":1},{"id":"GO:0061049","count":1}]},{"hash":"1457467714917451869","title":"Neurodevelopmental signaling and morphogenesis","description":"The top GO terms center on neural development and signaling\u2014neurotrophin TRK receptor signaling, optic nerve morphogenesis, and face development\u2014indicating a cohesive neural development/morphogenesis theme. Supporting pathways like PI3K/AKT signaling and modulation of Wnt signaling further tie these proteins to growth, survival, and patterning in neural tissues. A couple of peripheral terms exist, but they do not override the core neural-focused pattern.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":16},{"id":"GO:0090090","count":16},{"id":"GO:0020021","count":16},{"id":"GO:0071469","count":16},{"id":"GO:0060324","count":16}]},{"hash":"1302800889104908761","title":"Plant floral and seed development with hormone signaling","description":"The cluster prominently features GO terms tied to plant developmental programs such as bract development, seed development, floral meristem growth, and phyllotactic patterning, along with DNA-templated transcription, suggesting transcriptional regulation of developmental processes. Additionally, hormone signaling terms (ethylene-activated and abscisic acid-activated pathways) indicate hormonal control of these developmental events, with wax/cutin biosynthesis regulation hinting at coordinating cuticle formation during tissue differentiation. Together, these terms point to a cohesive set of proteins involved in regulating floral and seed development under hormonal guidance.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010200","count":1},{"id":"GO:0010432","count":1},{"id":"GO:0048316","count":1},{"id":"GO:0060774","count":1},{"id":"GO:0010451","count":1}]},{"hash":"359816344870754390","title":"Innate Immune Response and Xenophagy Activation","description":"Most top GO terms point to innate immune responses and pathogen handling: responses to LPS, defense against Gram-positive bacteria, dsRNA response, and positive regulation of xenophagy. A couple of terms relate to neural or behavioral responses, which appear as outliers. Overall, the cluster centers on innate immune defense and autophagic clearance of pathogens, hence this label.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1903351","count":5},{"id":"GO:0043330","count":5},{"id":"GO:0071222","count":5},{"id":"GO:1904417","count":5},{"id":"GO:0050830","count":5}]},{"hash":"577658287596006863","title":"Unknown","description":"Top terms are a mix of intracellular transport, transcription, immune response, development, and cell-cycle regulation, with no single dominant process linking them. Edges are absent, so the proteins do not form a coherent functional module. Hence Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051436","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0032495","count":2},{"id":"GO:0006888","count":1},{"id":"GO:0042147","count":1}]},{"hash":"194981882504403694","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":5},{"id":"GO:0090615","count":4},{"id":"GO:0090502","count":4},{"id":"GO:0090617","count":4},{"id":"GO:0009451","count":4}]},{"hash":"1755745737962796419","title":"Jasmonate signaling and plant defense","description":"This cluster\u2019s GO terms are dominated by jasmonic acid signaling and defense responses (regulation of jasmonic acid signaling, response to jasmonic acid, regulation of systemic acquired resistance, response to wounding), indicating a jasmonate-driven defense program in plants. The presence of developmental terms like somatic embryogenesis and microgametogenesis suggests jasmonate involvement in plant development as well, providing a cohesive theme around JA-mediated signaling coordinating both defense and development. A few terms (e.g., certain glycosylation or epithelial-to-mesenchymal transition) are less central and can be considered incidental. Overall, the cluster aligns best with jasmonate signaling linked to plant defense and development.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045466","count":2},{"id":"GO:0055046","count":2},{"id":"GO:0010262","count":2},{"id":"GO:0010112","count":2},{"id":"GO:2000022","count":2}]},{"hash":"1239870074822718222","title":"Unknown","description":"The top GO terms include immune processes (regulation of phagocytosis, B cell receptor signaling), vesicle trafficking, neural development (reelin signaling, cortical migration), and various basic cellular processes (antibiotic response, aging-related stress, transcription, insulin secretion, mRNA export), with no single cohesive function tying them together.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0050764","count":4},{"id":"GO:0006906","count":4},{"id":"GO:0050861","count":4},{"id":"GO:0021814","count":4},{"id":"GO:0071236","count":4}]},{"hash":"599047323819463170","title":"Unknown","description":"The GO terms span neural development, immune signaling, cytoskeletal remodeling, proteasomal degradation, peroxisome targeting, and plant pollen tube guidance, with no single cohesive function tying them together. This dispersion suggests disparate processes rather than a unified cluster function, so a generic Unknown label is most appropriate.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051402","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0010183","count":2},{"id":"GO:0050853","count":2}]},{"hash":"432086319213510806","title":"Oxidative Stress Response and Redox Homeostasis","description":"This cluster is driven by GO terms for cellular oxidant detoxification, redox homeostasis, and response to hydrogen peroxide, indicating a core function in managing oxidative stress. While it also includes metabolic and transport processes (lipid metabolism and intracellular protein transport) and regulatory signals, the strongest signals center on detoxification and redox regulation, making oxidative stress response the most representative label for the cluster.","confidence":"High","size":15,"edges":25,"triangles":35,"max_degree":6,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0098869","count":5},{"id":"GO:0045454","count":5},{"id":"GO:2000255","count":4},{"id":"GO:0070301","count":4},{"id":"GO:0006886","count":3}]},{"hash":"504176576244148418","title":"Keratinocyte Development and Glucocorticoid Signaling Network","description":"The cluster is enriched for keratinocyte development and differentiation, and prominent glucocorticoid-related signaling terms, indicating a skin/differentiation and steroid-signaling module. Other terms (insulin response, cytochrome c release, cortical development) are present but add less cohesion, suggesting broader stress-response and signaling roles rather than a single pathway.","confidence":"Medium","size":15,"edges":18,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001836","count":4},{"id":"GO:0032869","count":4},{"id":"GO:0051291","count":4},{"id":"GO:0003334","count":3},{"id":"GO:0000079","count":3}]},{"hash":"1546281204024286292","title":"Plant hormone signaling and stress responses","description":"This cluster centers on plant-specific signaling and stress-related processes, with GO terms for cytokinin-activated and gibberellin-mediated signaling, nodulation, defense against biotic stimuli, osmotic stress responses, water homeostasis, and ion transport, suggesting a cohesive plant regulatory network under stress and biotic interactions. Translation appears as a general housekeeping process but does not override the plant signaling theme.","confidence":"Medium","size":15,"edges":12,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0009992","count":3},{"id":"GO:0071470","count":3},{"id":"GO:0034220","count":3},{"id":"GO:0009607","count":3}]},{"hash":"2083588033659895717","title":"Unknown","description":"The GO terms are heterogeneous (transcription, ERAD/ER-to-Golgi transport, peroxisome targeting, development, and cytoskeletal processes) with no single dominant shared function, so a clear, specific label for the cluster isn\u2019t supported.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006888","count":2},{"id":"GO:2001162","count":1},{"id":"GO:0006625","count":1}]},{"hash":"868595609964701070","title":"Genome Integrity and Development","description":"The cluster is dominated by DNA maintenance terms (DNA replication, nucleotide-excision repair, DNA topology/topological changes, DNA unwinding) and mRNA quality control (nonsense-mediated decay), pointing to genome stability processes. The presence of hair cell differentiation and embryonic organ development suggests these genome maintenance functions are linked with developmental programs. Together, these indicate a coherent theme around genome integrity during development, hence the label Genome Integrity and Development.","confidence":"Medium","size":15,"edges":6,"triangles":1,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000184","count":10},{"id":"GO:0006260","count":8},{"id":"GO:0035315","count":6},{"id":"GO:0000717","count":6},{"id":"GO:0006289","count":6}]},{"hash":"1423010324048973480","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":27,"triangles":11,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0042793","count":2},{"id":"GO:0034414","count":2},{"id":"GO:0090503","count":2}]},{"hash":"730769757631354429","title":"Photosynthesis Light Harvesting and Light Response","description":"This cluster is enriched for GO terms about photosynthesis and light-related processes (light harvesting in photosystem I and II, nonphotochemical quenching, responses to red light, UV-A, and light intensity changes), suggesting a cohesive group of proteins involved in capturing and modulating light energy.","confidence":"High","size":15,"edges":34,"triangles":17,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0009768","count":1},{"id":"GO:0009645","count":1},{"id":"GO:0071486","count":1}]},{"hash":"1953867084099005017","title":"Diverse metabolite biosynthesis and redox processes","description":"This cluster\u2019s top GO terms point to biosynthesis of varied metabolites (strigolactone, biotin, menaquinone, antibiotics) alongside redox-related activities (oxidation-reduction and detoxification). The presence of developmental (secondary shoot formation) and cellular organization (nuclear envelope) terms suggests a broad metabolic cluster rather than a single specific pathway. Confidence reflects this as a generalized metabolic-redox theme.","confidence":"Medium","size":15,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:1901601","count":2},{"id":"GO:0010223","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0009234","count":2}]},{"hash":"336565270050633051","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006415","count":3},{"id":"GO:0046656","count":2},{"id":"GO:0044205","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1273368022192184924","title":"Chloroplast photoprotection and UV response","description":"The top terms cluster around light-driven processes and stress responses in photosynthetic systems: cellular response to UV-A, photosynthesis, nonphotochemical quenching, unfolded protein response, and related protein folding and secretion regulation. This pattern points to components that safeguard the photosynthetic machinery under UV/light stress, consistent with a chloroplast photoprotection/UV-response cluster.","confidence":"High","size":15,"edges":13,"triangles":0,"max_degree":6,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0071492","count":3},{"id":"GO:0015979","count":3},{"id":"GO:0000413","count":2},{"id":"GO:0050714","count":2},{"id":"GO:0010196","count":2}]},{"hash":"451738176676803323","title":"RNA Processing and Respiratory Complex Assembly","description":"This cluster centers on RNA modification/processing (pseudouridine synthases for rRNA and tRNA, polycistronic mRNA processing) and assembly of energy-related complexes (mitochondrial complex I and cytochrome b6f complex). The co-occurrence suggests a link between RNA maturation machinery and assembly of respiratory components, though other terms like stress response and dormancy hint at broader roles. ","confidence":"Medium","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032981","count":2},{"id":"GO:0031426","count":2},{"id":"GO:0031119","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0085014","count":1}]},{"hash":"1513978142800681445","title":"Plant organelle RNA editing and processing","description":"This cluster is dominated by GO terms for RNA editing and processing in plant organelles: cytidine-to-uridine editing, mitochondrial mRNA modification and processing, chloroplast RNA modification/processing, plastid transcription, and polycistronic mRNA processing. The strong enrichment across mitochondrial and chloroplast/plastid terms points to a cohesive role in post-transcriptional regulation of organellar gene expression in plants, with the embryo development term likely reflecting developmental connections to plastid function. Confidence reflects a clear, coherent theme across related processes.","confidence":"High","size":15,"edges":78,"triangles":220,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":9},{"id":"GO:0080156","count":9},{"id":"GO:0000961","count":9},{"id":"GO:1905639","count":9},{"id":"GO:1900865","count":9}]},{"hash":"334438814419206656","title":"Developmental signaling and cell cycle regulation","description":"Top GO terms point to roles in developmental processes (angiogenesis, myoblast fusion, multicellular organism development) and neural/tissue development (visual perception, excitatory postsynaptic potential), together with core signaling and cell-cycle activities (protein phosphorylation, positive regulation of DNA binding, G2/M transition). The mix across systems suggests proteins coordinating development through signaling and cell-cycle control.","confidence":"Medium","size":15,"edges":64,"triangles":122,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043388","count":11},{"id":"GO:0006468","count":11},{"id":"GO:0007275","count":11},{"id":"GO:0001525","count":11},{"id":"GO:0009738","count":11}]},{"hash":"1121338066686571754","title":"Sugars and Ethanol Metabolism","description":"Top GO terms indicate a focus on carbohydrate and aldehyde metabolism (fructose biosynthesis, sorbitol catabolic, furaldehyde, retinol metabolism) and ethanol-related pathways (pyruvate fermentation to ethanol, ethanol oxidation). Associated stress terms (response to nitrosative stress, response to lipopolysaccharide) hint at broader cellular stress responses but do not override the metabolic theme. Thus, the cluster is best described as sugars and ethanol metabolism with related aldehyde turnover.","confidence":"Medium","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0042572","count":10},{"id":"GO:0046370","count":10},{"id":"GO:0055114","count":9},{"id":"GO:0033859","count":8},{"id":"GO:0006062","count":8}]},{"hash":"177984971680399006","title":"RNA processing and translation in mucosal innate immunity","description":"This cluster centers on core RNA biology\u2014translation, translation reinitiation, mRNA export, alternative splicing, and polyadenylation\u2014as well as immune functions linked to mucosal surfaces (innate immune response in mucosa and antibacterial humoral response). The combination suggests a functional grouping where RNA processing and protein synthesis intersect with mucosal defense, with additional hints from viral translation-related terms. Some terms are obsolete, but the overall theme remains RNA metabolism coupled to innate immunity at mucosal sites.","confidence":"Medium","size":15,"edges":11,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:1901407","count":2},{"id":"GO:0019731","count":1},{"id":"GO:0002227","count":1},{"id":"GO:1900363","count":1}]},{"hash":"1349137819114557310","title":"mRNA processing, splicing, and export regulation","description":"The top GO terms cluster around post-transcriptional RNA processing: spliceosome-mediated splicing (including alternative and cis splicing), mRNA export from the nucleus, and regulation of polyadenylation/stability in stress conditions. The presence of translation reinitiation terms hints at a connection to translational control, but the dominant theme is mRNA maturation and processing.","confidence":"High","size":15,"edges":20,"triangles":17,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":6},{"id":"GO:1900363","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0075525","count":5},{"id":"GO:0006378","count":5}]},{"hash":"1256629708022480461","title":"Amino acid and cofactor biosynthesis","description":"This cluster is dominated by biosynthetic and metabolic processes, especially amino acid biosynthesis (tyrosine, phenylalanine, lysine), vitamin cofactors (biotin), and related pathways (heme, sphinganine, oxaloacetate metabolism), with transcription as a minor outlier. The overall theme appears to be metabolic biosynthesis rather than a single signaling or structural function.","confidence":"Medium","size":15,"edges":21,"triangles":19,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0006107","count":5},{"id":"GO:0015908","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0033585","count":4}]},{"hash":"1328711727554778457","title":"Unknown","description":"The top GO terms cover apoptosis, cocaine response, Schwann cell development, kinetochore localization, excitatory synaptic potential, various cell-cycle stages, DNA replication, root development, and centrosome separation. This diverse mix across apoptosis, neural, developmental, and plant processes shows no single cohesive function or pathway tying the proteins together, so an Unknown label with no confidence is appropriate.","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043065","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0014044","count":3},{"id":"GO:0034501","count":3},{"id":"GO:0060079","count":3}]},{"hash":"106414158098295893","title":"Flowering time regulation and inflorescence development","description":"The cluster is dominated by GO terms tied to flowering biology, including regulation of the vegetative-to-reproductive transition, short-day photoperiodism, and inflorescence/flower development (with both positive and negative regulation). This points to proteins that control flowering time and floral organ formation; a few unrelated terms may appear among annotations, but the main signal centers on plant reproductive development.","confidence":"Medium","size":15,"edges":3,"triangles":0,"max_degree":2,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0048510","count":3},{"id":"GO:0048575","count":3},{"id":"GO:0042755","count":3},{"id":"GO:0010229","count":3},{"id":"GO:0010951","count":3}]},{"hash":"763111575437289701","title":"Mitotic Regulation and DNA Repair","description":"Explanation: The terms cluster around mitotic control (G2/M transition, exit from mitosis, chromosome segregation) and genome maintenance (NER, NHEJ, translesion synthesis), coupled with ubiquitin-proteasome regulation (SCF-dependent ubiquitination, K48-linked ubiquitination) and apoptosis. This suggests a cohesive module linking cell-cycle progression with DNA repair and protein turnover; the viral process term may reflect virus-host interactions influencing these pathways, but the core theme remains mitosis and genome integrity.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0010458","count":15},{"id":"GO:0000086","count":15},{"id":"GO:0016032","count":15},{"id":"GO:0070911","count":15},{"id":"GO:0031146","count":15}]},{"hash":"1085755021373473074","title":"Neural development signaling pathways","description":"This cluster is dominated by GO terms linked to neural development and growth signaling: neurotrophin TRK receptor signaling, optic nerve morphogenesis, and face development point to neural patterning and craniofacial development, while FGFR apoptotic signaling and PI3K/AKT signaling indicate growth factor\u2013mediated pathways that support neural differentiation and survival. The negative regulation of Wnt signaling also fits developmental regulation of tissue patterning. A few terms (e.g., symbiont-mediated transformation of host cells, alkaline pH response) are less aligned and likely represent incidental or pleiotropic roles, but the core signal remains neural development and associated signaling.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":6},{"id":"GO:0090090","count":6},{"id":"GO:0020021","count":6},{"id":"GO:0071469","count":6},{"id":"GO:0060324","count":6}]},{"hash":"897074242567429233","title":"Unknown","description":"The GO terms are highly diverse (polycistronic mRNA processing, chlorophyll catabolic, intestinal absorption) plus several lipid-related processes (triglyceride and diacylglycerol biosynthesis, monoacylglycerol catabolic, ceramide metabolism) and detoxification, with no single dominant theme and no network connections, so there is no clear, representative label beyond Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031426","count":2},{"id":"GO:0015996","count":1},{"id":"GO:0050892","count":1},{"id":"GO:0019432","count":1},{"id":"GO:0098869","count":1}]},{"hash":"1865052431141688893","title":"Diverse developmental processes","description":"This cluster\u2019s top GO terms span embryonic and organ development across animals and plants (primitive streak formation; ventricular cardiac muscle cell differentiation; endochondral ossification; floral meristem determinacy; floral whorl structure; regulation of double fertilization forming a zygote and endosperm) and immune-related development (germinal center formation). The mix suggests proteins involved in broad regulatory aspects of development and differentiation across taxa rather than a single pathway. Therefore, a label reflecting multi-taxa developmental processes is most representative.","confidence":"Medium","size":15,"edges":87,"triangles":268,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090009","count":11},{"id":"GO:0055012","count":9},{"id":"GO:0001958","count":9},{"id":"GO:2000111","count":9},{"id":"GO:0010582","count":9}]},{"hash":"645298673190788009","title":"Neuronal gene expression and dendrite morphogenesis","description":"The top terms indicate regulation of transcription and nuclear transport, plus neuronal-focused processes like dendrite morphogenesis and response to cocaine, with supporting metabolic signals (glucose metabolism, potassium transport). Although a placenta development term appears, the strongest, consistent themes center on neuronal gene expression and neuron morphogenesis/signaling, suggesting proteins function together in neural development and regulation.","confidence":"Medium","size":15,"edges":82,"triangles":229,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":10},{"id":"GO:0043552","count":8},{"id":"GO:0006813","count":8},{"id":"GO:0006351","count":8},{"id":"GO:0033160","count":8}]},{"hash":"1356031924997684950","title":"Diverse biosynthetic pathways","description":"Top terms indicate involvement in a wide range of biosynthetic processes, including lipopolysaccharide and exopolysaccharide (colanic acid, GDP-mannose, dTDP-rhamnose), various secondary metabolite biosyntheses (anthocyanin-containing compounds, phenylpropanoid, poly-hydroxybutyrate), antibiotic biosynthesis, and sporulation. This pattern suggests the cluster groups enzymes associated with multiple biosynthetic pathways rather than a single, cohesive function, making a high-level label like \u201cDiverse biosynthetic pathways\u201d appropriate. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0009718","count":7},{"id":"GO:0042619","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0030435","count":5}]},{"hash":"1236834538843722635","title":"RNA processing and translation initiation","description":"This cluster is dominated by GO terms related to mRNA processing (splicing, snoRNA splicing, polyadenylation) and translation initiation (preinitiation complex formation, translation reinitiation). While signaling terms (EGF response, p38 MAPK) appear, the strongest signals center on RNA metabolism and initiation of protein synthesis, suggesting these proteins function together in RNA processing and translation control.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006378","count":5},{"id":"GO:0002188","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0045292","count":4},{"id":"GO:0071364","count":3}]},{"hash":"953172386149811540","title":"Unknown","description":"The top terms are a diverse mix of biosynthetic, catabolic, developmental, and regulatory processes across different biological contexts (biotin and antibiotic biosynthesis, retina development, detoxification, raffinose biosynthesis, acetylcholine and neurotransmitter-related catabolic processes, cellulose breakdown). With no connecting theme and no edges linking proteins, there isn't a single coherent function to label this cluster beyond Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0060041","count":5},{"id":"GO:0098869","count":4},{"id":"GO:0010325","count":4}]},{"hash":"321087135716002697","title":"Synaptic Vesicle Trafficking and Receptor Localization","description":"The Top GO terms point to vesicular transport routes between endosomes and the Golgi, Golgi-to-vacuole transport, and vesicle fusion with the Golgi, plus explicit references to localization and insertion of neurotransmitter receptors at the postsynaptic membrane. Together these indicate a cohesive function in neuronal vesicle trafficking and targeted receptor delivery to the synapse, with added support from terms about receptor localization to synapse and postsynaptic membrane insertion. Some unrelated terms appear in the set, but the dominant signal is synaptic trafficking and receptor targeting.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034498","count":3},{"id":"GO:0007565","count":2},{"id":"GO:1902685","count":2},{"id":"GO:0010811","count":2},{"id":"GO:1903575","count":2}]},{"hash":"2303813030756506944","title":"Unknown","description":"Top GO terms point to highly diverse themes, including cell cycle regulation, proton transport, plant hormone response, multiple organ development processes, Wnt signaling modulation, vacuole inheritance, and pseudopodium/cytoskeletal dynamics. This broad and scattered mix provides no single unifying function or pathway to label the cluster with high confidence, so a precise, representative name cannot be assigned. Therefore, Unknown with None confidence.","confidence":"","size":15,"edges":87,"triangles":277,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007050","count":10},{"id":"GO:0015991","count":9},{"id":"GO:0071681","count":8},{"id":"GO:0061380","count":8},{"id":"GO:0000011","count":8}]},{"hash":"785795901802872334","title":"Unknown","description":"The top GO terms span transcription regulation, transport processes, and plant-specific roles (root cap development, ethylene signaling), with an outlier like brain morphogenesis, indicating no cohesive shared function across the cluster. This appears to be a heterogeneous set without a single representative theme.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0015707","count":2},{"id":"GO:0048829","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0009873","count":2}]},{"hash":"520125896993394447","title":"Plant Hormone Signaling and Development","description":"The terms cluster around plant development (bract, seed, floral meristem growth) and hormone signaling pathways (ethylene, ABA, auxin) with transcriptional regulation, indicating a cohesive theme of developmental regulation modulated by hormonal signals, with a minor defensome signal (chitin) that may reflect crosstalk.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0010200","count":2},{"id":"GO:0010432","count":2},{"id":"GO:0048316","count":2},{"id":"GO:0060774","count":2}]},{"hash":"1191286081693425259","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0000448","count":2},{"id":"GO:0030900","count":2}]},{"hash":"493642711294658885","title":"Cytoskeleton Remodeling and Vesicle Trafficking","description":"Top terms cluster around actin filament regulation (capping and depolymerization) and ER-to-Golgi vesicle transport, with additional links to nuclear pore localization and peroxisomal targeting, plus development-related processes. This suggests proteins involved in intracellular trafficking and cytoskeletal dynamics as a coherent theme, though some developmental or fertilization terms appear as broader contexts.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051016","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0010226","count":2},{"id":"GO:2001162","count":2},{"id":"GO:0006625","count":2}]},{"hash":"65990178981994114","title":"Developmental transcriptional regulation","description":"The cluster\u2019s most prominent GO terms center on DNA-templated transcription and its regulation, including multicellular organism development and regulation of transcription. This suggests a core theme of transcriptional control during development, even though the set also includes terms related to cytoskeleton dynamics, ribosome maturation, organelle inheritance, and stress responses that may reflect broader multifunctional roles or annotation noise.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0043547","count":2},{"id":"GO:2000601","count":2}]},{"hash":"1887306895809782010","title":"Wnt-regulated Development and Regeneration","description":"The cluster centers on negative regulation of the canonical Wnt signaling pathway, with associated terms for face development, angiogenesis, and animal organ regeneration, suggesting a theme of Wnt-controlled developmental and regenerative processes. Additional terms related to inflammatory responses and receptor turnover align with Wnt pathway cross-talk to immune signaling, reinforcing a cohesive, albeit broad, developmental-regenerative/inflammatory theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090090","count":15},{"id":"GO:0060324","count":15},{"id":"GO:0009636","count":15},{"id":"GO:0001525","count":15},{"id":"GO:0031100","count":15}]},{"hash":"1861902514082615926","title":"Lipid catabolism and endocannabinoid signaling","description":"The cluster's GO terms are dominated by lipid metabolism\u2014monoacylglycerol catabolic process, triglyceride catabolic process, phosphatidylserine catabolic process\u2014and by regulation of endocannabinoid signaling; sebaceous gland development also aligns with lipid biology, supporting a theme of lipid metabolism and skin signaling. Some terms like DNA-templated transcription and seminiferous tubule development appear unrelated noise.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061087","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0072520","count":2},{"id":"GO:0045490","count":2},{"id":"GO:0009405","count":2}]},{"hash":"1004916129078271795","title":"TLR/MyD88-Mediated Immune Activation","description":"The cluster\u2019s GO terms are dominated by innate immune signaling: MyD88-dependent TLR pathway, detection of lipopolysaccharide, defense response to virus, and regulation of dendritic cell cytokine production, pointing to an innate immune activation theme. The neural development terms appear less central and may reflect broader pleiotropy or annotation overlap rather than a unified neural function across the proteins.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002755","count":2},{"id":"GO:0032497","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0048846","count":2},{"id":"GO:0007169","count":2}]},{"hash":"2165949579782405743","title":"Stress Response and Transcription Regulation","description":"This cluster centers on cellular responses to stress and damage (response to toxic substances, cadmium ion, ER stress leading to apoptotic signaling) and includes transcription-related processes (DNA-templated transcription), suggesting a theme of stress signaling coupled with transcriptional control; a few development terms appear but do not dominate the overall pattern.","confidence":"Medium","size":15,"edges":34,"triangles":45,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009636","count":13},{"id":"GO:0050830","count":12},{"id":"GO:0046827","count":12},{"id":"GO:0006349","count":12},{"id":"GO:0001403","count":12}]},{"hash":"1307761363990359024","title":"Fungal filamentous growth and cell polarity","description":"The terms cluster around morphogenesis and polarity in fungal cells: pseudohyphal and invasive growth, budding/apical growth, and signaling for filamentous growth, with supporting roles for cytoskeletal localization and cell shape polarity. Some unrelated terms (e.g., vertebrate immune signaling) appear, but the dominant theme is fungal filamentous growth and polarity.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035372","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0045087","count":2},{"id":"GO:1990872","count":2},{"id":"GO:0001403","count":2}]},{"hash":"82260741546032029","title":"Developmental Signaling and Tissue Differentiation","description":"The top terms cluster around developmental processes across multiple tissues (ovarian follicle development, intestinal epithelial development, imaginal disc-derived leg segmentation, hypochord development) and regulatory signaling (positive regulation of Notch signaling), with related reproductive maturation in female meiosis. While a few terms (cell wall organization, O-glycan biosynthesis) are less directly developmental, they can relate to cellular differentiation processes. Overall, the set points to general developmental regulation and tissue differentiation.","confidence":"Medium","size":15,"edges":35,"triangles":21,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0001541","count":3},{"id":"GO:0045747","count":3},{"id":"GO:0007143","count":3},{"id":"GO:0032092","count":3}]},{"hash":"2009594128137794699","title":"Chloroplast/mitochondrial RNA editing and processing","description":"The top GO terms cluster around RNA modification and editing (cytidine to uridine) in chloroplasts and mitochondria, along with chloroplast RNA processing and chloroplast-nucleus signaling, suggesting a plant-specific set of organellar RNA editing/processing factors that may influence seed development. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":6},{"id":"GO:0016554","count":6},{"id":"GO:0080156","count":6},{"id":"GO:0000961","count":6},{"id":"GO:1905639","count":6}]},{"hash":"1451741096848881356","title":"Lipid catabolism and stress/detox responses","description":"This cluster is dominated by glycerolipid and fatty acid catabolic terms (triglyceride and monoacylglycerol catabolism, acyl-chain remodeling, phosphatidylserine catabolic) and lipid signaling regulation (endocannabinoid pathway), along with general stress and detox responses, indicating a cohesive lipid metabolism and cellular defense theme despite one outlier term.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":5},{"id":"GO:0019433","count":5},{"id":"GO:0085014","count":4},{"id":"GO:0006950","count":4},{"id":"GO:0052651","count":4}]},{"hash":"2036603477297192647","title":"Plant morphogenesis and nutrient transport","description":"These proteins show GO terms centered on plant development (organ boundary specification between lateral organs and the meristem; petal development; lateral root branching) together with transport and nutrient utilization processes (ammonium transport, nitrogen utilization, carbon dioxide transport). The inclusion of transcription-related terms (DNA-templated transcription and its regulation) suggests a regulatory program coordinating development and metabolic transport. Overall, they reflect a cohesive theme of plant organ development linked to nutrient transport/growth responses.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010199","count":2},{"id":"GO:0048441","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0006353","count":1},{"id":"GO:0006355","count":1}]},{"hash":"2276758385645399302","title":"Vascular Development and Regeneration Signaling","description":"The terms point to key signaling pathways (Wnt; activin/TGF-beta with SMAD links), endothelial development (tube morphogenesis; migration), and tissue regeneration (liver regeneration), indicating a common theme of signaling networks governing vascular formation and tissue regeneration. Some terms are broader cellular processes, but the core appears focused on vascular development and regenerative signaling.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032927","count":1},{"id":"GO:0016055","count":1},{"id":"GO:0043537","count":1},{"id":"GO:0006359","count":1},{"id":"GO:0051101","count":1}]},{"hash":"2173685880740956635","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"The Top Terms show a strong focus on oocyte maturation (GO:0001556), spindle assembly in female meiosis I (GO:0007057), and ubiquitin-proteasome\u2013dependent proteolysis (GO:0031146, GO:0046785), indicating meiotic progression and microtubule-based spindle organization in oocytes, with protein turnover as a regulatory mechanism. Some terms also reference neural tube and ventricle development, but the dominant signal is meiosis-related processes in oocytes, justifying this label.","confidence":"High","size":15,"edges":58,"triangles":67,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":15},{"id":"GO:0021678","count":15},{"id":"GO:0006516","count":15},{"id":"GO:0051436","count":15},{"id":"GO:0046785","count":15}]},{"hash":"351936235209226501","title":"Ubiquitin-dependent TNF/NF-kappaB signaling and apoptosis regulation","description":"This cluster is strongly characterized by ubiquitin-related processes (ubiquitin-dependent protein catabolic process, autoubiquitination, K63-linked ubiquitination) and TNF-mediated signaling with activation of NF-kappaB and regulation of apoptosis, plus links to immune-related processes like V(D)J recombination. Together these terms point to a cohesive module of ubiquitin-driven signaling and cell fate decisions in the immune context.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":12},{"id":"GO:0051865","count":10},{"id":"GO:0033209","count":9},{"id":"GO:0042981","count":9},{"id":"GO:0007250","count":9}]},{"hash":"1406589169206248303","title":"Retinoic acid metabolism in female reproductive development","description":"The top GO terms point strongly to retinoic acid metabolism (biosynthesis and catabolic processes) and to development of female reproductive structures (uterus, female gonad, and female genitalia). This pattern suggests a cluster of proteins involved in retinoic acid\u2013dependent signaling that governs female reproductive development. Some terms related to xenobiotic metabolism (carbazole, isoquinoline alkaloid) and calcitriol biosynthesis appear, which may reflect broader metabolic roles or annotation noise, but the core connection is retinoic acid metabolism linked to female reproductive development.","confidence":"High","size":15,"edges":32,"triangles":21,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0071615","count":13},{"id":"GO:0042904","count":13},{"id":"GO:0060065","count":13},{"id":"GO:0008585","count":13},{"id":"GO:0034653","count":13}]},{"hash":"575360718991146084","title":"Unknown","description":"The terms are a mix of reproductive development (placenta, uterus, prostate) with stress responses, immune signaling, senescence, and host-symbiont dormancy. There is no clear, single biological theme that cohesively explains all terms, so a reliable, specific label cannot be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001890","count":2},{"id":"GO:0085014","count":1},{"id":"GO:0006950","count":1},{"id":"GO:0060065","count":1},{"id":"GO:0030890","count":1}]},{"hash":"1210961390503715196","title":"Female reproductive development and retinoid/vitamin D metabolism","description":"This cluster is enriched for female reproductive development terms (uterus, female gonad, female genitalia) alongside retinoic acid and calcitriol biosynthesis/catabolism, suggesting a coordinated role in female reproductive development tied to retinoid and vitamin D signaling. While some terms point to xenobiotic metabolism, the core pattern points to reproductive development linked to retinoid/vitamin D pathways.","confidence":"Medium","size":15,"edges":11,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071615","count":12},{"id":"GO:0042904","count":12},{"id":"GO:0060065","count":12},{"id":"GO:0008585","count":12},{"id":"GO:0034653","count":12}]},{"hash":"1596394865565038373","title":"Lipid hormone biosynthesis in female development","description":"Reasoning: The cluster is dominated by prostaglandin biosynthesis, retinoic acid biosynthesis/catabolism, and calcitriol biosynthesis, alongside terms for uterus and female gonad development. This points to lipid-derived signaling molecules (lipid hormones) driving female reproductive development, with some additional metabolic terms that may reflect broader aromatic or steroid metabolism.","confidence":"High","size":15,"edges":11,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":15},{"id":"GO:0071615","count":14},{"id":"GO:0042904","count":14},{"id":"GO:0060065","count":14},{"id":"GO:0008585","count":14}]},{"hash":"2100949192614810304","title":"TGF-\u03b2/BMP Signaling Regulation","description":"The top GO terms cluster around BMP and TGF-\u03b2 signaling regulation, including negative regulation of BMP signaling, negative regulation of TGF-\u03b2 receptor signaling, cellular response to TGF-\u03b2, SMAD-related regulation, and peptidyl-threonine dephosphorylation, indicating a common function in modulating TGF-\u03b2/BMP pathway activity. Some terms about meristem identity and vacuole fusion are present but do not outweigh the strong signal of TGF-\u03b2/BMP pathway modulation.","confidence":"High","size":15,"edges":54,"triangles":79,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0030514","count":14},{"id":"GO:0042347","count":14},{"id":"GO:0061191","count":14},{"id":"GO:0000173","count":14},{"id":"GO:0046827","count":14}]},{"hash":"465218558788778599","title":"Pollen Tube Growth and Guidance","description":"Based on the prominent GO terms related to pollen tube growth and guidance, along with cell wall modification and pectin metabolism (pectin catabolic and mucilage pectin biosynthetic processes), the cluster appears to coordinate pollen tube elongation and navigation through wall remodeling and signaling. The presence of intracellular signal transduction and pollen tube guidance supports a coordinated growth and targeting function in the reproductive process.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0045490","count":2},{"id":"GO:0048358","count":2},{"id":"GO:0042545","count":2},{"id":"GO:0080092","count":2}]},{"hash":"2154969340683958893","title":"Plant cell wall remodeling and pollen development","description":"Top GO terms cluster around plant-specific processes: pectin and polysaccharide catabolism and cell wall organization, plus developmental terms like flower phyllotactic patterning and microsporogenesis. This suggests a theme of carbohydrate metabolism-driven cell wall remodeling during plant growth and reproductive development, with pollen formation and floral patterning as representative functions. Some entries are obsolete DNA repair terms and may reflect annotation noise.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":4},{"id":"GO:0060773","count":4},{"id":"GO:0071555","count":4},{"id":"GO:0042121","count":2},{"id":"GO:0009556","count":2}]},{"hash":"1996107201856043386","title":"Actin-driven organelle inheritance and cytokinesis","description":"The top GO terms are dominated by actin-related processes: vesicle transport along actin filaments, mitotic contractile ring actin filament bundle assembly and localization, budding apical growth, and inheritance of organelles such as mitochondria, vacuoles, and peroxisomes, plus brush border assembly. This suggests a cohesive theme of actin-based cytoskeleton organization coordinating organelle distribution and cell division/morphogenesis.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043388","count":2},{"id":"GO:1903477","count":2},{"id":"GO:0000011","count":2},{"id":"GO:0030050","count":2},{"id":"GO:0048496","count":2}]},{"hash":"1536830337357709605","title":"MVB-mediated protein turnover in cell division","description":"The terms show strong representation of multivesicular body (MVB) sorting and ubiquitin-dependent/independent protein catabolic processes via the MVB pathway, i.e., endosomal degradation of proteins. Additional terms concern mitotic exit, cell division, abscission, and apoptosis, suggesting the cluster links regulated protein turnover with cell cycle and cytokinesis. A concise label capturing this MVB-driven protein degradation during cell division best represents the cluster.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902188","count":2},{"id":"GO:0010458","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0009838","count":2}]},{"hash":"485640407132922601","title":"Unknown","description":"The top GO terms are spread across plant defense signaling, cardiac electrophysiology, RNA processing, membrane protein localization, NOD signaling, kinase regulation, neuroendocrine secretion, heart morphogenesis, thermoception, and spindle assembly, showing no single cohesive function for the cluster.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000031","count":2},{"id":"GO:1900827","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0072660","count":2},{"id":"GO:0070427","count":2}]},{"hash":"2186787581603044387","title":"Membrane Signaling and Lipid Metabolism","description":"The cluster is dominated by membrane- and signaling-related terms: cholesterol biosynthetic process, calcium ion import across the plasma membrane, vasopressin secretion, maintenance of protein localization in the plasma membrane, and related signaling pathways. While there are outliers (hemopoiesis, mRNA processing), the prevailing theme centers on membrane dynamics, lipid metabolism, and calcium-mediated signaling.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030097","count":2},{"id":"GO:0006695","count":2},{"id":"GO:0098703","count":2},{"id":"GO:2000031","count":1},{"id":"GO:1900827","count":1}]},{"hash":"1684183414250838686","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035269","count":2},{"id":"GO:0045948","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0000288","count":2},{"id":"GO:0031990","count":2}]},{"hash":"1800495982677803074","title":"Unknown","description":"The top GO terms are highly diverse (translation, nail development, pollen hydration, circadian rhythm, starch catabolism, etc.) and there are no shared edges or a unifying biological theme linking these proteins. With no coherent function tying the terms together, 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":[{"id":"GO:0006412","count":1},{"id":"GO:0035878","count":1},{"id":"GO:0001403","count":1},{"id":"GO:0007165","count":1},{"id":"GO:0006633","count":1}]},{"hash":"101165079786093765","title":"Proteasomal Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are focused on ubiquitin tagging and degradation via the proteasome (SCF-dependent ubiquitinylation, K48-linked ubiquitination, and general ubiquitin-dependent proteolysis), with an ERAD connection. This points to a core function of targeted protein degradation, consistent across the cluster, with a few outliers related to receptor turnover or growth regulation.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":6},{"id":"GO:0070936","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0038018","count":4}]},{"hash":"872267243760901099","title":"Fungal cell wall biosynthesis and remodeling","description":"The cluster includes multiple GO terms tied to fungal-type cell wall organization/assembly and beta-D-glucan biosynthesis, as well as catabolic processes for cellulose and pectin, indicating both construction and remodeling of fungal cell walls. The presence of a biofilm formation term suggests involvement in surface adherence and biofilm-related wall dynamics, making a cohesive theme around fungal cell wall metabolism and surface-associated growth.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":2},{"id":"GO:0000917","count":2},{"id":"GO:0006076","count":2},{"id":"GO:0031505","count":2},{"id":"GO:0071940","count":2}]},{"hash":"1217378043691423593","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010252","count":2},{"id":"GO:2000344","count":1},{"id":"GO:0007283","count":1},{"id":"GO:0045493","count":1},{"id":"GO:0016042","count":1}]},{"hash":"2029677351265721627","title":"Neural development signaling and craniofacial morphogenesis","description":"This cluster centers on neural development and craniofacial morphogenesis, highlighted by neurotrophin receptor signaling (TRK), optic nerve morphogenesis, and face development, with supporting growth/survival pathways such as FGFR-apoptotic signaling and PI3K/AKT, along with Wnt pathway regulation. While a few terms like response to alkaline pH or symbiont-mediated transformation are less directly connected, the dominant theme reflects neural crest\u2013related development and signaling.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":15},{"id":"GO:0090090","count":15},{"id":"GO:0020021","count":15},{"id":"GO:0071469","count":15},{"id":"GO:0060324","count":15}]},{"hash":"2175958885846969803","title":"Glutamatergic synaptic transmission","description":"The top GO terms point to neuronal signaling at glutamatergic synapses: glutamatergic synaptic transmission, excitatory postsynaptic potentials, and receptor clustering, plus related ion transport (Na+/K+ channels) that underpins excitability. While a few terms are more general (transcription, vacuole fusion), the core cluster theme centers on glutamatergic synapse function and excitatory signaling.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0008542","count":2}]},{"hash":"1847093408796617093","title":"Plant Hormone Biosynthesis and Stress Signaling","description":"The cluster shows multiple GO terms tied to plant hormone biology (salicylic acid signaling, ethylene and gibberellin biosynthesis, auxin catabolic processes) and stress responses (hydrogen peroxide\u2013mediated programmed cell death, regulation of proline transport) along with a flavonoid biosynthesis term (proanthocyanidin). Together these indicate a theme of hormone-regulated growth and defense signaling in plants; a single outlier term (penicillin biosynthesis) is likely noise.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009863","count":2},{"id":"GO:0009693","count":1},{"id":"GO:1902835","count":1},{"id":"GO:0042318","count":1},{"id":"GO:0055114","count":1}]},{"hash":"236805647695004281","title":"Cytoskeleton assembly and cell division","description":"Most frequent terms point to cytoskeletal organization and cell division (tubulin complex assembly, mitotic cell cycle, protein heterooligomerization) with related processes such as keratinization and Golgi localization, plus some brain-region development signals. The dominant theme across the cluster is cytoskeleton/matrix assembly and cell cycle progression.","confidence":"Medium","size":14,"edges":44,"triangles":51,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0007021","count":2},{"id":"GO:0003334","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0031424","count":2}]},{"hash":"470839757459992391","title":"Neurodevelopment and cell proliferation","description":"The cluster centers on core proliferative processes (DNA replication, mitotic cell cycle) while also emphasizing neural development features (optic nerve morphogenesis, face development) and neural signaling pathways (neurotrophin TRK signaling, Wnt regulatory influence). Other terms may be ancillary contexts, but the dominant theme ties neural development to cell proliferation.","confidence":"High","size":14,"edges":11,"triangles":7,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":12},{"id":"GO:2000251","count":11},{"id":"GO:0071333","count":11},{"id":"GO:0000278","count":11},{"id":"GO:0048011","count":10}]},{"hash":"1309528902105010139","title":"DNA Replication and Cell Cycle","description":"Dominant GO terms point to core DNA replication and cell cycle processes, including cell cycle progression, DNA replication, mitotic sister chromatid cohesion, and regulation of DNA-directed DNA polymerase activity. While a few terms touch on translation, collagen regulation, vesicle fusion, and Ras signaling, the strongest signals describe genome duplication and chromosome segregation, suggesting a cluster of proteins involved in DNA maintenance during cell division.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0035753","count":1},{"id":"GO:1900264","count":1}]},{"hash":"40146835251496734","title":"Regulated mRNA Splicing and Export","description":"The top GO terms cluster around mRNA processing and regulation, including positive/alternative splicing via the spliceosome and mRNA export from the nucleus, with additional signals related to polyadenylation regulation and ncRNA-mediated silencing. This suggests a cohesive theme of controlled mRNA maturation and trafficking rather than a single enzymatic activity. ","confidence":"Medium","size":14,"edges":14,"triangles":11,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":6},{"id":"GO:0031047","count":6},{"id":"GO:1900363","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0075525","count":5}]},{"hash":"1203390698243351298","title":"Plant Development and Hormone Signaling","description":"The cluster\u2019s GO terms center on transcriptional regulation and plant development (DNA-templated transcription; multicellular development; bract, seed, and floral meristem growth), anchored by abscisic acid signaling, with additional hints of auxin signaling and stress responses (cold acclimation, chitin response) and cutin biosynthesis. This combination suggests proteins involved in developmental programs modulated by plant hormones, with some overlap into stress and defense pathways, making a concise label reflecting plant development plus hormone signaling appropriate.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0009631","count":2},{"id":"GO:0010200","count":1}]},{"hash":"544625034549087636","title":"Oocyte maturation and meiotic spindle assembly","description":"This cluster is dominated by GO terms tied to female meiosis and oocyte maturation, including spindle assembly in meiosis I, microtubule polymerization, and processes involving ubiquitin-proteasome\u2013mediated protein degradation that regulate cell cycle progression. While a couple terms refer to broader developmental events, the strongest and most consistent signal is meiosis/oocyte maturation and the associated spindle dynamics, making this a concise and representative label.","confidence":"High","size":14,"edges":19,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":14},{"id":"GO:0006516","count":14},{"id":"GO:0008285","count":14},{"id":"GO:0007057","count":14},{"id":"GO:0051436","count":14}]},{"hash":"973347545625769841","title":"Plant floral meristem identity maintenance","description":"The cluster shows strong representation of GO terms for maintaining inflorescence and floral meristem identity, pointing to a role in floral development. DNA damage repair and cell cycle terms appear at lower counts, so the primary theme is floral meristem maintenance in plants.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009610","count":2},{"id":"GO:0010077","count":2},{"id":"GO:0010076","count":2},{"id":"GO:0010792","count":1},{"id":"GO:1990898","count":1}]},{"hash":"76807720438996013","title":"Nuclear RNA processing and cell cycle regulation","description":"It centers on nuclear RNA maturation and processing steps\u2014splicing regulation, ncRNA-mediated silencing, rRNA processing, poly(A) tail maturation and mRNA export\u2014and on mitotic processes such as spindle assembly and sister chromatid cohesion, plus DNA replication. Taken together, these terms point to a cohort of nuclear functions that couple RNA processing with genome replication and chromosome segregation. The viral genome replication term appears as a peripheral hint rather than a defining function.","confidence":"Medium","size":14,"edges":30,"triangles":22,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0000464","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0006406","count":3}]},{"hash":"2122942095363270406","title":"Ubiquitin-Proteasome Degradation and Antiviral Signaling","description":"Proteins in this cluster are dominated by ubiquitin-dependent proteolysis and proteasomal degradation (SCF pathway, K48-linked ubiquitination, ERAD) and immune signaling (TNF-mediated pathways, antiviral defense). The presence of peroxisome import and intracellular transport regulation terms suggests links to broader protein quality control and trafficking, but the central theme remains protein turnover coupled with antiviral/immune responses.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0031146","count":9},{"id":"GO:0016558","count":8},{"id":"GO:0030433","count":8},{"id":"GO:0051607","count":7},{"id":"GO:0051092","count":7}]},{"hash":"1656426204865321463","title":"Developmental signaling and mitotic cell cycle","description":"The GO terms point to developmental processes (ossification/bone maturation, multicellular and skin development) alongside fundamental cell-cycle steps (mitotic cell cycle, spindle assembly). The inclusion of small GTPase\u2013mediated signaling and its positive regulation suggests these proteins coordinate signaling with cell division during development, indicating a theme of developmentally linked cell-cycle regulation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043931","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0007264","count":4},{"id":"GO:0007275","count":4}]},{"hash":"295760787684039575","title":"TLR-NF-kB Innate Immunity","description":"The top GO terms center on innate immune signaling via Toll-like receptors (MyD88-dependent and TLR4), NF-kB pathway regulation, and defense against viruses and lipopolysaccharide. This suggests a cohesive function around TLR/NF-kB\u2013driven antiviral and inflammatory responses, with some peripheral terms (dendrite morphogenesis, neuron homeostasis) possibly reflecting broader cellular roles or cross-talk. Overall, the dominant theme is TLR/NF-kB\u2013mediated innate immunity.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0043123","count":14},{"id":"GO:0051607","count":13},{"id":"GO:0051092","count":13},{"id":"GO:0090073","count":13},{"id":"GO:0070050","count":13}]},{"hash":"1683288021559764474","title":"Chloroplast and mitochondrial transcription and ribosome biogenesis","description":"The cluster shows strong enrichment for organellar gene expression: chloroplast/plastid and mitochondrial transcription, mitochondrial ribosome assembly, and chloroplast organization, plus photosynthesis-related terms. These points converge on regulation and execution of organellar gene expression and biogenesis, with some RNA processing terms that can occur in organelles. The presence of an outlier like cell wall organization is peripheral but does not overwhelm the central theme.","confidence":"Medium","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0009658","count":2},{"id":"GO:0042794","count":2},{"id":"GO:0061668","count":2},{"id":"GO:0006393","count":2}]},{"hash":"57941621101559997","title":"Unknown","description":"The GO terms show a mix of photosynthesis, lipopolysaccharide biosynthesis, various ion transports, membrane-related processes, and signaling responses (pheromone, testosterone), spanning diverse organisms and functions. There is no single coherent function linking these proteins, so a specific label isn\u2019t justifiable.","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0070574","count":3},{"id":"GO:1990938","count":3},{"id":"GO:0033292","count":3}]},{"hash":"1979360669424347280","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":49,"triangles":51,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":7},{"id":"GO:0090617","count":7},{"id":"GO:0080156","count":7},{"id":"GO:0000961","count":7},{"id":"GO:0009793","count":7}]},{"hash":"1465403751916260419","title":"Chloroplast RNA editing and processing","description":"Dominant pattern is chloroplast RNA metabolism: chloroplast RNA modification, chloroplast RNA processing, and C-to-U RNA editing, with related chloroplast-nucleus signaling. Some mitochondrial RNA regulation terms appear but do not outweigh the chloroplast-focused terms. Thus label reflects chloroplast RNA editing and processing.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:1903026","count":2},{"id":"GO:0009451","count":2},{"id":"GO:1905639","count":2},{"id":"GO:0080156","count":2}]},{"hash":"1423638142056069391","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0006605","count":3},{"id":"GO:0017038","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0098789","count":3}]},{"hash":"142100831337934294","title":"Amino acid metabolism and central metabolism","description":"The top GO terms are dominated by amino acid biosynthesis/catabolism (L-serine, L-threonine, L-cysteine), transsulfuration, and related intermediates like 2-oxobutyrate, alongside the TCA cycle. This suggests the cluster centers on core metabolic processes with a focus on amino acid pathways, with a broader transcription term appearing less cohesively. Confidence: Medium","confidence":"","size":14,"edges":82,"triangles":274,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006099","count":4},{"id":"GO:0018871","count":3},{"id":"GO:0046360","count":3},{"id":"GO:0043418","count":3}]},{"hash":"1836093391301002411","title":"Lipid Hormone Biosynthesis and Female Reproductive Development","description":"The top GO terms point to biosynthesis of lipid-derived signaling molecules (prostaglandins, retinoic acid, calcitriol) and to female reproductive development (uterus and gonad development), suggesting a cluster of proteins involved in lipid hormone production linked to reproductive tissue processes. Some terms (alkaloid metabolism) may be incidental noise, but the core theme is lipid/hormone biosynthesis with reproductive context.","confidence":"Medium","size":14,"edges":39,"triangles":45,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":10},{"id":"GO:0071615","count":9},{"id":"GO:0042904","count":9},{"id":"GO:0060065","count":9},{"id":"GO:0008585","count":9}]},{"hash":"1078408371615676118","title":"Diverse metabolite and cofactor biosynthesis","description":"The top GO terms span biosynthetic pathways for vitamins (biotin, thiamine), pigments/retinoids (retinal, retinol), steroids (testosterone, androgen), porphyrin/heme precursor, and antibiotics. This cluster seems enriched for proteins involved in the synthesis of various metabolites and cofactors rather than a single pathway. Therefore, a concise label covering multiple biosynthetic processes fits best.","confidence":"High","size":14,"edges":41,"triangles":49,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0006782","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0019878","count":3},{"id":"GO:0009228","count":3}]},{"hash":"370125496498154169","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0090617","count":1},{"id":"GO:0001889","count":1},{"id":"GO:0009451","count":1}]},{"hash":"706515302350108066","title":"Metal Ion Transport and Antigen Processing","description":"The top terms point to transmembrane transport of various metal ions (cadmium, iron, nitrite, arginine) and iron homeostasis, suggesting a core function in ion transport and metal balance. Immune-related terms (MHC class II biosynthesis, dendritic cell antigen presentation, interleukin-3 production) appear as secondary annotations, implying a possible link to antigen-presenting cell activity. Overall, metal ion transport/homeostasis is the strongest theme with immune processing as a secondary association, so the label Metal Ion Transport and Antigen Processing is appropriate.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":2},{"id":"GO:0002606","count":2},{"id":"GO:0015707","count":2},{"id":"GO:0043091","count":2},{"id":"GO:0060586","count":2}]},{"hash":"433003409573617689","title":"Spliceosome-Driven mRNA Processing","description":"This cluster is dominated by GO terms related to mRNA splicing by the spliceosome (including regulation and alternative splicing), mRNA processing steps such as export from the nucleus and polyadenylation regulation, and links to translation reinitiation and ncRNA-mediated gene silencing, pointing to a coherent role in RNA maturation and post-transcriptional regulation.","confidence":"High","size":14,"edges":38,"triangles":45,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:1900363","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0075525","count":3}]},{"hash":"1366937559826804997","title":"Ribosome biogenesis and translation","description":"Based on the GO terms, the cluster is dominated by processes tied to ribosome assembly, cytoplasmic translation, and SRP-dependent cotranslational targeting to the membrane, pointing to components of the protein synthesis machinery. A few terms reflect stress or pollen-related processes, but the core signal is clearly translation/ ribosome biogenesis, supporting a concise label around ribosome function.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006614","count":1},{"id":"GO:0071353","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0032147","count":1}]},{"hash":"874004819780748757","title":"Spliceosome-Driven mRNA Processing and Export","description":"Top terms reveal a strong emphasis on post-transcriptional RNA processing: mRNA splicing via the spliceosome (including alternative splicing), mRNA export, regulation of mRNA stability under stress, and polyadenylation; plus related translation reinitiation steps. This points to a cohesive cluster of proteins involved in mRNA maturation, processing, and export.","confidence":"High","size":14,"edges":61,"triangles":176,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":9},{"id":"GO:0006378","count":8},{"id":"GO:0045292","count":8},{"id":"GO:1900363","count":6},{"id":"GO:0002188","count":6}]},{"hash":"1024304806005783857","title":"Chromatin remodeling and RNA processing","description":"These proteins show a theme around nuclear chromatin dynamics (chromatin remodeling, nucleosome positioning, DNA topology changes) and RNA metabolism (regulatory ncRNA silencing, snoRNA processing, splicing regulation, protein targeting to RNAs), suggesting a cohesive role in chromatin regulation linked with RNA processing and expression control.","confidence":"Medium","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":14},{"id":"GO:0048026","count":14},{"id":"GO:0006265","count":12},{"id":"GO:0016584","count":12},{"id":"GO:1990417","count":12}]},{"hash":"91139004387384688","title":"Mitochondrial Metabolite Transport and Energy Regulation","description":"The cluster is strongly characterized by GO terms for transmembrane transport of metabolites into mitochondria (citrate, ornithine, CoA) and the malate-aspartate shuttle, indicating mitochondrial carrier activity and energy metabolism. Additional terms reference nutrient signaling and cellular responses to insulin/IGF, fatty acids, and amino acid starvation, suggesting coordinated metabolic regulation centered on mitochondrial transport and utilization.","confidence":"High","size":14,"edges":37,"triangles":33,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0061179","count":13},{"id":"GO:1990314","count":12},{"id":"GO:0070542","count":12},{"id":"GO:0048250","count":12},{"id":"GO:0034198","count":12}]},{"hash":"752011216611387181","title":"Developmental Processes with Neural Signaling","description":"The cluster\u2019s top GO terms cover multicellular development, angiogenesis, Schwann cell development, myoblast fusion, visual perception, and synaptic activity (long-term potentiation and excitatory postsynaptic potential), pointing to a broad developmental program with emphasis on neural differentiation and synaptic function. The inclusion of an ABA-signaling term likely reflects cross-ontology noise rather than a cohesive plant-specific pathway, so the core theme remains animal development and neural signaling. Overall, these terms coherently suggest developmental processes with neural maturation and synaptic activity.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":5},{"id":"GO:0001525","count":5},{"id":"GO:0009738","count":5},{"id":"GO:0007601","count":5},{"id":"GO:0060079","count":5}]},{"hash":"1885487005107685696","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":8},{"id":"GO:0000398","count":7},{"id":"GO:0002188","count":7},{"id":"GO:0000480","count":5},{"id":"GO:0042273","count":5}]},{"hash":"1376209743129637465","title":"Biosynthesis and Metabolic Processes","description":"This cluster centers on a variety of biosynthetic and metabolic pathways, including fatty acid and glucose metabolism, lipoteichoic acid and other lipid-related biosynthesis, and secondary metabolite (anthocyanin) biosynthesis, plus antibiotic metabolism. The shared theme is enzymes and proteins involved in generating diverse biomolecules and fundamental metabolism, rather than a single specific pathway. Confidence: Medium","confidence":"","size":14,"edges":27,"triangles":21,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009718","count":4},{"id":"GO:0070395","count":3},{"id":"GO:0030259","count":3},{"id":"GO:0016999","count":3}]},{"hash":"488699944526784959","title":"Central carbon metabolism","description":"This cluster is strongly enriched for core energy pathways: glycolysis, TCA cycle, gluconeogenesis, and the pentose phosphate shunt, with additional associations to related carbon metabolism and thiamine biosynthesis. These terms together point to a cohesive theme of central carbon metabolism and energy production, with some nonessential (obsolete) annotations. Confidence: High","confidence":"","size":14,"edges":63,"triangles":138,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":7},{"id":"GO:0006096","count":6},{"id":"GO:0006094","count":5},{"id":"GO:0051289","count":5},{"id":"GO:0055114","count":5}]},{"hash":"52545693555383813","title":"Neural and muscular developmental transcriptional regulation","description":"This cluster combines terms tied to transcriptional control (RNA polymerase II), muscle morphogenesis and cardioblast migration, and neural differentiation (subpallium neuron fate, amacrine cell differentiation, astrocyte regulation) with integrin-mediated adhesion and circadian regulation of gene expression, suggesting a theme of coordinated transcriptional programs governing development in neural and muscular lineages rather than a single tissue-specific process.","confidence":"Medium","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":9},{"id":"GO:0060415","count":7},{"id":"GO:0060163","count":7},{"id":"GO:0033627","count":7},{"id":"GO:0032922","count":7}]},{"hash":"1702133723002398410","title":"Neural and vascular development","description":"This cluster is enriched for angiogenesis, heart development, axonogenesis, and Schwann cell development, which point to neural and cardiovascular differentiation processes. Additional terms related to cell cycle progression and apoptosis reflect growth control during development. One term appears plant-specific or noisy, but the overall theme centers on tissue development and differentiation in neural/vascular contexts.","confidence":"Medium","size":14,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001525","count":13},{"id":"GO:0046827","count":13},{"id":"GO:0009738","count":13},{"id":"GO:0000086","count":13},{"id":"GO:0043065","count":13}]},{"hash":"1023938890806387362","title":"Epigenetic Regulation of Development","description":"Dominated by chromatin modification and transcriptional control (histone H3 acetylation, CENP-A chromatin assembly) alongside various developmental processes (brain development, osteoblast differentiation, male gonad development, fertilization, organismal growth). This pattern suggests a cluster of proteins involved in epigenetic regulation that drives developmental programs. A few terms (defense response) are less central to the main theme but do not override the core epigenetic-development link.","confidence":"High","size":14,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043966","count":7},{"id":"GO:0000122","count":6},{"id":"GO:0007338","count":6},{"id":"GO:0035264","count":6},{"id":"GO:0008584","count":6}]},{"hash":"1928833562042471736","title":"Multi-substrate membrane transporters","description":"This cluster is driven by a set of GO terms describing transmembrane transport of diverse substrates (xenobiotics, vitamins, ions, sugars, nitrite) and related cellular responses (osmotic stress, insulin-stimulated glucose import, fructose response). The common theme is membrane transporter activity with broad substrate specificity, indicating a cohesive group of transporter proteins rather than a single substrate type. ","confidence":"High","size":14,"edges":46,"triangles":53,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":14},{"id":"GO:0035461","count":14},{"id":"GO:0042908","count":12},{"id":"GO:0071805","count":12},{"id":"GO:0042891","count":12}]},{"hash":"129335693390494592","title":"Plant defense signaling and nitrogen metabolism","description":"The cluster centers on plant-like defense signaling (defense response to fungus and calcium-mediated signaling) integrated with nitrogen metabolism (ureide catabolism, allantoin assimilation, purine and arginine biosynthesis). While a few terms (like lipid transport) are less connected, the strongest signals point to immune signaling coupled with nitrogen mobilization and metabolism. Overall, a coherent theme of plant defense linked to nitrogen processing best describes the set.","confidence":"Medium","size":14,"edges":16,"triangles":3,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0010136","count":2},{"id":"GO:0010951","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0006869","count":2},{"id":"GO:0019722","count":2}]},{"hash":"1512346459519091137","title":"Diverse Lipid and Cofactor Biosynthesis","description":"The top GO terms point to multiple biosynthetic processes across lipids, cofactors, and related metabolites (poly-hydroxybutyrate, mycolic acid, tetrahydrobiopterin, phylloquinone, retinal, and steroid-related metabolism), with additional references to antibiotic biosynthesis and response pathways. This pattern suggests a cluster whose proteins participate in a variety of biosynthetic and metabolic steps rather than a single, cohesive function, best captured by a broad label like diverse lipid and cofactor biosynthesis.","confidence":"Medium","size":14,"edges":24,"triangles":8,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":13},{"id":"GO:0042619","count":13},{"id":"GO:0017000","count":13},{"id":"GO:0031427","count":12},{"id":"GO:0006710","count":12}]},{"hash":"127200653659284380","title":"Plant hormone biosynthesis and fruit ripening","description":"This cluster is dominated by GO terms for plant hormone biosynthesis (ethylene, gibberellin, auxin) and the ripening process, with additional links to secondary metabolite biosynthesis and stress-related responses. The co-occurrence of multiple hormone-related biosynthesis terms and fruit ripening points to a cohesive hormone-regulated fruit development module.","confidence":"High","size":14,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009693","count":14},{"id":"GO:0042318","count":14},{"id":"GO:0055114","count":14},{"id":"GO:0009686","count":14},{"id":"GO:0045487","count":14}]},{"hash":"46393240250915067","title":"Floral Meristem Development and Wax Biosynthesis Regulation","description":"This cluster centers on plant developmental regulation, with GO terms emphasizing floral/meristem growth (bract development, seed development, regulation of DNA-templated transcription, ethylene signaling) and epidermal lipid metabolism (positive regulation of cutin biosynthesis, wax biosynthesis regulation). The combination suggests a cohesive module of transcriptional regulators and signaling components coordinating floral meristem activity with cuticle-related lipid remodeling, rather than a random assortment. A defense term (response to chitin) may reflect broader plant stress links but does not dominate the theme. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0010200","count":3},{"id":"GO:0010432","count":3},{"id":"GO:0048316","count":3},{"id":"GO:0060774","count":3}]},{"hash":"1150706495625547506","title":"Prostaglandin, retinoid, and vitamin D metabolism","description":"These proteins cluster around lipid-derived hormone pathways: prostaglandin biosynthesis, retinoic acid biosynthesis/catabolism, and calcitriol (vitamin D) biosynthesis, with supporting signals of detoxification and reproductive development (uterus and female gonad development). The overlap suggests a functional group focused on lipid signaling molecules and their metabolic regulation, potentially impacting reproductive development. Some terms (detoxification, aromatic compound metabolism) reflect broader xenobiotic processing common to metabolic enzymes. Overall, a coherent theme of lipid hormone production and turnover linked to development emerges. ","confidence":"Medium","size":14,"edges":50,"triangles":91,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":5},{"id":"GO:0098869","count":4},{"id":"GO:0071615","count":4},{"id":"GO:0042904","count":4},{"id":"GO:0060065","count":4}]},{"hash":"1974411601957863283","title":"Neuronal morphogenesis and synaptic function","description":"The top terms converge on neural development and synaptic activity, including branching morphogenesis of nerves, postsynaptic density assembly, and regulation of synaptic transmission. Additional terms point to corpus callosum development and trans-synaptic signaling, with related adhesion and lipid signaling pathways. Taken together, the cluster appears to represent neuronal wiring and synaptic communication.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048755","count":1},{"id":"GO:0051835","count":1},{"id":"GO:0097107","count":1},{"id":"GO:0033628","count":1},{"id":"GO:0022038","count":1}]},{"hash":"680963014922602180","title":"Unknown","description":"GO terms are highly diverse: photosynthesis and carbon fixation related terms co-occur with meiotic chromatid cohesion and Golgi nucleotide-sugar transport. The lack of a single cohesive function or pathway, and no network connectivity (edges/triangles=0), suggests no unified theme tying these proteins together.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051754","count":2},{"id":"GO:0006196","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0019509","count":1},{"id":"GO:0019253","count":1}]},{"hash":"1315470178989090567","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034063","count":1},{"id":"GO:0061157","count":1},{"id":"GO:1902039","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000288","count":1}]},{"hash":"428754474288285222","title":"Transcription and Translation Core with Ribosome Biogenesis","description":"This cluster centers on core gene expression processes: transcription by RNA polymerase II and III, transcription elongation and termination, RNA-templated transcription, ribosome biogenesis, and translation initiation/translation. The convergence on transcription-to-translation machinery and ribosome assembly suggests these proteins collectively form the gene expression core from transcription through ribosome assembly.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006354","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0070893","count":1}]},{"hash":"398410157357678465","title":"Unknown","description":"The top terms span a wide range of unrelated physiological processes (aging, muscle contraction, digestion development, leukocyte migration, erythrocyte and energy homeostasis, B cell proliferation, penile erection, mucus secretion), with no clear shared pathway or cellular context. The absence of edges/triangles suggests little convergent interaction within the cluster, making a cohesive functional label inappropriate; GO:0007568 is obsolete, further indicating noisy or diverse annotations. Confidence: None.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:0006157","count":2},{"id":"GO:0045987","count":2},{"id":"GO:0048566","count":2},{"id":"GO:0002686","count":2}]},{"hash":"709923750467733606","title":"DNA replication and repair machinery","description":"The cluster shows strong representation of DNA replication (GO:0006260), base-excision repair (GO:0006284), replication-born DSB repair via sister chromatid exchange (GO:1990414), and meiotic cell cycle (GO:0051321), plus translesion synthesis and somatic hypermutation signals, all pointing to genome maintenance and repair processes during replication and recombination. Some terms appear obsolete or noise (e.g., memory), but the core theme is genome integrity. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035753","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1990414","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0090502","count":2}]},{"hash":"469969929670819459","title":"Female reproductive development and retinoic acid metabolism","description":"This cluster shows strong representation of female reproductive development terms (uterus, female gonad, female genitalia) and retinoic acid biosynthesis/catabolic processes, suggesting a theme around retinoid signaling in female reproductive development, with some auxiliary xenobiotic metabolism terms.","confidence":"Medium","size":14,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0071615","count":5},{"id":"GO:0042904","count":5},{"id":"GO:0060065","count":5},{"id":"GO:0008585","count":5},{"id":"GO:0034653","count":5}]},{"hash":"1899465158394821311","title":"Unknown","description":"This cluster shows a mix of disparate GO terms spanning transcription and chromatin regulation (DNA-templated transcription, histone methylation), nuclear transport (nuclear pore localization), and several developmental and cellular processes (forebrain/retina development, peroxisome targeting, fertilization, actin dynamics, SREBP signaling). The lack of a clear, cohesive functional theme across proteins suggests no single interpretable function for the cluster, so it is best labeled Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:2001162","count":5},{"id":"GO:0006625","count":5},{"id":"GO:0030900","count":5},{"id":"GO:0030042","count":5}]},{"hash":"711868857349818526","title":"Metabolic and Synaptic Signaling","description":"The top GO terms point to several metabolic/catabolic processes (nicotine, cellulose, glycolysis, nitrate assimilation, raffinose biosynthesis) alongside neuronal/synaptic functions (acetylcholine catabolic process in the synaptic cleft, synaptic transmission regulation, glutamatergic signaling, dendritic spine morphogenesis). This suggests a cluster that spans both metabolism and neuronal signaling, rather than a single cohesive function. Therefore, a label that captures both domains is appropriate.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019608","count":3},{"id":"GO:0030245","count":3},{"id":"GO:0018013","count":3},{"id":"GO:0006096","count":2},{"id":"GO:0042128","count":2}]},{"hash":"898448174387866104","title":"Neural development and growth factor signaling","description":"The top GO terms cluster around neural development and growth factor pathways (neurotrophin TRK receptor signaling, optic nerve morphogenesis, face development, and FGFR apoptotic signaling, plus regulation of Wnt signaling), suggesting a developmental, neurobiologically oriented module. Some terms reflect broader stress or immune responses (response to toxic substances, alkaline pH, defense against virus) that are less central. The lack of edges implies these proteins share these annotations but do not form a tight interaction network in this dataset.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":14},{"id":"GO:0090090","count":14},{"id":"GO:0020021","count":14},{"id":"GO:0071469","count":14},{"id":"GO:0051607","count":14}]},{"hash":"470194589823440421","title":"Developmental Signaling and Cell Fate Regulation","description":"This cluster centers on developmental and growth-control signaling: forebrain development, hippo signaling, Wnt pathway regulation (both positive and negative), neurotrophin signaling, and differentiation processes like keratinocyte differentiation, plus apoptosis. Together, these terms point to networks governing tissue growth, neural development, and cell fate decisions. Some terms are peripheral, but the dominant theme is developmental signaling and cell proliferation/differentiation balance.","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030900","count":14},{"id":"GO:0060044","count":14},{"id":"GO:0035329","count":14},{"id":"GO:0030216","count":14},{"id":"GO:0090263","count":14}]},{"hash":"720369005152191492","title":"Neurodevelopmental signaling","description":"The top GO terms cluster around neural development and signaling: neurotrophin TRK receptor signaling, optic nerve morphogenesis, and face development hint at neural and craniofacial patterning, while PI3K/AKT and FGFR-related signaling and Wnt regulation reinforce a theme of neuronal growth and receptor-mediated pathways. A few terms (e.g., symbiont-mediated transformation, alkaline pH response) are less directly related but do not override the dominant neural-development signal.","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":13},{"id":"GO:0090090","count":13},{"id":"GO:0020021","count":13},{"id":"GO:0071469","count":13},{"id":"GO:0060324","count":13}]},{"hash":"1603741969433051600","title":"Cadmium Detoxification and Zinc Ion Homeostasis","description":"The top GO terms are dominated by cadmium detoxification and zinc ion handling, including cadmium ion transmembrane transport, intracellular zinc ion homeostasis, zinc ion transmembrane transport, and response to zinc ion, with related terms like zinc sequestration and negative regulation of zinc import. This pattern points to a cohesive metal ion detoxification/maintenance module focused on cadmium and zinc rather than unrelated processes.","confidence":"High","size":14,"edges":26,"triangles":14,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0098849","count":7},{"id":"GO:0070574","count":7},{"id":"GO:0006876","count":7},{"id":"GO:0061090","count":7},{"id":"GO:0032119","count":7}]},{"hash":"844483571280387350","title":"Neurodevelopmental Growth Factor Signaling","description":"This cluster is dominated by neural development and growth-factor\u2013mediated signaling terms: neurotrophin TRK receptor signaling, FGFR apoptotic signaling, PI3K/AKT signaling, optic nerve morphogenesis, and face development, suggesting a shared role in neural differentiation, survival, and morphogenesis driven by growth factor pathways. Negative regulation of Wnt signaling also fits into developmental regulation, while other terms like response to toxic substances or alkaline pH appear as broader cellular responses that may accompany development. Overall, the theme centers on neural development and growth factor signaling networks.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":13},{"id":"GO:0090090","count":13},{"id":"GO:0020021","count":13},{"id":"GO:0071469","count":13},{"id":"GO:0060324","count":13}]},{"hash":"1422845648504022170","title":"Neural and Visual Development","description":"The top GO terms cluster around brain development, forebrain development, and retina development, suggesting the proteins share roles in neural and eye formation. Additional terms point to general cellular processes, but the dominant signal is neural/visual development, supporting a label focused on brain and eye formation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:2001162","count":3},{"id":"GO:0006625","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0030042","count":3}]},{"hash":"1479312751742056414","title":"RNA Splicing, Processing, and mRNA Export","description":"The terms point to mRNA maturation (cis/alternative splicing, polyadenylation), mRNA export, and related nuclear transport, with a minor note of translation reinitiation and occasional noise.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:1901407","count":2},{"id":"GO:1900363","count":1},{"id":"GO:0002188","count":1}]},{"hash":"1433311091566915585","title":"Lipid catabolism and endocannabinoid signaling","description":"Most of the top GO terms describe lipid metabolism and signaling: monoacylglycerol and triglyceride catabolic processes, phosphatidylserine catabolism, epoxygenase P450 pathway, and regulation of endocannabinoid signaling. There is also a neural signaling angle (excitatory postsynaptic potential, response to morphine) consistent with endocannabinoid modulation of synaptic transmission. Some terms (secondary shoot formation, alkaloid metabolism, lymphangiogenesis) are plant/lymph-related and likely annotation noise. Overall, the cluster seems tied together by lipid-based signaling and metabolism, especially endocannabinoid pathways.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010223","count":3},{"id":"GO:0009820","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0043278","count":3},{"id":"GO:0001946","count":3}]},{"hash":"2166451356029437060","title":"Epigenetic Chromatin Modification and Nucleosome Assembly","description":"The top GO terms are dominated by histone modification (H3K4/H3K27 methylation) and nucleosome assembly, pointing to chromatin regulation as the core theme of this cluster. While angiogenesis and immune tolerance terms appear, the strongest signal centers on epigenetic machinery and chromatin dynamics, justifying this label.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":3},{"id":"GO:2000791","count":2},{"id":"GO:0044648","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0002458","count":2}]},{"hash":"537746814809673066","title":"Metal ion transport and homeostasis","description":"The cluster is dominated by GO terms related to transport and detoxification of multiple metal ions (copper, zinc, iron, mercury, cadmium) and intracellular metal homeostasis (e.g., copper export, copper homeostasis, regulation of iron transport, mercury detoxification). This suggests a cohesive functional module focused on metal ion handling and oxidative stress response; the occasional DNA-templated transcription term likely reflects regulatory proteins in the same cluster rather than a central function. High","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0070574","count":1},{"id":"GO:0050787","count":1},{"id":"GO:0015680","count":1},{"id":"GO:0015694","count":1}]},{"hash":"783548030442601813","title":"Plant pectin metabolism and pollen tube growth","description":"This cluster is enriched for pectin-related processes (pectin catabolic process; mucilage pectin biosynthetic process) and cell wall modification, plus pollen tube growth, pointing to plant-specific wall remodeling that supports pollen tube elongation and mucilage production. Other terms indicate regulatory mechanisms (negative regulation of catalytic activity; negative regulation of endopeptidase activity) and associated processes like lipid transport and defense responses to fungi, consistent with coordinated remodeling during reproduction and defense readiness.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045736","count":2},{"id":"GO:0045490","count":2},{"id":"GO:0048358","count":2},{"id":"GO:0009860","count":2},{"id":"GO:0043086","count":2}]},{"hash":"19134968262704722","title":"Plant organellar RNA editing and processing","description":"This cluster is strongly enriched for RNA modification and processing terms in plant organelles, especially chloroplast and mitochondrial RNA editing (cytidine to uridine editing; mitochondrial and chloroplast RNA processing), plus chloroplast-nucleus signaling, with one seed dormancy development term aligning to plant development tied to organelle function.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":10},{"id":"GO:0016554","count":10},{"id":"GO:0080156","count":10},{"id":"GO:0000961","count":10},{"id":"GO:1905639","count":10}]},{"hash":"1874996538850227174","title":"Actin-Driven Polarity and Vesicle Trafficking","description":"The listed GO terms center on podosome assembly, microvillus assembly, intralumenal vesicle formation, and pinocytosis, plus regulation of cell polarity and centrosome localization. This points to a common theme of actin cytoskeleton remodeling and polarized membrane trafficking that supports adhesion structures and vesicle dynamics. Development-related terms like bone and adipose development are present but likely incidental to this cluster.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071800","count":1},{"id":"GO:1904179","count":1},{"id":"GO:0071539","count":1},{"id":"GO:0032534","count":1},{"id":"GO:0048310","count":1}]},{"hash":"530598157567114556","title":"Plant Development and Autophagy","description":"The GO terms predominantly point to plant developmental processes\u2014meristem development, somatic embryogenesis, abaxial cell fate specification, longitudinal axis specification, and flower development\u2014indicating a plant-development center. Autophagy-related terms (autophagosome assembly, aggrephagy) suggest cellular remodeling linked to development, while meiosis I and meiotic cell cycle reflect reproductive transitions. Overall, the cluster represents plant developmental biology with an autophagy-related facet.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000045","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0007127","count":1},{"id":"GO:0035973","count":1},{"id":"GO:0051321","count":1}]},{"hash":"2039895267400032461","title":"Oocyte maturation and meiotic spindle","description":"This cluster is dominated by terms tied to oocyte maturation and meiosis I spindle assembly (GO:0001556, GO:0007057) and microtubule dynamics (GO:0046785), with supportive involvement of ubiquitin-mediated protein degradation (GO:0031146) that governs cell-cycle progression during meiosis. Some neural-development terms seem less connected to the core meiotic theme, likely incidental. ","confidence":"High","size":13,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0001556","count":7},{"id":"GO:0006516","count":7},{"id":"GO:0008285","count":7},{"id":"GO:0007057","count":7}]},{"hash":"1441403435322221168","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is enriched for ubiquitination and ubiquitin-dependent proteolysis, with multiple terms for K48-/K11-/K6-linked ubiquitination and ubiquitin-dependent protein catabolic process, implying proteasome-mediated protein turnover as the core function. Some associated terms (histone catabolic process, neuron maturation, TNF signaling, exosomal regulation, mitochondrial fission) may reflect broader roles of ubiquitination in chromatin, development, and organelle dynamics.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0070936","count":10},{"id":"GO:0085020","count":10},{"id":"GO:1903265","count":10},{"id":"GO:0051865","count":10}]},{"hash":"49530793003659932","title":"Organelle RNA Editing and Processing","description":"The GO terms are dominated by RNA modification and processing in mitochondria and chloroplasts (cytidine to uridine editing; mitochondrial and chloroplast mRNA modification/processing) and chloroplast-nucleus signaling, suggesting a cohesive role in organellar RNA maturation and inter-organelle communication. A minor subset about ubiquitination appears, but the core theme centers on organellar RNA handling.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0000961","count":2}]},{"hash":"817789358421237387","title":"Organelle RNA Editing and Processing","description":"The cluster shows enrichment for RNA modification and editing in mitochondria and chloroplasts (cytidine to uridine editing; chloroplast RNA processing/modification; mitochondrial mRNA modification), and chloroplast-nucleus signaling, pointing to coordinated RNA maturation within organelles and cross-talk with the nucleus. While there are also terms for cytosolic ribosome assembly and transcription regulation, the core signal is organelle RNA editing/processing.","confidence":"High","size":13,"edges":77,"triangles":275,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0042256","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2}]},{"hash":"1852952269990844843","title":"Neural signaling and development","description":"The cluster centers on neural-related signaling and development, highlighted by neurotrophin TRK receptor signaling, JNK cascade regulation, and multicellular development terms. Additional enrichment in response to cocaine and translation/proteasomal regulation suggests coordinated control of signaling and protein homeostasis during neural development and responses to stimuli. Some terms (telomere maintenance, symbiont-related host interactions) are broader, but the overall pattern points to neural signaling and developmental regulation.","confidence":"Medium","size":13,"edges":69,"triangles":205,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032436","count":6},{"id":"GO:0042220","count":5},{"id":"GO:0051973","count":5},{"id":"GO:0032212","count":5},{"id":"GO:0046330","count":4}]},{"hash":"355481975546788893","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":5},{"id":"GO:0080156","count":5},{"id":"GO:0000961","count":5},{"id":"GO:1905639","count":5},{"id":"GO:1900865","count":5}]},{"hash":"606851929303072824","title":"Organelle RNA editing and processing","description":"This cluster centers on RNA metabolism in organelles, with strong representation of chloroplast and mitochondrial RNA modification, editing (C-to-U), and processing, plus related translation in organelles and organelle-nucleus signaling. The terms consistently point to organelle RNA maturation and regulation, justifying a focused label on organelle RNA editing/processing.","confidence":"High","size":13,"edges":43,"triangles":54,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0000961","count":3}]},{"hash":"1528969563090402409","title":"mRNA Splicing and Translation Initiation","description":"This cluster centers on mRNA processing and translation readiness, as evidenced by multiple GO terms for spliceosome-mediated splicing, mRNA export, and formation of translation preinitiation complexes, as well as translation reinitiation. The co-occurrence of splicing and translation initiation terms suggests proteins coordinating mRNA maturation with translation control.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1900363","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0075525","count":5},{"id":"GO:0006378","count":5},{"id":"GO:0006406","count":5}]},{"hash":"994965765404407581","title":"Organelle RNA editing and processing (mitochondria & chloroplasts)","description":"These terms cluster around organellar RNA metabolism in plants: mitochondrial ribosome assembly, mitochondrial mRNA processing, and RNA modification, including cytidine-to-uridine editing, along with chloroplast RNA modification/processing and chloroplast-nucleus signaling. The shared pattern suggests a module of proteins that regulate post-transcriptional maturation and editing of mitochondrial and chloroplast transcripts.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061668","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0000961","count":2}]},{"hash":"1618859241286690571","title":"RNA and protein methyltransferases","description":"This cluster is strongly enriched for methylation-related GO terms, including tRNA methylation, rRNA methylation/ modification, tRNA wobble uridine modification, and peptidyl-lysine methylation (mono- and di-). While a few biosynthetic terms (cobalamin, menaquinone, chlorophyll) appear, the dominant signal points to enzymes that transfer methyl groups to RNA and to lysine residues on proteins.","confidence":"High","size":13,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0018026","count":3},{"id":"GO:0031167","count":3},{"id":"GO:0002098","count":2}]},{"hash":"436082950395315514","title":"Central Carbon Metabolism and Insulin Signaling","description":"Enriched GO terms cluster around energy metabolism: glycolysis, TCA cycle, and pyruvate/acetyl\u2011CoA biosynthesis, plus regulation of pyruvate decarboxylation and glucose metabolic process. The inclusion of cellular response to insulin stimulus supports a metabolic-regulatory module linking energy production to signaling. An outlier term for olfactory bulb development is likely incidental noise.","confidence":"Medium","size":13,"edges":46,"triangles":79,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":4},{"id":"GO:0006096","count":4},{"id":"GO:0032869","count":4},{"id":"GO:0061732","count":3},{"id":"GO:0010510","count":3}]},{"hash":"2006735141935057183","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":39,"triangles":55,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009231","count":3},{"id":"GO:0071548","count":3},{"id":"GO:0010043","count":3},{"id":"GO:0044210","count":3},{"id":"GO:0006207","count":3}]},{"hash":"1750823028021558104","title":"ER Stress Response and Protein Quality Control","description":"The cluster centers on proteostasis under stress, with terms for unfolded protein response, translation initiation during ER stress, chaperone-assisted refolding, protein maturation and targeting, transport of misfolded proteins, and ubiquitin-proteasome\u2013mediated nuclear quality control. Despite some obsolete terms, the overall theme ties together how cells detect and manage misfolded or damaged proteins across compartments during stress.","confidence":"High","size":13,"edges":75,"triangles":254,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0036494","count":5},{"id":"GO:0006626","count":5},{"id":"GO:0006986","count":5},{"id":"GO:0070389","count":5},{"id":"GO:0070843","count":4}]},{"hash":"1415466419731456244","title":"Cytoplasmic translation and ribosome biogenesis","description":"The cluster is dominated by GO terms for translation (GO:0006412), cytoplasmic translation, ribosome biogenesis and small subunit assembly, and tRNA modification, pointing to components of the ribosome and the protein-synthesis machinery. Some cell-cycle terms appear, but the prevailing signal is ribosome function and translation.","confidence":"High","size":13,"edges":54,"triangles":115,"max_degree":12,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0046677","count":3},{"id":"GO:0002181","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000028","count":2}]},{"hash":"1195352098141706516","title":"Craniofacial and optic nerve morphogenesis","description":"This cluster is dominated by GO terms tied to embryonic cranial skeleton morphogenesis, face development, and optic nerve morphogenesis, with supporting pathways like neurotrophin signaling, Wnt regulation, and FGF-related signaling, indicating a cohesive theme of craniofacial and neural tissue development during embryogenesis. The DNA replication term suggests cell proliferation common in developing tissues but does not outweigh the developmental focus. ","confidence":"High","size":13,"edges":59,"triangles":128,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":12},{"id":"GO:0006260","count":12},{"id":"GO:0048011","count":9},{"id":"GO:0090090","count":9},{"id":"GO:0020021","count":9}]},{"hash":"1745495649299375288","title":"Membrane Transporters and Mitochondrial Ion Homeostasis","description":"The top GO terms cluster around diverse transmembrane transport processes (vitamin, xenobiotic, manganese, proton) and a mitochondrial electron transport step (ubiquinol to cytochrome c), with supporting ion homeostasis terms. This suggests a cohesive theme centered on membrane transport and regulation of metal ions, including mitochondrial energy-related activity. Some terms are obsolete, but the core signature remains transporter activity and ion balance across membranes.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0006855","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0006122","count":2}]},{"hash":"1049574768141398967","title":"Innate immune regulation and RNA processing","description":"The top terms show innate immune modulation (negative regulation of interferon-beta production, negative regulation of LPS signaling, and cellular response to lipopolysaccharide) alongside RNA metabolism processes (maturation of LSU/SSU rRNA and mRNA splicing via spliceosome). The inclusion of DNA replication and cell division suggests a broader involvement with cell-cycle dynamics. Together, these indicate a cluster tied to host innate immune regulation intertwined with RNA processing/ribosome biogenesis rather than a single, narrow function.","confidence":"Medium","size":13,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071222","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0019062","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0039520","count":2}]},{"hash":"787461132486992816","title":"Chromatin remodeling and transcription regulation in development","description":"The cluster is enriched for chromatin remodeling and transcription-related GO terms (DNA-templated transcription, transcription regulation by RNA Polymerase II, DNA topology changes) alongside a developmental process (embryonic cranial skeleton morphogenesis), suggesting proteins that remodel chromatin to regulate transcription during development; some members touch on nucleosome positioning and RNA processing steps.","confidence":"High","size":13,"edges":13,"triangles":3,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043044","count":4},{"id":"GO:0048701","count":4},{"id":"GO:0045944","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0006265","count":3}]},{"hash":"793302726527461961","title":"Unknown","description":"The top GO terms span plant development, transcription regulation, RNA modification, epithelial maturation, and immune signaling, with several obsolete terms, and there are no edges among the proteins. This dispersion suggests no single coherent function unites the cluster, so a specific label cannot be confidently assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048507","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0002943","count":1},{"id":"GO:0055114","count":1}]},{"hash":"1997550095727144442","title":"DNA Damage Response and Ubiquitin-Chromatin Regulation","description":"The cluster consistently features GO terms tied to DNA damage repair (NHEJ), meiotic DSB formation, synaptonemal complex organization, and multiple ubiquitination processes affecting histones and protein turnover, plus cell-cycle exit and apoptosis. This suggests a cohesive module of DNA damage response with chromatin modification and cell fate decisions.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0070936","count":13},{"id":"GO:0010458","count":13},{"id":"GO:0006303","count":13},{"id":"GO:0006915","count":13},{"id":"GO:0042276","count":13}]},{"hash":"954501569813503619","title":"Nuclear transcriptional regulation and chromatin dynamics","description":"The top GO terms point to regulation of gene expression within the nucleus: protein phosphorylation affecting signaling, positive regulation of transcription by RNA Pol II, splicing regulation, and chromatin remodeling (histone exchange), along with nuclear import and NF-kappaB signaling. Developmental terms for muscle and substantia nigra likely reflect tissue-specific contexts of these regulatory proteins. Together, these signals converge on nuclear control of transcription and chromatin state.","confidence":"Medium","size":13,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006468","count":4},{"id":"GO:0043123","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0048741","count":3},{"id":"GO:0021762","count":3}]},{"hash":"1641770010221396931","title":"Retroviral lifecycle and host RNA processing","description":"The top GO terms point to retroviral processes (DNA integration, proviral latency, ESCRT-mediated budding) and host RNA biology (translation, splicing, miRNA turnover), suggesting a theme of virus\u2013host interactions and the retroviral lifecycle; a few terms are broad host functions, but the core signal is retroviral lifecycle plus dependence on host gene expression.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0075713","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0072756","count":1}]},{"hash":"2115322239685886480","title":"Neuronal development and proteostasis","description":"This cluster centers on neural development and neuron-specific morphogenesis (nervous system development, cell differentiation, dendrite morphogenesis, multicellular organism development) and is enriched for protein turnover via the ubiquitin-proteasome system (SCF-dependent and ubiquitin-dependent proteolysis), indicating proteostasis in neurons. The presence of an intrinsic apoptotic ER-stress pathway suggests stress-response links that could impact neural differentiation and maintenance, reinforcing the neural development plus proteostasis theme.","confidence":"High","size":13,"edges":50,"triangles":88,"max_degree":10,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0070059","count":6},{"id":"GO:0031146","count":6},{"id":"GO:0007399","count":6},{"id":"GO:0030154","count":6},{"id":"GO:0070050","count":6}]},{"hash":"1102446144162872216","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007595","count":2},{"id":"GO:0032869","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0006002","count":2},{"id":"GO:0061621","count":2}]},{"hash":"852654624919233099","title":"Floral development and transcription regulation","description":"The cluster is dominated by plant-focused developmental GO terms: floral meristem determinacy, floral organ number specification, floral whorl structural organization, and ovule development, along with DNA-templated transcription, indicating a group of proteins tied to floral organogenesis and transcriptional control. Some animal development terms appear as outliers, but the plant terms prevail, supporting this theme.","confidence":"High","size":13,"edges":57,"triangles":154,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010582","count":6},{"id":"GO:0090009","count":6},{"id":"GO:0048833","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0048481","count":6}]},{"hash":"2067742704305098366","title":"Ubiquitin-regulated immune signaling and lymphocyte development","description":"The terms point to ubiquitin-dependent protein turnover, NF-kB and TNF signaling, and lymphocyte biology (T cell homeostasis, V(D)J recombination), with circadian and apoptotic regulation indicating broader stress- and transcription-control roles. Chromatin modification terms (histone ubiquitination/acetylation) further support a coordinated regulatory module governing immune activation and lymphocyte development via ubiquitin pathways and transcriptional control.","confidence":"High","size":13,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0043029","count":5},{"id":"GO:0042752","count":5},{"id":"GO:0042981","count":5},{"id":"GO:0033151","count":5}]},{"hash":"599660150133089156","title":"Pollen wall biosynthesis","description":"The top GO terms are dominated by sporopollenin biosynthesis, chalcone and flavonoid biosynthetic processes, and cell wall layer assembly, all of which point to pollen exine formation and related lipid/fatty-acid components. This combination strongly suggests a functional cluster around pollen wall construction rather than general metabolism. Thus, a concise label is \u201cPollen wall biosynthesis.\u201d","confidence":"High","size":13,"edges":61,"triangles":148,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0071770","count":5},{"id":"GO:0006633","count":5},{"id":"GO:0080110","count":5},{"id":"GO:0009715","count":5},{"id":"GO:0009813","count":5}]},{"hash":"1324095590397342100","title":"Plant cell wall biosynthesis and fungal-type wall organization","description":"This cluster is dominated by GO terms related to plant cell wall biogenesis and remodeling (cell wall biogenesis, xyloglucan metabolic process, plant-type cell wall modification) and includes fungal-type cell wall organization and detection of molecules of fungal origin, indicating a functional group involved in cell wall construction and plant defense against fungi. The presence of stamen filament development reinforces a plant-specific context, while a single outlier term (B cell chemotaxis) likely reflects annotation noise. Overall, the proteins appear tied to plant cell wall processes with a fungal-response angle.","confidence":"Medium","size":13,"edges":22,"triangles":6,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0080086","count":6},{"id":"GO:0009831","count":6},{"id":"GO:0031505","count":6},{"id":"GO:0010411","count":6},{"id":"GO:0032491","count":6}]},{"hash":"599796314463534282","title":"Spliceosome-Mediated mRNA Processing","description":"The GO terms cluster around mRNA splicing via the spliceosome, spliceosomal snRNP assembly, P-body assembly, and mRNA decay, with additional regulation of mRNA splicing. This points to a cohesive function in splicing-driven mRNA processing and turnover.","confidence":"High","size":13,"edges":67,"triangles":194,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0033962","count":3},{"id":"GO:0000387","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0042274","count":2}]},{"hash":"1849585034775701029","title":"Ubiquitin-Proteasome Pathway and ERAD","description":"This cluster is centered on ubiquitination-related processes that tag proteins for degradation, including autoubiquitination, ubiquitin-dependent ERAD, and K48-linked ubiquitination, as well as ubiquitin-driven protein catabolic processes. Additional terms reflect downstream consequences like Wnt receptor degradation and transcriptional regulation, with peroxisomal protein import tied to ubiquitin-mediated recycling of the receptor. Some GO terms are obsolete or broad, but the common thread is proteostasis via the ubiquitin-proteasome system.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":7},{"id":"GO:0030433","count":7},{"id":"GO:0070936","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0046621","count":5}]},{"hash":"177652819966114455","title":"Nucleobase transport across plasma membrane","description":"The Top Terms show transport across the plasma membrane for nucleobases and related purines/pyrimidines (adenine, guanine, uracil, hypoxanthine, xanthine, urate), suggesting a cohesive function as nucleobase transporters; a couple of unrelated terms (sucrose catabolic process, thrombocyte differentiation) appear but do not override the dominant transport theme.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098702","count":3},{"id":"GO:0015747","count":3},{"id":"GO:0098710","count":3},{"id":"GO:0070904","count":3},{"id":"GO:0098721","count":3}]},{"hash":"1078663570378227228","title":"CNS development and dendrite morphogenesis","description":"The top GO terms are strongly weighted toward nervous system development, forebrain development, CNS formation, and dendrite morphogenesis, suggesting the cluster centers on neuronal development and dendritic structuring. There are a few outliers (e.g., plant hypersensitive response, methylation cycle, G1 DNA damage checkpoint signaling, TGF-beta response, cardiac apoptotic process), but the dominant theme remains neural development. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0051260","count":11},{"id":"GO:0033353","count":10},{"id":"GO:0048813","count":10},{"id":"GO:0030900","count":10},{"id":"GO:0021556","count":10}]},{"hash":"665704697316736449","title":"Plant phenylpropanoid biosynthesis and plasmodesmata transport","description":"The top GO terms cluster around plant-specific secondary metabolism (lignin biosynthesis and flavonoid/anthocyanin pathways) and plasmodesmata-mediated intercellular transport, suggesting a module tied to cell-wall biosynthesis and cell-to-cell movement. Anomalous paranode axon localization is likely noise. ","confidence":"Medium","size":13,"edges":17,"triangles":8,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0010497","count":6},{"id":"GO:0033609","count":6},{"id":"GO:0002175","count":5},{"id":"GO:0030259","count":5},{"id":"GO:0009808","count":5}]},{"hash":"946125413761194535","title":"Unknown","description":"The top GO terms span transcriptional regulation, development (maternal axis specification, photoreceptor maintenance), signaling (I-kappaB phosphorylation), metabolism (cytochrome assembly, prolyl hydroxylation), protein secretion, red blood cell/homeostasis, and detoxification. The terms cover diverse, seemingly unrelated processes with no clear single functional theme for the cluster, suggesting the proteins do not share a cohesive primary function. Therefore, Unknown with no clear representative label.","confidence":"","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903026","count":2},{"id":"GO:0045494","count":2},{"id":"GO:0007313","count":2},{"id":"GO:0007252","count":2},{"id":"GO:0050709","count":2}]},{"hash":"1203593523293274924","title":"Iron and manganese ion homeostasis and stress response","description":"Top GO terms indicate iron and manganese ion homeostasis and transport (intracellular manganese ion homeostasis, manganese ion transmembrane transport) and iron-sulfur cluster assembly, alongside stress-related and plant-associated terms (cellular response to stress, cellular response to ethylene, endosperm development). No single unified function emerges, and several terms are plant- or symbiont-related. The label captures the central motif of metal ion metabolism tied to stress signaling rather than a narrow pathway.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:0085014","count":1},{"id":"GO:0006950","count":1},{"id":"GO:0030026","count":1},{"id":"GO:0071421","count":1}]},{"hash":"1131966632699252424","title":"Innate immune signaling and neuronal axon guidance","description":"The top GO terms combine innate immune signaling (MyD88-dependent TLR signaling, LPS detection, defense response to virus) with neuronal development processes (axonogenesis, axon extension in axon guidance, axonal fasciculation). A kinase signaling/negative regulation of kinase activity term links these signaling events. One term for kidney development appears peripheral. Together, the cluster seems to represent proteins involved in immune signaling that intersect with axon guidance pathways, hence the combined label. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":5},{"id":"GO:0007409","count":4},{"id":"GO:0002755","count":3},{"id":"GO:0032497","count":3},{"id":"GO:0051607","count":3}]},{"hash":"2121543459913454168","title":"Neural and optic development signaling","description":"The top GO terms cluster around neural signaling and development of ocular/craniofacial structures (neurotrophin TRK receptor signaling, optic nerve morphogenesis, face development) with related signaling pathways (FGFR apoptotic signaling, PI3K/AKT, actin cytoskeleton) and regulatory processes, suggesting a cohesive theme of neural/eye development and associated signaling networks.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":5},{"id":"GO:0090090","count":5},{"id":"GO:0020021","count":5},{"id":"GO:0071469","count":5},{"id":"GO:0060324","count":5}]},{"hash":"1333322459950760785","title":"Negative regulation of ubiquitin-proteasome and vesicle trafficking","description":"The top GO terms cluster around deubiquitination, ERAD, negative regulation of endocytosis and vesicle formation, and suppression of proteasomal degradation and ER stress\u2013induced apoptotic signaling. This points to a group of proteins that collectively dampen protein turnover and intracellular trafficking, with some links to immune signaling and developmental processes. Confidence: Medium","confidence":"","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":9},{"id":"GO:0030433","count":8},{"id":"GO:0034140","count":7},{"id":"GO:1904049","count":7},{"id":"GO:0045648","count":7}]},{"hash":"2208826790967299777","title":"Chromatin remodeling and transcription regulation","description":"The top GO terms cluster around chromatin remodeling and nucleosome disassembly, suggesting these proteins function in modifying chromatin structure to regulate gene expression. The presence of terms related to transcriptional regulation, growth signaling, and nutrient response aligns with a cohesive theme where chromatin state modulates transcription in response to environmental cues. While some terms reflect specific yeast processes (mating-type switching, invasive growth) or host\u2013virus interactions, these can be downstream effects or context-specific expansions of chromatin-mediated regulation, supporting a label focused on chromatin remodeling and transcription control.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005987","count":2},{"id":"GO:2000219","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0006337","count":2},{"id":"GO:0043923","count":2}]},{"hash":"1371757790316972544","title":"Unknown","description":"The Top Terms span membrane ion transport, transcription regulation, cell wall processes, synaptic transmission, and various development/immune terms, with no clear shared function or pathway. There are no edges or interactions in the cluster, indicating a heterogeneous grouping rather than a cohesive functional module. Therefore, this cluster cannot be assigned a confident, specific label.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0016998","count":2}]},{"hash":"1193563850875539418","title":"Protein and polyamine acetylation","description":"The top GO terms are dominated by acetylation-related processes, including peptidyl-lysine N6-acetylation, N-terminal acetylation, spermidine and putrescine acetylation, and histone H4 acetylation, pointing to enzymes or substrates involved in acetyl group transfer. While other terms like arginine and mycothiol biosynthesis appear, they can be linked to broader metabolic contexts that accompany acetylation pathways. Overall, the cluster centers on acetylation activities and acetylated substrates, justifying the label \"Protein and polyamine acetylation.\"","confidence":"High","size":13,"edges":18,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":5},{"id":"GO:0018003","count":5},{"id":"GO:0032918","count":4},{"id":"GO:0043967","count":4},{"id":"GO:0006526","count":4}]},{"hash":"416556243955696183","title":"Neuronal morphogenesis and ER organization","description":"The cluster is dominated by neural development terms (axon fasciculation, branching morphogenesis of a nerve, negative regulation of axon extension) alongside terms for endoplasmic reticulum tubular network formation and membrane organization, suggesting a shared theme of neuronal morphogenesis linked to ER structure. A few terms (nuclear pore complex assembly, steroid biosynthesis, plant-type secondary cell wall biogenesis) appear noisy relative to the main theme. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":2},{"id":"GO:0071787","count":1},{"id":"GO:0007413","count":1},{"id":"GO:2000172","count":1},{"id":"GO:0060317","count":1}]},{"hash":"1705334372939435008","title":"Ubiquitin-mediated transcriptional and cell fate regulation","description":"Based on GO terms, this cluster centers on negative regulation of transcription by RNA Pol II, ubiquitination (polyubiquitination), and modulation of apoptotic/necroptotic pathways, with additional signals related to TLR signaling and cell cycle control. This suggests a cohesive theme of ubiquitin-dependent regulation of transcription and cell fate decisions, rather than a single linear pathway. Some meiosis-related terms appear but do not define the core function.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0060544","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0043066","count":2},{"id":"GO:0034121","count":2}]},{"hash":"500367722025286626","title":"Developmental signaling and cell proliferation","description":"The top GO terms point to tissue development (multicellular organism development, skin development) and pathways that promote growth and division (positive regulation of GTPase activity, protein autophosphorylation, serine/threonine kinase activity, mitotic cell cycle, positive regulation of cell population proliferation). Taken together, they suggest a module of developmental signaling that drives cell proliferation and tissue formation, especially in skin or epithelia. Some terms like mRNA transport or aging appear ancillary and do not define the core theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0043588","count":5},{"id":"GO:0031954","count":4},{"id":"GO:0071456","count":4}]},{"hash":"1934582249536177282","title":"Seed coat mucilage biosynthesis and embryogenesis","description":"This cluster centers on seed coat mucilage/polysaccharide-related processes (pectin biosynthetic and catabolic) and cell wall modification, with somatic embryogenesis and axis specification suggesting developmental regulation during embryo formation; ABA signaling and nitric oxide responses further support plant developmental signaling contexts.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0045490","count":3},{"id":"GO:0048358","count":3},{"id":"GO:0042545","count":3},{"id":"GO:0006355","count":3}]},{"hash":"1610525751057169299","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster centers on ubiquitination and downstream proteolysis: autoubiquitination, ubiquitin-dependent ERAD, K48-linked ubiquitination, and general ubiquitin-dependent protein catabolic processes. It also touches on related signaling and turnover roles, such as NF-kappaB activation, Wnt receptor degradation, and regulation of apoptosis, with additional hints from chromatin-related ubiquitination and V(D)J recombination. Together, these terms point to the ubiquitin-proteasome system governing protein turnover and signaling, justifying a label focused on ubiquitination and degradation.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":12},{"id":"GO:0030433","count":11},{"id":"GO:0042787","count":11},{"id":"GO:0070936","count":10},{"id":"GO:0042981","count":9}]},{"hash":"2067118644673238764","title":"Oocyte maturation and meiotic spindle assembly","description":"The top GO terms strongly point to oocyte development, particularly oocyte maturation and spindle assembly in female meiosis I, coupled with ubiquitin-proteasome\u2013mediated protein turnover and microtubule dynamics. This suggests a cohesive theme of meiosis control and spindle formation in oocytes, with some neural-development terms likely representing broader developmental regulation or annotation noise. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":7},{"id":"GO:0001556","count":6},{"id":"GO:0006516","count":6},{"id":"GO:0008285","count":6},{"id":"GO:0007057","count":6}]},{"hash":"1653259035055240790","title":"Neural Development Signaling and Growth Factors","description":"The top GO terms center on neurotrophin TRK receptor signaling, FGFR-mediated pathways, PI3K/AKT signaling, and morphogenesis of neural structures (optic nerve) and craniofacial features (face development), suggesting a cluster tied to neural development guided by growth-factor signaling. Some terms appear peripheral (e.g., response to alkaline pH), but the dominant theme is neural development and growth-factor\u2013driven signaling networks.","confidence":"Medium","size":13,"edges":12,"triangles":5,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":13},{"id":"GO:0090090","count":13},{"id":"GO:0020021","count":13},{"id":"GO:0071469","count":13},{"id":"GO:0060324","count":13}]},{"hash":"989458207855171529","title":"Intracellular Signaling and Ubiquitin Regulation","description":"The cluster centers on intracellular signal transduction and polyubiquitination, with connections to related signaling pathways (NOD2 signaling, NF-\u03baB regulation) and cell migration. While some terms are development- or obsolete-terminology, the dominant themes point to signaling networks modulated by ubiquitin, suggesting a cohesive focus on ubiquitin-regulated signaling processes.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":3},{"id":"GO:0000209","count":3},{"id":"GO:0007205","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0016477","count":2}]},{"hash":"237031982609126468","title":"Unknown","description":"The terms are highly heterogeneous, spanning intracellular transport, multiple metabolism pathways (glucose metabolism, amino acid catabolism, bacillithiol biosynthesis), lipopolysaccharide and fungal cell wall biosynthesis, and environmental stress/behavioral annotations, with an obsolete glycosylation term as well. This mix across organisms and processes provides no clear cohesive function for the cluster, so a single, representative label cannot be determined.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0042219","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0009413","count":1},{"id":"GO:0033577","count":1}]},{"hash":"2034235493248247023","title":"Mucosal glycosylation and gut immune processes","description":"This cluster converges on glycosylation and proteoglycan biosynthesis (UDP-xylose, heparin proteoglycan) and mucosal-immune functions (immunoglobulin production in mucosal tissue, leukocyte tethering/rolling, intestinal absorption), along with tissue morphogenesis. Together, these terms point to roles in mucosal barrier glycosylation and immune/tissue remodeling at mucosal sites.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006486","count":4},{"id":"GO:0034116","count":3},{"id":"GO:0032868","count":3},{"id":"GO:0050901","count":3},{"id":"GO:0050892","count":3}]},{"hash":"1274899227843067942","title":"Intracellular trafficking and localization","description":"Top terms indicate a focus on intracellular transport and localization, including ER-to-Golgi vesicle transport, peroxisomal targeting, nuclear pore localization, and cytoskeletal remodeling, suggesting these proteins collectively participate in moving and positioning other proteins within the cell. Some terms about neural development and lipid signaling may reflect broader roles of trafficking components rather than a single pathway, but the dominant theme is intracellular transport/localization.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:2001162","count":2},{"id":"GO:0006625","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0030042","count":2}]},{"hash":"784681461365289352","title":"Proteolysis and ubiquitin-dependent degradation","description":"The top GO terms cluster around protein catabolic processes and proteolysis, including ubiquitin-proteasome\u2013mediated degradation (SCF-dependent ubiquitin\u2013proteasomal pathway) and maturation steps like insulin processing. While a few terms relate to plant-specific processes, the dominant theme across the terms is protein turnover through proteolysis and ubiquitin pathways, justifying a label focused on degradation. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009405","count":1},{"id":"GO:1905182","count":1},{"id":"GO:0006807","count":1},{"id":"GO:0030163","count":1},{"id":"GO:0045493","count":1}]},{"hash":"676751466008300434","title":"Lipid metabolism and adipose development","description":"This cluster is dominated by GO terms tied to lipid droplets and adipose tissue development, pointing to a core function in fat cell biology and energy storage. Additional terms relating to mitochondrial membrane potential and peroxisome inheritance suggest broader metabolic regulation, while neuromuscular development and BMP signaling relate to developmental pathways; however, the strongest signal centers on lipid metabolism and adipogenesis.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030514","count":2},{"id":"GO:0034389","count":2},{"id":"GO:0009838","count":2},{"id":"GO:0048698","count":2},{"id":"GO:0060612","count":2}]},{"hash":"1257192552903747420","title":"Glycan and carbohydrate catabolism","description":"Top GO terms indicate a clear emphasis on the breakdown and remodeling of carbohydrates and glycans (galactose catabolic/metabolic, cellulose and polysaccharide catabolism, keratan sulfate proteoglycan catabolic, glycosphingolipid metabolism). This suggests the cluster centers on glycan metabolism. A few terms about cell surface receptor signaling and synapse assembly imply possible membrane-associated roles or annotation noise; the fungal-type cell wall organization term seems out of place and may reflect cross-species annotation quirks. Overall, the strongest signal is glycan and carbohydrate catabolism.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031505","count":4},{"id":"GO:0042220","count":2},{"id":"GO:0042340","count":2},{"id":"GO:0006687","count":2},{"id":"GO:0007166","count":2}]},{"hash":"427044624898175716","title":"Mitochondrial import and membrane regulation","description":"The Top Terms show a clear enrichment for mitochondrial-related processes: protein import into the mitochondrial matrix and regulation of mitochondrial membrane permeability. There are additional hints of lipid metabolism (triglyceride biosynthesis) and transcription/RNA processing terms that may be peripheral or reflect broad cellular processes, but the strongest signal centers on mitochondria. The mixture of obsolete terms and a few unrelated annotations reduces certainty, so a moderate confidence is appropriate.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":4},{"id":"GO:0046902","count":3},{"id":"GO:0010867","count":3},{"id":"GO:1903740","count":3},{"id":"GO:2000134","count":3}]},{"hash":"1543666243411542580","title":"Plant flavonoid biosynthesis and karrikin response","description":"The terms point to flavonoid biosynthetic activity and a plant-specific response to karrikin, suggesting a plant secondary metabolism/signaling theme. Because each term is represented by a single protein, the connection is tentative.","confidence":"Low","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080167","count":1},{"id":"GO:0009813","count":1}]},{"hash":"1340860748384378576","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0052889","count":3},{"id":"GO:2000344","count":3},{"id":"GO:0016042","count":3},{"id":"GO:0015979","count":1},{"id":"GO:0019684","count":1}]},{"hash":"2192034421920672926","title":"Plant transcriptional regulation and chromatin remodeling","description":"The dominant GO terms point to transcriptional control and chromatin remodeling (regulation of DNA-templated transcription, chromatin remodeling, positive regulation of miRNA transcription), suggesting a core role in gene expression regulation. Supporting terms involve development (organ boundary specification) and stress responses/metabolism (defense to fungus, invasive growth in response to glucose limitation, sugar and glucan catabolic processes), indicating this cluster integrates development with environmental responsiveness through transcriptional control.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010199","count":2},{"id":"GO:0030308","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0006076","count":1}]},{"hash":"929182264245718953","title":"Pollen Tube Growth and Guidance Signaling","description":"This cluster is dominated by terms tied to pollen tube growth and guidance, suggesting a plant-specific signaling module that controls directional growth and target navigation. The presence of intracellular signal transduction and Ras/GPCR-related pathways supports a coordinated signaling network, while a few outlier terms reflect broader or cross-species annotations.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":8},{"id":"GO:0080092","count":6},{"id":"GO:0010183","count":6},{"id":"GO:0007205","count":5},{"id":"GO:0016477","count":5}]},{"hash":"2036432769992228376","title":"Plant Golgi glycosylation and sugar nucleotide transport","description":"This cluster is driven by GO terms for importing sugar nucleotides into the Golgi (GDP-fucose, UDP-glucose) and for Golgi-based protein glycosylation (fucosylation, O- and N-glycosylation). A few development terms (root hair and lateral root development) appear, but the dominant signal points to Golgi glycosylation and nucleotide-sugar transport in plants.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048527","count":1},{"id":"GO:0036066","count":1},{"id":"GO:0080147","count":1},{"id":"GO:0036071","count":1},{"id":"GO:0036085","count":1}]},{"hash":"835790098471346588","title":"Neuroinflammation and neuronal development","description":"These proteins are enriched for innate immune signaling (NF-kappaB, MyD88-dependent TLR signaling, LPS detection, defense against virus) alongside neuronal development processes (brain development, dendrite morphogenesis, neuron cellular homeostasis), suggesting a link between neuroinflammatory pathways and neural development/maintenance.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0043123","count":5},{"id":"GO:0090073","count":5},{"id":"GO:0070050","count":5},{"id":"GO:0007420","count":4},{"id":"GO:0002755","count":3}]},{"hash":"860503533339654128","title":"GTPase-driven vesicle trafficking and membrane organization","description":"Top terms indicate a recurring theme of small GTPase signaling and regulation, vesicle transport (including Golgi/lysosome-related pathways), and membrane-associated processes like lysosomal membrane organization and podosome assembly. While other terms (ribosome biogenesis, cell division) appear, the strongest signal centers on GTPase-mediated trafficking and membrane organization, suggesting this as the cluster\u2019s core function. ","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0007264","count":4},{"id":"GO:0055108","count":3},{"id":"GO:0097284","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1904963772048829726","title":"Plant Defense and Hormone Signaling","description":"The cluster is dominated by plant-related defense and biotic-stimulus response terms (defense response, response to biotic stimulus, nodulation) and multiple hormone signaling pathways (cytokinin, gibberellin, abscisic acid), suggesting proteins involved in immune and developmental signaling in plants. A few notes like short-day photoperiodism and a likely annotation artifact (synaptic plasticity) are outliers, but do not override the main theme. Confidence: High.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009607","count":3},{"id":"GO:0009736","count":3},{"id":"GO:0006952","count":3},{"id":"GO:0009740","count":3},{"id":"GO:0009877","count":3}]},{"hash":"526316735778401515","title":"Heat-Responsive Cell Cycle and Metabolism","description":"This cluster is enriched for terms related to cell division and centriole dynamics (cell division, positive regulation of centriole elongation) alongside energy metabolism and heat response (oxidative phosphorylation, ATP biosynthetic process, cellular heat acclimation), and mRNA export/gene expression (mRNA export from nucleus, transcription preinitiation complex assembly). The combination suggests a coordinated program of cell-cycle progression with upregulated energy production in response to heat stress, despite a few outliers such as viral genome replication.","confidence":"Medium","size":12,"edges":9,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1903724","count":3},{"id":"GO:0070370","count":3},{"id":"GO:0019079","count":3},{"id":"GO:0051301","count":3},{"id":"GO:1903862","count":3}]},{"hash":"1883163477716066146","title":"Nervous system development and dendrite morphogenesis","description":"The top GO terms are dominated by neural development processes, especially dendrite morphogenesis, forebrain development, and nervous system development, suggesting the proteins cluster around neuronal development. Other terms related to immune or stress responses appear secondary and may reflect pleiotropy or cross-talk rather than defining the core function. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0048813","count":7},{"id":"GO:0030900","count":7},{"id":"GO:0007399","count":7},{"id":"GO:0007275","count":7},{"id":"GO:1903351","count":7}]},{"hash":"148745001298646754","title":"Negative regulation of signaling and trafficking pathways","description":"Most top GO terms point to the suppression of diverse signaling and trafficking processes (TLR3 signaling, clathrin-dependent endocytosis, store-operated calcium channel activity, vesicle formation, ER stress\u2013induced apoptotic signaling, proteasomal protein catabolic process). Some terms touch development or differentiation (hypothalamus GnRH neuron development, erythrocyte differentiation) and TNF signaling, which can be viewed within a broader regulatory context. Overall, the cluster seems enriched for proteins that function as regulators dampening signaling and intracellular transport rather than promoting a single pathway.","confidence":"High","size":12,"edges":41,"triangles":70,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0034140","count":7},{"id":"GO:1904049","count":7},{"id":"GO:0045648","count":7},{"id":"GO:1901799","count":7},{"id":"GO:1905366","count":7}]},{"hash":"1140318336682841713","title":"Developmental gene regulation and stress responses","description":"These proteins show enrichment for developmental processes (forebrain, multicellular organism, skeletal system development) alongside core gene expression steps (DNA-templated transcription, formation of translation preinitiation complex). The presence of stress-related terms (ER stress\u2013induced apoptotic signaling, cellular response to cadmium) and an immune defense term suggests roles in interfacing development with stress signaling. Overall, the cluster most coherently reflects developmental gene regulation with associated stress responses.","confidence":"Medium","size":12,"edges":54,"triangles":130,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030900","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0001501","count":3},{"id":"GO:0050830","count":3}]},{"hash":"134843757153545259","title":"Synaptic Transmission and Plasticity Regulation","description":"The cluster shows a clear focus on neuronal signaling and plasticity, with terms for synaptic transmission (glutamatergic), long-term potentiation, and both positive and negative regulation of synaptic plasticity, suggesting core involvement in synaptic function; additional terms related to apoptotic regulation may reflect context in neural cell survival but do not override the primary neuronal signaling theme.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001324","count":3},{"id":"GO:0034351","count":3},{"id":"GO:0060963","count":3},{"id":"GO:0009738","count":3},{"id":"GO:0035249","count":3}]},{"hash":"497249136022356714","title":"Chloroplast Photosynthesis and Redox Homeostasis","description":"The top GO terms are dominated by photosynthesis-related processes (photosynthetic electron transport in PSI, photosynthesis, light reactions, light harvesting) and redox balance, with cytochrome complex assembly pointing to the electron transport chain. A couple of terms (ER protein folding and valyl-tRNA aminoacylation) are more general housekeeping processes or dual-targeted, but the strongest signal centers on chloroplast photosystem I activity and redox regulation.","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0017004","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0006438","count":2},{"id":"GO:0009773","count":2}]},{"hash":"1745435723306494271","title":"Central Metabolism: Glycolysis and Lysine Biosynthesis","description":"The cluster shows strong representation of glycolytic process and gluconeogenesis, plus diaminopimelate (lysine) biosynthesis, pointing to core metabolic pathways. Some terms are obsolete or unrelated (e.g., peroxisome import, chromatin organization), which likely reflect historical annotations rather than a single cohesive function, but the dominant theme remains central carbon and amino acid metabolism.","confidence":"High","size":12,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019877","count":3},{"id":"GO:0009089","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006096","count":2},{"id":"GO:0016558","count":2}]},{"hash":"725629878054692660","title":"Plant auxin signaling and organelle RNA editing","description":"The cluster is dominated by auxin-related terms: auxin-activated signaling pathway, auxin polar transport, and response to auxin, along with regulation of organ growth, pointing to an auxin-regulated development module. The presence of chloroplast and mitochondrial RNA modification and RNA editing terms suggests a link to organelle gene expression and RNA processing. Together, these indicate a theme of plant growth regulation tied to organelle RNA processing, giving a coherent but compact label.","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046620","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0009926","count":1},{"id":"GO:0009733","count":1}]},{"hash":"1835897427988318206","title":"Translation and tRNA modification","description":"This cluster is dominated by GO terms tied to protein synthesis and tRNA maturation, including cytosolic and mitochondrial translation, wobble uridine modification, and tRNA methylation, suggesting a core theme around the translation machinery. Other terms like redox homeostasis, capsule biosynthesis, isoleucine catabolism, and muscle differentiation are present but less represented, indicating some functional noise outside the main theme.","confidence":"Medium","size":12,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0002098","count":2},{"id":"GO:0030488","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0045227","count":2}]},{"hash":"498994243014698693","title":"DNA repair and xenobiotic stress response","description":"The cluster\u2019s terms center on DNA maintenance and damage response (base-excision repair, DNA recombination, depyrimidination) along with cellular responses to xenobiotic stimuli and cadmium, plus anti-apoptotic regulation, suggesting a core theme of DNA repair and stress survival. Proteoglycan biosynthesis and cell wall organization are less directly connected but may reflect broader remodeling processes; overall, the dominant signal is DNA repair and stress response.","confidence":"Medium","size":12,"edges":22,"triangles":17,"max_degree":9,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0006284","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0050650","count":3}]},{"hash":"130376752406180595","title":"Mitochondrial fission and apoptotic signaling","description":"The terms point to mitochondrial dynamics and apoptosis, with multiple hits on mitochondrial fission (GO:0000266), cytochrome c release (GO:0090200), apoptosis (GO:0006915), and mitochondrion localization (GO:0034643). While some terms touch on immune signaling and muscle physiology, the central cluster centers on mitochondrial fission and apoptotic pathways, suggesting a shared functional module around mitochondrial integrity and programmed cell death.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":6},{"id":"GO:0002031","count":6},{"id":"GO:0090200","count":6},{"id":"GO:1900756","count":6},{"id":"GO:0034340","count":6}]},{"hash":"330317391022700366","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":58,"triangles":150,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0006382","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0009240","count":1},{"id":"GO:0034656","count":1}]},{"hash":"1181271750518083686","title":"Unknown","description":"The cluster includes both DNA damage response and nucleotide-excision repair terms and a variety of membrane transport terms (lipids, vitamins, teichoic acids, metals), plus an immune presentation term. This mixture does not point to a single coherent biological function, so a specific label isn\u2019t identifiable.","confidence":"","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0015777","count":2},{"id":"GO:0015910","count":2},{"id":"GO:0017004","count":2}]},{"hash":"1462194491933787564","title":"Heterochromatin Formation and Chromatin Maintenance","description":"The top terms are dominated by heterochromatin formation at rDNA, pericentric and subtelomeric regions, plus maintenance of mitotic sister chromatid cohesion. These point to a shared role in chromatin organization and genome stability. A few terms about innate immunity or fertilization seem peripheral noise rather than core to the cluster.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":4},{"id":"GO:0070481","count":3},{"id":"GO:0033128","count":3},{"id":"GO:0034184","count":3},{"id":"GO:0031508","count":3}]},{"hash":"1014312633148598783","title":"Floral development and hormone signaling in plants","description":"This cluster centers on plant reproductive development and patterning, with strong representation of floral meristem growth, bract and seed development, and auxin-related phyllotactic signaling. It is complemented by hormone signaling pathways (ethylene and ABA) and processes for cuticle biosynthesis (wax/cutin), plus transcriptional regulation, indicating a cohesive theme of development coordinated by hormonal cues, with some defense-related responses as a secondary facet.","confidence":"Medium","size":12,"edges":20,"triangles":16,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010200","count":3},{"id":"GO:0010432","count":3},{"id":"GO:0048316","count":3},{"id":"GO:0060774","count":3},{"id":"GO:0010451","count":3}]},{"hash":"1712869719326616171","title":"Developmental Regulation and Transcription","description":"The cluster is enriched for developmental terms (multicellular organism development, forebrain development, skeletal system development) and transcription-related processes (DNA-templated transcription), suggesting a core theme of developmental regulation and gene expression control. Other terms point to growth and stress responses, but development-focused terms are dominant.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0030900","count":2},{"id":"GO:0007338","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0001501","count":2}]},{"hash":"1169129147986348116","title":"Neural development signaling and morphogenesis","description":"The top GO terms point strongly to neural development and tissue morphogenesis, including neurotrophin TRK receptor signaling, optic nerve morphogenesis, and face development, with supporting signaling pathways like Wnt regulation, PI3K/AKT, and FGFR-associated signaling. While a few broader or peripheral terms (e.g., response to toxic substances, alkaline pH) appear, the core pattern is signaling networks guiding neural tissue formation and craniofacial morphogenesis, justifying a label focused on neural development and morphogenesis.","confidence":"High","size":12,"edges":57,"triangles":148,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":12},{"id":"GO:0090090","count":12},{"id":"GO:0020021","count":12},{"id":"GO:0071469","count":12},{"id":"GO:0060324","count":12}]},{"hash":"500156359156283179","title":"Drosophila Developmental Signaling and Gene Regulation","description":"Top GO terms indicate involvement in developmental processes (eye morphogenesis, vitellogenesis, osteoblast proliferation) alongside core regulatory mechanisms (calcium signaling, SMAD signaling, transcription by RNA polymerase II, histone deacetylation). This pattern suggests a cluster of proteins functioning in development through signaling cascades and transcriptional regulation, rather than a single pathway.","confidence":"Medium","size":12,"edges":61,"triangles":180,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071277","count":7},{"id":"GO:2001016","count":5},{"id":"GO:0006366","count":5},{"id":"GO:0031063","count":4},{"id":"GO:0034670","count":4}]},{"hash":"1565870680778570405","title":"Stress-Responsive Proteostasis and Protein Quality Control","description":"Top terms indicate proteome quality control under stress: ER-stress\u2013driven translation, misfolded protein transport, nuclear ubiquitin-proteasome\u2013mediated QC, and coordinated protein targeting/transport. The presence of stress and heat response modulation and cell-cycle links supports a general theme of maintaining proteostasis under cellular stress.","confidence":"Medium","size":12,"edges":16,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":2},{"id":"GO:0036494","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0070843","count":1},{"id":"GO:0071630","count":1}]},{"hash":"2074168712195140815","title":"Plant Hormone Biosynthesis and Stress Responses","description":"The top GO terms cluster around plant hormone biosynthesis (ethylene, gibberellin, auxin, salicylic acid) and related stress signaling (hydrogen peroxide\u2013mediated PCD) along with auxiliary secondary metabolite pathways, suggesting a cohesive theme of hormone metabolism and stress response in plants, despite one potentially unrelated term.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009693","count":3},{"id":"GO:1902835","count":3},{"id":"GO:0042318","count":3},{"id":"GO:0009686","count":3}]},{"hash":"224914565362792528","title":"MAPK Pathway Phosphatases Modulating Host Signaling","description":"This cluster is dominated by GO terms for dephosphorylation (tyrosine and threonine) and negative regulation of ERK/MAPK cascades, as well as suppression of T cell receptor signaling and host interaction, pointing to phosphatases that dampen MAPK-driven signaling and modulate host immunity. Additional terms on cyclin-dependent kinase activity and kinetochore localization suggest links to cell cycle and stress responses, supporting a cohesive role in regulating signaling and host interaction. ","confidence":"High","size":12,"edges":27,"triangles":39,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":7},{"id":"GO:0035970","count":5},{"id":"GO:0044119","count":4},{"id":"GO:0050860","count":4},{"id":"GO:0000200","count":4}]},{"hash":"299205943729920472","title":"Mitotic spindle and cytokinesis regulation","description":"This cluster is dominated by GO terms tied to mitosis and cell division machinery: attachment of spindle microtubules to kinetochores and regulation of protein localization to the division site involved in cytokinesis, indicating a core theme of mitotic control and cytokinesis. Other terms (cell-cell adhesion, transcription termination, neuronal differentiation, stress responses) may reflect ancillary roles of these proteins in broader cellular contexts, but the strongest signal centers on spindle dynamics and cytokinesis. ","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0098609","count":12},{"id":"GO:0005979","count":12},{"id":"GO:0030846","count":12},{"id":"GO:1901901","count":12},{"id":"GO:0051315","count":12}]},{"hash":"246057472955217333","title":"Developmental signaling and morphogenesis","description":"The cluster features terms centered on development and tissue patterning (face development, optic nerve morphogenesis, apical bud growth) along with key signaling pathways (neurotrophin TRK signaling, Wnt signaling regulation, FGF receptor\u2013related signaling). Although a few terms touch on stress responses, the dominant signal is developmental signaling and morphogenesis, suggesting proteins function together in shaping neural and craniofacial tissues.","confidence":"High","size":12,"edges":44,"triangles":76,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007118","count":12},{"id":"GO:0048011","count":11},{"id":"GO:0090090","count":11},{"id":"GO:0020021","count":11},{"id":"GO:0071469","count":11}]},{"hash":"450887173512078924","title":"Transcription and RNA Processing Regulation","description":"The cluster centers on core gene-expression control mechanisms, with GO terms spanning DNA-templated transcription, chromatin remodeling, transcription termination regulation, and multiple RNA processing steps (pre-miRNA processing, mRNA splicing, miRNA catabolism) as well as mRNA stabilization. This cohesive set suggests a role in coordinating transcriptional activity with RNA maturation and turnover, possibly including context-specific regulatory states such as proviral latency.","confidence":"High","size":12,"edges":24,"triangles":1,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0043044","count":2},{"id":"GO:0070934","count":1},{"id":"GO:0075713","count":1},{"id":"GO:0031054","count":1}]},{"hash":"1962328803081118680","title":"Cardiac electrophysiology and ion transport","description":"The cluster is dominated by terms tied to cardiac muscle electrical activity and ion handling: membrane depolarization in Purkinje/myocyte cells, ventricular repolarization, left ventricular morphogenesis, and regulation of potassium export. Additional terms like vasopressin secretion and DNA-templated transcription hint at broader regulatory contexts, while caffeine- and clozapine-related responses are less central but can reflect general signaling cross-talk. Overall, this cluster centers on cardiac electrophysiology and ion transport.","confidence":"Medium","size":12,"edges":11,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071313","count":2},{"id":"GO:0060453","count":2},{"id":"GO:0060307","count":2},{"id":"GO:0048016","count":2},{"id":"GO:0086047","count":2}]},{"hash":"343751277384589300","title":"Unknown","description":"The Top Terms include lipopolysaccharide biosynthesis, metal ion transport (copper, cadmium), several biosynthetic and metabolic processes (glycolate, N-acetylneuraminate, carbohydrate metabolism), a P450 epoxygenase pathway, dephosphorylation, and a testosterone response. This broad, cross-species mix does not reveal a single, coherent functional theme for the cluster, so a unified label isn\u2019t supported.","confidence":"","size":12,"edges":36,"triangles":54,"max_degree":10,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0009103","count":5},{"id":"GO:0070574","count":5},{"id":"GO:0046295","count":5},{"id":"GO:0046380","count":5},{"id":"GO:0006825","count":5}]},{"hash":"1421639512150421616","title":"Chromatin modification and ribosome biogenesis","description":"The top terms center on histone methylation (H3K4/H3K79) and DNA-templated transcription, indicating chromatin regulation and gene expression, while ribosome biogenesis and rRNA maturation point to a nuclear program for ribosome production. Some terms (peroxisome targeting, eye development) appear as outliers, but the core theme combines chromatin modification with ribosome assembly.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051568","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0034729","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000463","count":4}]},{"hash":"1308326562562762869","title":"Plant Hormone Signaling and Defense Responses","description":"These proteins show enrichment for responses to salicylic acid, chitin, gibberellin, and the ethylene precursor ACC, coupled with transcriptional regulation and pigment biosynthesis, pointing to a core of plant hormone signaling and defense/stress pathways.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009751","count":3},{"id":"GO:0010200","count":3},{"id":"GO:0009739","count":3},{"id":"GO:0009718","count":2},{"id":"GO:0055114","count":2}]},{"hash":"924291629544320169","title":"Diverse Metabolic Biosynthesis and Catabolism","description":"The cluster includes terms spanning biosynthetic processes (biotin, antibiotic, methionine biosynthesis) and various catabolic processes (stilbene, chlorophyll, monoacylglycerol catabolism), along with detoxification and response to toxic substances, plus nitrogen utilization. This suggests proteins involved in broad metabolic pathways with both synthesis and degradation roles, as well as detox-related functions, rather than a single focused function. ","confidence":"Medium","size":12,"edges":10,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0009086","count":5},{"id":"GO:0046272","count":5},{"id":"GO:0015996","count":4}]},{"hash":"415916767997118501","title":"Chromatin regulation and RNA processing","description":"The cluster\u2019s top GO terms cluster around histone modification (H3K27 methylation, H3K4 dimethylation), nucleosome assembly, transcription, and mRNA splicing, suggesting a shared role in epigenetic control of gene expression and RNA processing. The presence of brain development, monocyte/immune differentiation, and centrosome cycle terms likely reflects broader developmental and cell-cycle contexts of chromatin-regulating factors. Overall, chromatin regulation with transcription and RNA processing is the most coherent theme across the terms.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061087","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0045657","count":2}]},{"hash":"2118779118556193378","title":"Membrane Transport of Ions and Metabolites","description":"The top GO terms are centered on transmembrane transport of various ions and metabolites (nitrite, nitrate, phosphate, sialic acid, vitamins) and related assimilation processes, with an additional note of neurotransmitter loading into vesicles. This pattern points to a cohesive function around membrane transport and nutrient uptake, with vesicular transport as a related aspect. ","confidence":"High","size":12,"edges":11,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":3},{"id":"GO:0098700","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0015706","count":3},{"id":"GO:0006004","count":3}]},{"hash":"2064169839343724789","title":"ER-Golgi trafficking and protein secretion","description":"The top GO terms cluster around the secretory pathway: ER retention/export, COPI vesicle budding, Golgi ribbon formation, and regulation of secretion (including Wnt proteins). While some terms touch on development, the dominant theme ties to vesicle trafficking and ER-to-Golgi export, consistent with a secretion-related cluster.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009664","count":4},{"id":"GO:0006621","count":2},{"id":"GO:0001893","count":2},{"id":"GO:1902003","count":2},{"id":"GO:0070863","count":2}]},{"hash":"1301663260474926545","title":"RNA Pol II Transcription Repression","description":"Most top GO terms point to negative regulation of transcription by RNA polymerase II and general DNA-templated transcription, indicating a cluster of nuclear transcription regulators. ER stress and protein folding terms appear but are less central, suggesting secondary involvement in broader cellular stress responses. The low connectivity (edge 1) reinforces a core transcriptional regulatory theme rather than a tightly cohesive pathway cluster.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0061087","count":2},{"id":"GO:1903026","count":1},{"id":"GO:0034976","count":1}]},{"hash":"2200606825299638529","title":"Plant development transcription and secondary cell wall biogenesis","description":"The dominant GO terms point to transcriptional regulation in plants, with specific emphasis on plant-type secondary cell wall biosynthesis, protoxylem and root cap development, callus formation, and organ formation timing, alongside hormone responses (salicylic acid and gibberellin). This suggests a coherent module of transcription factors controlling developmental programs and cell-wall formation in plants.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:1901348","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0009751","count":3},{"id":"GO:0009739","count":3}]},{"hash":"259934161758722255","title":"Nucleotide Transport and RNA Processing","description":"This cluster shows GO terms for RNA processing (mRNA splicing via spliceosome, DNA-templated transcription) alongside multiple nucleobase transport terms (adenine, guanine, uracil, urate, xanthine, hypoxanthine imports), suggesting a shared focus on nucleotide handling and RNA synthesis/modification.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0098702","count":1},{"id":"GO:0015747","count":1},{"id":"GO:0098710","count":1}]},{"hash":"1815954415901951829","title":"Developmental transcription regulators","description":"The top GO terms cluster around transcription regulation (DNA-templated transcription and its regulation) with several development-related terms (uterus development, inner ear morphogenesis, multicellular organism development, neuronal commitment). This pattern suggests these proteins function mainly as regulators of gene expression during development, making \"Developmental transcription regulators\" an intuitive, representative label.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0006351","count":4},{"id":"GO:1901348","count":3},{"id":"GO:0060065","count":2},{"id":"GO:0042472","count":2}]},{"hash":"2082767313223365835","title":"ER-Golgi Trafficking and Developmental Signaling","description":"The terms cluster around the early secretory pathway components (ER retention/exit, COPI vesicle budding, Golgi ribbon formation) and secretion-related processes (Wnt protein secretion), coupled with maternal developmental patterning terms (axis specification, placenta development, egg-laying). This suggests a coherent group of proteins involved in ER-Golgi trafficking that modulates developmental signaling.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006621","count":2},{"id":"GO:0001893","count":2},{"id":"GO:1902003","count":2},{"id":"GO:0070863","count":2},{"id":"GO:0032525","count":2}]},{"hash":"1656873019086556771","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":2},{"id":"GO:2000641","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0001682","count":2},{"id":"GO:0048011","count":1}]},{"hash":"1918216078599767985","title":"Neurodevelopment and eye morphogenesis signaling","description":"The top GO terms cluster around neural signaling and development, including neurotrophin/TRK signaling, PI3K/AKT signaling, FGFR apoptotic signaling, optic nerve morphogenesis, and face development, suggesting a cohesive theme of neural/eye and craniofacial morphogenesis and associated signaling pathways. While there are a few ancillary terms, the core pattern points to neural development and eye/face morphogenesis networks.","confidence":"Medium","size":12,"edges":22,"triangles":7,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0048011","count":2},{"id":"GO:0090090","count":2},{"id":"GO:0020021","count":2},{"id":"GO:0071469","count":2},{"id":"GO:0060324","count":2}]},{"hash":"392282900620378855","title":"Neural development and growth factor signaling","description":"This cluster centers on nervous system development and signaling pathways: neurotrophin Trk receptor signaling, optic nerve morphogenesis, and face development, with FGFR and PI3K/AKT signaling also represented. Wnt pathway regulation and toxin response support developmental signaling context. One outlier GO term may reflect a multifunctional protein; overall, the theme is neural development and growth-factor signaling.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":12},{"id":"GO:0090090","count":12},{"id":"GO:0020021","count":12},{"id":"GO:0071469","count":12},{"id":"GO:0060324","count":12}]},{"hash":"1463979694570045978","title":"Pollen tube growth and fertilization","description":"The cluster shows strong enrichment for plant reproductive processes: pollen tube growth, pollination, and double fertilization, supported by related cell wall remodeling (pectin metabolism) terms, pointing to a shared role in pollen tube function and fertilization. Some auxiliary terms (cell wall modification, protein localization) align with these processes, reinforcing the theme.","confidence":"High","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":2},{"id":"GO:0048358","count":2},{"id":"GO:0009860","count":2},{"id":"GO:0043086","count":2},{"id":"GO:0042545","count":2}]},{"hash":"1215356943139651831","title":"Developmental gene expression and RNA processing","description":"This cluster combines GO terms centered on development and morphogenesis (embryonic cranial skeleton morphogenesis, fat cell differentiation, response to muscle stretch) with core gene expression processes (DNA-templated transcription, mRNA processing) and regulatory activities (protein export from nucleus, telomere maintenance/capping, CDK activity regulation), suggesting proteins coordinating developmental programs through transcriptional/RNA processing control, with some cell-cycle and telomere-related regulation.","confidence":"Medium","size":12,"edges":11,"triangles":5,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":7},{"id":"GO:0046827","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0032212","count":6},{"id":"GO:0045736","count":6}]},{"hash":"2096050889287537790","title":"Nuclear import and cell cycle signaling","description":"The cluster centers on NLS-bearing protein import into the nucleus and regulation of signaling pathways (GTPase activity, MAPK), with associations to mitotic sister chromatid separation and ciliogenesis-related transport, suggesting a cohesive role in coordinating nuclear import with cell cycle\u2013related signaling. ","confidence":"Medium","size":12,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0001938","count":2},{"id":"GO:0051306","count":2},{"id":"GO:0000188","count":2}]},{"hash":"1812568046121067960","title":"Craniofacial and neural morphogenesis signaling","description":"The most represented GO terms center on development of facial structures and the optic nerve, together with neural growth signaling (neurotrophin TRK, FGF receptor pathways) and regulation of pathways like Wnt, pointing to a coordinated craniofacial/neural morphogenesis program.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":12},{"id":"GO:0048011","count":11},{"id":"GO:0090090","count":11},{"id":"GO:0020021","count":11},{"id":"GO:0071469","count":11}]},{"hash":"269557828232282229","title":"Bacterial cell division and cell wall biosynthesis","description":"The top GO terms concentrate on cell division and cell cycle, with related cell shape regulation, and concurrent biosynthetic processes for peptidoglycan and capsule polysaccharides, pointing to proteins involved in bacterial division and cell-wall construction. A few non-bacterial metabolic terms appear but are less representative of the cluster\u2019s core function.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0008360","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0019516","count":4},{"id":"GO:0045227","count":4}]},{"hash":"258358014958256654","title":"Mitotic Cell Cycle Regulation","description":"Dominant GO terms focus on cell division and mitosis, including regulation of the mitotic cell cycle and metaphase/anaphase transition, suggesting proteins involved in mitotic progression. While a few terms like ciliary motility and stress responses appear, they are less represented, so the core theme is mitotic control.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0035884","count":3},{"id":"GO:0060296","count":3},{"id":"GO:0036494","count":3},{"id":"GO:2001162","count":3}]},{"hash":"1042611828425395588","title":"Ubiquitin-Proteasome\u2013Mediated Degradation","description":"The cluster is dominated by GO terms related to ubiquitination and proteasomal degradation (SCF-dependent ubiquitin-proteasome pathway, SCF complex assembly, ubiquitin-dependent and K63-linked ubiquitination, ERAD), indicating a module focused on tagging proteins for degradation and protein quality control. Some septin/bud-neck organization terms suggest a link to cell cycle\u2013related cytoskeletal remodeling, which is often regulated by targeted proteolysis. Despite a few broader terms (viral process, NER), the core signal is ubiquitin-mediated proteolysis.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0000921","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0070911","count":3},{"id":"GO:0010265","count":3}]},{"hash":"850137373976435930","title":"Oocyte meiosis and spindle assembly","description":"The top GO terms cluster around oocyte maturation, spindle assembly in female meiosis I, and microtubule dynamics, with a strong emphasis on proteasome- and ubiquitin-mediated protein degradation (SCF-dependent processes). This combination points to proteins coordinating meiosis progression, spindle formation, and cell-cycle regulation in oocytes, with some related developmental processes that may reflect broader roles in cell division and differentiation.","confidence":"High","size":12,"edges":6,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":11},{"id":"GO:0006516","count":11},{"id":"GO:0008285","count":11},{"id":"GO:0007057","count":11},{"id":"GO:0051436","count":11}]},{"hash":"2196508443699549407","title":"Regulation of transcription, apoptosis, and signaling","description":"This cluster centers on various regulatory processes rather than a single pathway: transcriptional control (negative regulation by RNA Pol II), apoptosis/necroptosis regulation, protein ubiquitination, immune signaling (TLR), and cell-cycle regulation, with a couple plant development terms suggesting cross-species annotations. The common thread is broad regulatory control over cellular fate and signaling rather than a specific function, so the label reflects a general regulatory theme.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071300","count":2},{"id":"GO:0000122","count":1},{"id":"GO:0060544","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0043066","count":1}]},{"hash":"571686918522306083","title":"TLR/MyD88-Driven Antiviral Cytokine Signaling","description":"The cluster centers on innate immune signaling: MyD88-dependent TLR pathways, defense against virus, dsRNA response, and cytokine (including IL-8) production. While a few terms touch on broader cellular processes, the dominant theme is TLR-mediated antiviral signaling and cytokine regulation, suggesting a cohesive innate immune module.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002755","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0002730","count":2},{"id":"GO:0035751","count":2},{"id":"GO:2000172","count":2}]},{"hash":"255271839009985568","title":"Unknown","description":"The provided GO terms span diverse developmental programs (pituitary gland, multicellular organism development, neuron maturation, erythrocyte differentiation) alongside varied metabolic and stress-related processes (quinolinate and tetrahydrofolate metabolism, mercury detoxification, LPS response). There isn\u2019t a single, coherent functional theme linking these terms, so a concise, specific label cannot be justified. ","confidence":"","size":12,"edges":17,"triangles":0,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":7},{"id":"GO:0042128","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0007275","count":5},{"id":"GO:0045648","count":5}]},{"hash":"951050798823036858","title":"Wnt Signaling in Developmental Patterning","description":"This cluster is enriched for GO terms related to canonical and negative regulation of Wnt signaling and multiple developmental processes across tissues (hair follicle placode formation, fungiform papilla formation, renal outer medulla development, and superior colliculus development), suggesting a function in Wnt-mediated developmental patterning. The presence of cell-cycle regulation also aligns with Wnt's roles in growth control, supporting a coherent theme around developmental signaling rather than a single tissue-specific process.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0007050","count":11},{"id":"GO:0071681","count":9},{"id":"GO:0061380","count":9},{"id":"GO:0000011","count":9},{"id":"GO:0044336","count":9}]},{"hash":"515711695903694320","title":"RNA Pol II Transcription Regulators with Oxidative Stress Response","description":"This cluster is dominated by GO terms related to RNA polymerase II\u2013dependent transcription and regulation of DNA binding, along with other nuclear processes such as protein export from the nucleus and cell-cycle transition. Oxidative stress\u2013related terms (cellular response to oxidative stress and oxidant detoxification) appear alongside transcriptional regulation, suggesting the proteins function as nuclear transcription regulators that respond to cellular redox state. The viral process term may reflect broader host\u2013pathogen interaction contexts but does not override the core theme of transcriptional control and nuclear signaling.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000122","count":4},{"id":"GO:0016032","count":3},{"id":"GO:0000082","count":3},{"id":"GO:1903026","count":2}]},{"hash":"1176151256106225007","title":"Golgi-ER vesicle trafficking and mitotic signaling","description":"The top GO terms are dominated by vesicle transport between the ER and Golgi, Golgi organization, and retrograde transport, pointing to a core Golgi/ER trafficking function. There are also mitosis-related terms (spindle assembly checkpoint signaling, kinetochore attachment), suggesting a secondary link to cell division. Plant-specific terms like pollen tube growth and autophagy-related Cvt pathway appear, but do not override the central trafficking theme.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009860","count":2},{"id":"GO:0006890","count":1},{"id":"GO:0000301","count":1},{"id":"GO:0033227","count":1},{"id":"GO:0007030","count":1}]},{"hash":"442703936863795835","title":"Organelle RNA Editing and Processing","description":"This cluster centers on RNA modification and editing events in organelles, notably chloroplast and mitochondrial mRNA modification/processing, with signals between chloroplasts and the nucleus. The presence of cytidine-to-uridine editing and organelle-specific RNA processing terms supports a unifying theme of organelle RNA biology in plants. The embryo dormancy term suggests a plant context but does not override the primary organellar RNA theme.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":6},{"id":"GO:0016554","count":6},{"id":"GO:0080156","count":6},{"id":"GO:0000961","count":6},{"id":"GO:1905639","count":6}]},{"hash":"2267648676683967911","title":"Plant Transcription Regulation and Hormone Signaling","description":"The dominant terms point to transcriptional control (DNA-templated transcription and its regulation) and regulation of catalytic activity, complemented by plant-specific processes (phytochelatin biosynthesis and cytokinin signaling), suggesting a plant transcription-regulatory signaling module; a few terms (response to morphine, blood pressure) may be non-specific annotations.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006508","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0043085","count":3},{"id":"GO:1904715","count":3},{"id":"GO:0046938","count":3}]},{"hash":"1215636036559764760","title":"Angiogenic and Immune Receptor Signaling","description":"The cluster is enriched for GO terms related to receptor-mediated signaling, especially angiogenesis (VEGF receptor signaling) and immune cell receptor pathways (B and T cell signaling), plus related serine/threonine kinase signaling. While some developmental terms appear, the dominant theme ties to surface receptor signaling coordinating vascular and immune responses.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001525","count":7},{"id":"GO:0048010","count":7},{"id":"GO:0051092","count":7},{"id":"GO:0007178","count":7},{"id":"GO:0022038","count":7}]},{"hash":"1397648599431950730","title":"ER-Golgi Vesicle Trafficking","description":"The top GO terms point to vesicle-mediated transport from the endoplasmic reticulum to the Golgi and to retrograde transport from endosomes to the Golgi, all within general protein transport of the secretory pathway. This makes \"ER-Golgi Vesicle Trafficking\" a concise, representative label for this cluster.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:0042147","count":1},{"id":"GO:0015031","count":1}]},{"hash":"605483162197097084","title":"Ubiquitin-regulated NF-kappaB immune signaling","description":"This cluster centers on ubiquitination events (autoubiquitination and K48-linked ubiquitination) that regulate signaling, notably NF-kappaB, and it also includes immune-related processes such as B cell proliferation and V(D)J recombination, pointing to lymphocyte development and activation. The combination suggests a theme of ubiquitin-mediated control of immune signaling pathways.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090073","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0043123","count":2},{"id":"GO:0002322","count":2},{"id":"GO:1903382","count":2}]},{"hash":"1544255096364403894","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"The GO terms are dominated by oocyte maturation and spindle assembly in female meiosis I, with supporting themes of microtubule polymerization and ubiquitin-proteasome\u2013mediated protein turnover that regulate the meiotic cell cycle. Some neural development terms appear, but the core signal is meiosis/cell-cycle regulation in oocytes.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":5},{"id":"GO:0006516","count":5},{"id":"GO:0008285","count":5},{"id":"GO:0007057","count":5},{"id":"GO:0051436","count":5}]},{"hash":"1011928799813450446","title":"Oocyte maturation and meiotic spindle dynamics","description":"This cluster is dominated by GO terms tied to oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization, with supporting signals from ubiquitin-proteasome\u2013mediated protein turnover that regulates the cell cycle. While a couple of neural development terms appear, the strongest pattern centers on meiosis entry and spindle/microtubule functions in oocytes, making this a coherent, specific cluster label.","confidence":"High","size":11,"edges":35,"triangles":51,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":11},{"id":"GO:0006516","count":11},{"id":"GO:0008285","count":11},{"id":"GO:0007057","count":11},{"id":"GO:0051436","count":11}]},{"hash":"1837901740972872347","title":"Unknown","description":"The top GO terms span very diverse processes across metabolism, transcription, biosynthesis, and development (e.g., proton transport, mitochondrial complex assembly, LPS and colanic acid biosynthesis, GDP-mannose metabolism, hair follicle and labyrinthine layer development). This broad mix across kingdoms and functions provides no single cohesive theme or function to label the cluster, so an Unknown label with None confidence is appropriate.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1902600","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0033617","count":2},{"id":"GO:0042774","count":2}]},{"hash":"1325711960571561007","title":"Innate Immune and Neuronal Signaling","description":"The proteins cluster around innate immune functions, including MyD88-dependent TLR signaling and defense against virus, yet also include neuronal-relevant processes (synaptic potential regulation, dopamine response) and endosomal trafficking regulation, suggesting a theme where immune signaling interfaces with neuronal activity and intracellular transport.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0090394","count":6},{"id":"GO:0071287","count":6},{"id":"GO:0002755","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0035751","count":5}]},{"hash":"886966969258495530","title":"Plant organellar RNA editing and processing","description":"These terms cluster around RNA modification/editing in plant organelles (mitochondria and chloroplasts), including cytidine-to-uridine editing and organellar RNA processing/modification, plus chloroplast-nucleus signaling. This points to plant organellar RNA-binding/processing proteins (e.g., PPR family) as the likely functional group; the embryo development term may be incidental. ","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":1},{"id":"GO:0016554","count":1},{"id":"GO:0080156","count":1},{"id":"GO:0000961","count":1},{"id":"GO:1905639","count":1}]},{"hash":"373204599615119501","title":"RNA processing and translation","description":"Dominant themes are mRNA processing (splicing, polyadenylation, export) and translation (cytoplasmic translation, translation reinitiation). The co-occurrence of spliceosome and export terms supports a cohesive RNA metabolism cluster with ribosome-associated protein synthesis. A minor link to cell cycle may reflect shared regulation rather than a core function.","confidence":"High","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0002181","count":3},{"id":"GO:0007049","count":3},{"id":"GO:1900363","count":2},{"id":"GO:0002188","count":2}]},{"hash":"1529329065246696831","title":"Visual system and craniofacial neural development","description":"The top terms cluster around eye/optic nerve development (optic nerve morphogenesis, visual perception), facial development, and neural signaling (neurotrophin TRK signaling), suggesting a cohesive theme of neural development specific to the visual system and craniofacial structures, with supporting processes like cell migration and mitosis. A few terms relate more broadly but do not override the central theme.","confidence":"High","size":11,"edges":33,"triangles":42,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007100","count":10},{"id":"GO:0007601","count":10},{"id":"GO:0016477","count":10},{"id":"GO:0000278","count":10},{"id":"GO:0048011","count":9}]},{"hash":"1142300873775303609","title":"Mitochondrial Translation and Xenobiotic Stress","description":"The cluster is anchored by translation terms, especially mitochondrial translation, indicating protein synthesis within mitochondria. In addition, there are several stress-related terms (response to xenobiotic stimulus, response to antibiotic, response to toxic substance) suggesting coordinated detox and stress adaptation. A few other terms (protein homooligomerization, skeletal muscle differentiation) hint at broader complex assembly and potential muscle-associated context, but the dominant signal is mitochondrial protein synthesis coupled with xenobiotic/toxic stress responses. ","confidence":"Medium","size":11,"edges":53,"triangles":147,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0055114","count":2}]},{"hash":"2202114514143676904","title":"Metabolism and Oxidative Xenobiotic Stress Response","description":"These proteins cluster around central metabolism (TCA cycle and 2-oxoglutarate\u2013related processes) and various stress-response pathways, including oxidative stress and responses to xenobiotics such as ethanol and glucocorticoids. The presence of tRNA methylation and protoporphyrinogen IX biosynthesis hints at 2-oxoglutarate\u2013dependent dioxygenase activities linking metabolism to RNA modification and heme biosynthesis, which together frame a theme of metabolic remodeling under redox and chemical stress. Overall, the terms point to a metabolic-stress response module rather than a single isolated pathway.","confidence":"Medium","size":11,"edges":39,"triangles":63,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":3},{"id":"GO:0006979","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0045471","count":2},{"id":"GO:0051384","count":2}]},{"hash":"1608402213106912895","title":"Organelle RNA Editing and Translation Regulation","description":"This cluster centers on RNA modification and editing in mitochondria and chloroplasts, including cytidine-to-uridine editing, chloroplast RNA processing, and regulation of mitochondrial translation. The inclusion of chloroplast-nucleus signaling points to coordinated organellar gene expression in plants. The embryo dormancy term is peripheral but does not override the main organellar RNA theme.","confidence":"High","size":11,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":5},{"id":"GO:0016554","count":5},{"id":"GO:0080156","count":5},{"id":"GO:0000961","count":5},{"id":"GO:1905639","count":5}]},{"hash":"1080318105495666893","title":"Auxin signaling and growth regulation","description":"The strongest shared signal is auxin-related biology: regulation of organ growth, auxin-activated signaling, auxin polar transport, and response to auxin, suggesting this cluster captures an auxin response/growth module. The translation and transcription elongation terms may reflect linked regulatory processes or basal cellular functions accompanying hormone signaling.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0046620","count":2},{"id":"GO:0009734","count":2},{"id":"GO:0009926","count":2},{"id":"GO:0009733","count":2},{"id":"GO:0006412","count":2}]},{"hash":"522189213419243160","title":"Organelle RNA editing in mitochondria and chloroplasts","description":"The GO terms show RNA modification and cytidine-to-uridine editing, with explicit mentions of mitochondrial mRNA modification, chloroplast RNA modification/processing, and chloroplast-nucleus signaling. This points to a cluster of proteins involved in RNA maturation and editing within organelles (mitochondria and chloroplasts), potentially linking nuclear transcription to organelle RNA processing. While transcription-related terms appear, the organelle RNA metabolism terms dominate, supporting a label centered on organelle RNA editing and processing.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006353","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2}]},{"hash":"2267483640997465452","title":"Retinoid and lipid metabolism in reproduction","description":"Top GO terms include triglyceride metabolism, prostaglandin biosynthesis, retinoic acid biosynthesis and catabolism, and calcitriol biosynthesis, along with uterus and female gonad development. These collectively point to lipid/retinoid signaling pathways that influence reproductive biology.","confidence":"High","size":11,"edges":26,"triangles":24,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006641","count":10},{"id":"GO:0001516","count":10},{"id":"GO:0071615","count":9},{"id":"GO:0042904","count":9},{"id":"GO:0060065","count":9}]},{"hash":"1795339622862256967","title":"Diverse Biosynthetic Pathways","description":"These GO terms point to a range of metabolite biosynthesis processes (menaquinone, various fatty acids, lipoteichoic acid, siderophores, phenylpropanoids, and nonribosomal peptides), indicating enzymes involved in producing diverse metabolites rather than a single function. The shared theme is biosynthetic activity across different metabolite classes, justifying a label of Diverse Biosynthetic Pathways.","confidence":"High","size":11,"edges":11,"triangles":5,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0043041","count":5},{"id":"GO:0009234","count":5},{"id":"GO:0036112","count":5},{"id":"GO:0009698","count":5}]},{"hash":"1838789588822995303","title":"RNA processing and RNP assembly","description":"This cluster is dominated by RNA metabolism and ribonucleoprotein assembly processes, including P-body assembly, histone mRNA metabolism, spliceosome assembly and mRNA splicing, tRNA processing, and rRNA maturation. The convergence on multiple steps of RNA processing and mRNA decay suggests a coherent function in RNA maturation and RNP complex biogenesis, with some chromatin-associated terms reflecting nuclear RNA-chromatin context. Overall, it represents RNA processing machinery and processing-body dynamics.","confidence":"High","size":11,"edges":37,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0033962","count":6},{"id":"GO:0008334","count":6},{"id":"GO:1990141","count":6},{"id":"GO:0000387","count":6},{"id":"GO:0045292","count":6}]},{"hash":"75713065275904104","title":"Glucocorticoid-regulated keratinocyte development","description":"The top GO terms point to skin-related processes (keratinocyte development and differentiation) and glucocorticoid signaling (nuclear receptor-mediated glucocorticoid signaling pathway, glucocorticoid catabolic process), suggesting a cluster of proteins involved in epidermal maturation under glucocorticoid regulation. Additional terms on protein targeting, kinase activity regulation, and mitochondrial cytochrome c release indicate broader regulatory and stress-response roles that may accompany glucocorticoid signaling. Overall, the dominant theme is glucocorticoid-regulated keratinocyte development, with moderate confidence due to heterogeneity in terms. ","confidence":"Medium","size":11,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0003334","count":3},{"id":"GO:0000079","count":3},{"id":"GO:0021987","count":3},{"id":"GO:0006605","count":3},{"id":"GO:0030216","count":3}]},{"hash":"2122355662563448129","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":6},{"id":"GO:0090617","count":6},{"id":"GO:0009451","count":6},{"id":"GO:0080156","count":6},{"id":"GO:0000961","count":6}]},{"hash":"1483383890362459859","title":"Chromatin regulation and transcription control","description":"The top GO terms cluster around chromatin dynamics and transcriptional regulation, including histone modification (H3-K4 methylation and H3 acetylation), chromatin assembly, and repression of transcription by RNA polymerase II, plus rDNA heterochromatin formation. This suggests proteins in this cluster are involved in establishing chromatin states that modulate transcription. Some terms appear less related (antibiotic biosynthesis, gibberellin signaling) and may reflect annotation noise, but the dominant signal is chromatin-mediated transcription control.","confidence":"Medium","size":11,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051572","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0009938","count":2}]},{"hash":"38241368973254315","title":"RNA processing and translation machinery","description":"This cluster centers on RNA metabolism and protein synthesis, with prominent terms for tRNA processing, mRNA splicing, transcription termination, ribosome biogenesis, and translation, plus spliceosome and P-body involvement. While a few terms touch on chromatin or stress responses, the dominant theme is RNA processing and the machinery for gene expression from transcription to translation.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":4},{"id":"GO:0045292","count":3},{"id":"GO:0006369","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0006412","count":3}]},{"hash":"1115711911070354537","title":"Ribosome biogenesis and translational fidelity","description":"This cluster is dominated by GO terms for ribosome biogenesis, translation, rRNA processing, and regulation/maintenance of translational fidelity, with a minor hint of mitochondrial translation. The common theme is assembly of ribosomes and ensuring accurate protein synthesis, rather than a single metabolic pathway, making this label appropriate.","confidence":"High","size":11,"edges":49,"triangles":122,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042254","count":5},{"id":"GO:0006407","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0000447","count":2}]},{"hash":"1700995732023457032","title":"Skeletal muscle Ca2+ signaling and contraction","description":"The cluster shows strong representation of calcium handling in skeletal muscle (Ca2+ transport into SR/ER, ER Ca2+ concentration regulation, SR import, T-tubule organization) along with regulation of contraction and relaxation, aligning with excitation-contraction coupling in fast-twitch muscle. A single unrelated term (lipopolysaccharide biosynthesis) appears but does not define the overall theme. ","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":5},{"id":"GO:0031448","count":5},{"id":"GO:0033292","count":5},{"id":"GO:1903515","count":5},{"id":"GO:0090076","count":5}]},{"hash":"1938701941332935653","title":"Ribosome Biogenesis and Cytokinesis","description":"The top GO terms are dominated by ribosome-related processes (ribosome biogenesis, ribosomal small subunit biogenesis, tRNA modification), suggesting a cluster centered on the translation machinery. The presence of cell cycle, cell division, and cell septum assembly terms indicates a link to bacterial cytokinesis and division. A few terms related to stress responses are present but secondary to the main theme. Therefore, a label like \"Ribosome Biogenesis and Cytokinesis\" best captures the core function represented by this cluster.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:1903833","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0051301","count":1}]},{"hash":"73762709002813692","title":"Ribosome biogenesis and translation initiation","description":"This cluster is dominated by translation- and ribosome-related GO terms: translation, cytoplasmic translation initiation complex formation, translational initiation, and regulation of translational fidelity, along with maturation of LSU/5.8S rRNA and RNA (guanine-N7)-methylation. Together these point to ribosome assembly and the early steps of protein synthesis in the cytoplasm, with rRNA processing and modifications supporting ribosome maturation. The mitotic cohesion term is less central and likely incidental. Overall, the cluster reflects ribosome biogenesis and translation processes.","confidence":"High","size":11,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0007064","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2}]},{"hash":"11683948503989551","title":"Viral translation initiation and mRNA processing","description":"The cluster centers on translation initiation and reinitiation, including IRES-dependent viral translation, with supporting terms for preinitiation complex formation and regulation of initiation. It also includes mRNA processing features such as mRNA export and spliceosome-mediated splicing, suggesting a broader link between mRNA maturation and translation, particularly in viral contexts.","confidence":"Medium","size":11,"edges":6,"triangles":0,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0002188","count":5},{"id":"GO:0075525","count":5},{"id":"GO:0006406","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0006446","count":5}]},{"hash":"1936939169219692640","title":"Epithelial organ development (kidney and tooth)","description":"The cluster\u2019s top GO terms are dominated by kidney development and morphogenesis of an epithelium, with an additional odontogenesis term, suggesting a theme of epithelial organ development focusing on kidney and dental tissues. Some other terms (ion transport, pH response, hormone responses) appear auxiliary or context-specific, but the core signals point to epithelial organ formation. The lack of interactions (edges) introduces some noise, so the label is moderately confident rather than definitive.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001822","count":2},{"id":"GO:0002009","count":2},{"id":"GO:0006796","count":1},{"id":"GO:0009691","count":1},{"id":"GO:2001225","count":1}]},{"hash":"1549418229724948626","title":"mRNA splicing and post-transcriptional regulation","description":"The top GO terms are dominated by spliceosome-mediated splicing activities (alternative splicing, cis splicing, and regulation of splicing), along with mRNA processing steps such as export and polyadenylation regulation and mRNA stability in response to stress. A few translation reinitiation terms appear, but the core signal points to post-transcriptional RNA maturation and regulation. This suggests the cluster represents proteins involved in mRNA processing, splicing, and export rather than transcriptional control.","confidence":"High","size":11,"edges":11,"triangles":6,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":7},{"id":"GO:1900363","count":6},{"id":"GO:0002188","count":6},{"id":"GO:0075525","count":6},{"id":"GO:0006378","count":6}]},{"hash":"2213770830481246484","title":"Unknown","description":"The top terms show a highly diverse mix of processes (plant cytokinin biosynthesis, bacterial lipid A biosynthesis, nucleotide and NAD salvage, glycolytic regulation, DNA damage signaling, gluconeogenesis, and intestinal development) with no clear shared function. The cluster also has no edges or triangles, suggesting it may be heterogeneous or artifactual, so a coherent, representative label cannot be assigned.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009691","count":2},{"id":"GO:0009245","count":2},{"id":"GO:0006218","count":2},{"id":"GO:0019358","count":2},{"id":"GO:0034356","count":2}]},{"hash":"2278530862715171345","title":"Organelle RNA modification and processing","description":"The cluster shows enrichment for RNA modification and editing in mitochondria and chloroplasts (cytidine to uridine editing; mitochondrial and chloroplast RNA modification/processing) and chloroplast-nucleus signaling, indicating a cohesive function in organellar RNA maturation and regulation. The embryo development term appears incidental to the main theme.","confidence":"High","size":11,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0000961","count":3},{"id":"GO:1905639","count":3}]},{"hash":"1520163611834516305","title":"Ribosome biogenesis and translation","description":"The dominant GO terms point to ribosomal large subunit assembly/biogenesis and translation, with associated preribosome assembly. A few terms touch cell cycle checkpoints, which can accompany ribosome production during cell growth. Retina-related terms appear incidental and do not define the main function of the cluster.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032781","count":2},{"id":"GO:0031290","count":2},{"id":"GO:0010458","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0007093","count":2}]},{"hash":"435920537239171062","title":"Glycogen and lipid metabolism","description":"The top GO terms are dominated by energy metabolism, especially carbohydrate and lipid pathways: glucose metabolic process, glycogen biosynthetic process, triglyceride catabolic process (and its positive regulation), and cholesterol biosynthetic process. This suggests a cohesive metabolic module focused on energy storage and lipid synthesis/degradation. Some other terms (e.g., smooth muscle contraction, axon regeneration) appear ancillary and not core to this theme.","confidence":"Medium","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006006","count":2},{"id":"GO:0005978","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0010898","count":2}]},{"hash":"1075315028247134156","title":"Cellular stress response and genome maintenance","description":"The terms point to a theme where proteins participate in responding to cellular stress (cadmium, ROS, innate immunity) while also engaging in metabolism (cholesterol and glucose pathways) and genome maintenance tasks (DNA repair, replication, and cell cycle). This suggests a cluster of proteins involved in coordinating stress responses with genome integrity and metabolic regulation.","confidence":"Medium","size":11,"edges":9,"triangles":3,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0006695","count":3},{"id":"GO:0006006","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0006281","count":3}]},{"hash":"1142687358923442432","title":"Steroid and lipid metabolism","description":"The top terms are dominated by steroid-related metabolism: androgen catabolic, C21-steroid hormone metabolic, and general steroid catabolic processes, indicating turnover of steroid hormones. Complementing this are diverse lipid-related biosynthetic and catabolic processes (mycolic acid, phylloquinone, retinal, methyl-branched fatty acids, tetrahydrobiopterin), suggesting a broader lipid metabolism theme. A few terms (drug response, obsolete redox) are peripheral, but do not override the core pattern. ","confidence":"High","size":11,"edges":11,"triangles":3,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0031427","count":5},{"id":"GO:0006710","count":5},{"id":"GO:0006729","count":5},{"id":"GO:0008207","count":5}]},{"hash":"1449809574870282182","title":"Amino acid and cofactor biosynthesis","description":"The top GO terms show multiple amino acid biosynthetic processes (histidine, tyrosine, phenylalanine, lysine, alanine) plus biosynthesis of cofactors like heme and biotin, with additional related lipid biosynthesis and transport terms. This suggests the cluster is enriched for enzymes and pathways involved in synthesizing amino acids and essential cofactors. ","confidence":"High","size":11,"edges":25,"triangles":27,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019551","count":5},{"id":"GO:0019878","count":4},{"id":"GO:0000105","count":4},{"id":"GO:0015908","count":3},{"id":"GO:0042853","count":3}]},{"hash":"625431880999915512","title":"Nucleotide Metabolism and RNA Editing","description":"This cluster centers on nucleotide metabolism and RNA editing activities, including UMP/uridine biosynthesis and salvage, cytidine/deoxycytidine catabolism, cytosine metabolism, and A-to-I RNA editing of tRNA. The presence of riboflavin biosynthesis and a ribonucleotide-related signal reinforces a broad nucleotide-processing theme, though there is one outlier term about mammary gland epithelial cell proliferation. Overall, the predominant functions tie to nucleotide metabolism and RNA editing rather than a single signaling pathway.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033601","count":2},{"id":"GO:0002100","count":2},{"id":"GO:0019858","count":2},{"id":"GO:0044206","count":2},{"id":"GO:0009972","count":2}]},{"hash":"542106440394695354","title":"Cell cycle control and developmental signaling","description":"The dominant GO terms cluster around DNA replication, kinetochore localization, and regulation of cyclin-dependent kinase activity, highlighting cell cycle control; additional terms related to development (face development, optic nerve morphogenesis) and signaling pathways (Wnt, FGF, TRK) suggest a broader link to developmental signaling networks.","confidence":"Medium","size":11,"edges":17,"triangles":11,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045736","count":9},{"id":"GO:0034501","count":9},{"id":"GO:0006260","count":7},{"id":"GO:0048011","count":6},{"id":"GO:0090090","count":6}]},{"hash":"1934930746845275748","title":"Neuronal development and synaptic signaling","description":"The cluster is dominated by terms related to nervous system development, axon growth, and hippocampal development, along with excitatory postsynaptic potential and dopamine-responsive signaling. The inclusion of ERK/JNK/MAPK cascade terms supports a neuronal signaling context, linking growth with synaptic transmission. This combination best describes a group focused on neuronal development and synaptic signaling.","confidence":"High","size":11,"edges":42,"triangles":76,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045773","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0007399","count":2},{"id":"GO:1903351","count":2},{"id":"GO:0070374","count":2}]},{"hash":"1517314293966846995","title":"Stimulus-Responsive Signaling","description":"The top GO terms cluster around cellular responses to various stimuli (insulin, epinephrine, cAMP) and signal transduction processes like protein phosphorylation, with supporting terms in development, angiogenesis, plant signaling, and neural activity. This suggests the proteins participate in diverse signaling networks governing growth, differentiation, and neural responses, rather than a single tightly defined function. Confidence: Medium","confidence":"","size":11,"edges":5,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0032869","count":5},{"id":"GO:0071872","count":4},{"id":"GO:0051591","count":4},{"id":"GO:0006468","count":3}]},{"hash":"779456738256566466","title":"Osmoregulation and ion transport","description":"Most of the top GO terms point to water and ion balance (intracellular water homeostasis; cellular hyperosmotic response; cellular response to water deprivation; potassium ion transmembrane transport; acetate transport; endosomal lumen acidification), suggesting a shared function in osmoregulation and ion homeostasis. A couple of terms like visual perception and pancreatic juice secretion appear as outliers, likely annotation breadth rather than core cluster function.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009992","count":11},{"id":"GO:0007601","count":11},{"id":"GO:0072232","count":11},{"id":"GO:0080029","count":11},{"id":"GO:0006846","count":11}]},{"hash":"1055570972211711564","title":"Wnt-Driven Development and Organogenesis","description":"The cluster shows strong enrichment for terms related to regulation of canonical Wnt signaling (both negative and positive) alongside multiple developmental processes such as hair follicle placode formation, fungiform papilla formation, renal outer medulla development, and superior colliculus development, suggesting a common function in Wnt-regulated organogenesis and tissue patterning. Some terms (e.g., indole-3-methanol response, vacuole inheritance) are less clearly connected, but the dominant theme is Wnt pathway modulation in developmental contexts.","confidence":"Medium","size":11,"edges":50,"triangles":126,"max_degree":10,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0071681","count":9},{"id":"GO:0061380","count":9},{"id":"GO:0000011","count":9},{"id":"GO:0044336","count":9},{"id":"GO:0090090","count":9}]},{"hash":"1838912569419337073","title":"Petal development and floral morphogenesis","description":"The top GO terms cluster around petal development, petal number specification, organ boundary specification between lateral organs and the meristem, and post-embryonic plant morphogenesis, pointing to a cohesive theme of floral organ formation and broader plant structure development. Some terms about chloroplast mRNA processing and ubiquinone biosynthesis suggest additional housekeeping roles in plastids, but the dominant signal is floral organogenesis, particularly petals, and overall plant morphogenesis.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010239","count":1},{"id":"GO:0048507","count":1},{"id":"GO:0006744","count":1},{"id":"GO:0043086","count":1},{"id":"GO:0031426","count":1}]},{"hash":"1589847204430754174","title":"Developmental signaling and morphogenesis","description":"The top GO terms cluster around signaling pathways pertinent to development (neurotrophin TRK receptor signaling, Wnt signaling, FGFR apoptotic signaling) and tissue formation (face development, optic nerve morphogenesis). There are also core cell cycle processes (DNA replication, mitotic cell cycle), which are commonly active during growth and morphogenesis. A few terms relate to stress or host interactions, but the dominant theme appears to be signaling guiding development and tissue patterning, with accompanying cell proliferation. ","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0000278","count":10},{"id":"GO:0048011","count":9},{"id":"GO:0090090","count":9},{"id":"GO:0020021","count":9}]},{"hash":"2305397529039100519","title":"Nutrient-sensing metabolism and signaling","description":"GO terms cluster around glucose response, insulin secretion, nitrogen/ammonia metabolism, and growth regulation, indicating a theme of nutrient sensing and metabolic control. Some entries (e.g., synaptic transmission, protein homooligomerization) may reflect broader signaling or assembly processes, but the dominant pattern links nutrient management to metabolic regulation.","confidence":"Medium","size":11,"edges":24,"triangles":20,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0010756","count":6},{"id":"GO:0051260","count":6},{"id":"GO:0019676","count":6},{"id":"GO:0050679","count":6},{"id":"GO:0009749","count":6}]},{"hash":"2265291260247191781","title":"miRNA Biogenesis and RNAi Machinery","description":"This cluster is dominated by GO terms for miRNA processing (primary and pre-miRNA processing), RISC complex assembly, and RNAi-related antiviral immunity, plus regulation of miRNA metabolism and mRNA processing. The combination points to a coherent RNA silencing/RNA interference pathway, centered on miRNA maturation and RISC-mediated gene silencing. The inclusion of flower development hints at plant-specific developmental roles linked to miRNA pathways, reinforcing the miRNA/RNAi theme rather than unrelated transcription factors.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0009908","count":2},{"id":"GO:0035280","count":1},{"id":"GO:0031054","count":1}]},{"hash":"1613911791316897997","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0009734","count":2},{"id":"GO:0006808","count":2},{"id":"GO:1990180","count":1}]},{"hash":"1279871335734140520","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072752","count":2},{"id":"GO:0034414","count":2},{"id":"GO:1990928","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0038202","count":2}]},{"hash":"878485748426917009","title":"Mitotic machinery and chromosome dynamics","description":"The top GO terms are dominated by mitosis-related processes (mitotic spindle assembly, sister chromatid cohesion, cell division, and mitotic DNA replication). While a few terms touch on actin dynamics, nuclear pore localization, vesicle trafficking, and intraciliary transport, these do not overshadow the core mitotic theme. Confidently captures the primary function of the cluster.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030042","count":3},{"id":"GO:0031081","count":3},{"id":"GO:1903461","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0007064","count":3}]},{"hash":"269585833972886426","title":"Neural Innate Immune Signaling","description":"This cluster shows strong signals of innate immune activation: cellular response to lipopolysaccharide, response to exogenous dsRNA, defense against Gram-positive bacteria, and innate immune response with interferon-beta production. The inclusion of neural-context terms such as cellular response to dopamine and corpus callosum development suggests potential neuroimmune cross-talk, so a label emphasizing neural innate immune signaling is representative of the dominant functions in the cluster.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:1903351","count":11},{"id":"GO:0043330","count":11},{"id":"GO:0071222","count":11},{"id":"GO:0050830","count":11},{"id":"GO:0045087","count":11}]},{"hash":"369249633394428849","title":"Unknown","description":"The GO terms cover a highly diverse set of processes (aging, GTPase regulation, transcription, chloroplast protein import, development, foam cell differentiation, protein localization, and pain response) with no clear shared function or pathway across the proteins. The absence of edges and the broad, disjoint terms suggest no coherent theme suitable for a specific label.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0034260","count":2},{"id":"GO:0006351","count":2},{"id":"GO:2000031","count":1}]},{"hash":"235178891428923923","title":"Neural development signaling and morphogenesis","description":"This cluster centers on neural development and signaling, with terms like optic nerve morphogenesis, face development, neurotrophin TRK receptor signaling, and FGFR apoptotic signaling, plus regulation of Wnt signaling, suggesting a shared role in neural patterning and morphogenesis. There are also general transcription-related terms, but several outliers (chemotaxis, symbiont-mediated host transformation) reduce coherence, yielding a moderate level of confidence.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":8},{"id":"GO:0006351","count":7},{"id":"GO:0006935","count":7},{"id":"GO:0048011","count":6},{"id":"GO:0090090","count":6}]},{"hash":"1379797703444250389","title":"CDK Regulation and PARylation in Cell Cycle","description":"This cluster centers on core cell cycle control, highlighted by GO terms for the cell cycle itself, poly-ADP-ribosylation (PARP activity), and negative regulation of cyclin-dependent kinase activity and related serine/threonine kinase activity. These indicate a coherent theme of coordinating cell cycle progression and DNA damage response via kinase modulation and PARP-mediated signaling. A few terms (e.g., vitamin D response, salicylic acid signaling, NOD1 signaling, mRNA processing) are more peripheral, suggesting some annotation noise relative to the dominant cell-cycle/par-kinase theme.","confidence":"Medium","size":11,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0070212","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0033280","count":2},{"id":"GO:2000031","count":1}]},{"hash":"240961198242511014","title":"Brain and Retina Development Proteins","description":"Most enriched terms are brain/forebrain/retina development, pointing to neural development as the cluster's central theme. Other terms (protein homooligomerization, actin depolymerization, peroxisome targeting, nuclear pore localization, fertilization-related terms) are more general or cross-species, introducing some noise. The lack of edges means the label is inferred from GO term frequencies rather than interactions, giving a moderate level of confidence in this neural-development-based label.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0048235","count":1},{"id":"GO:2001162","count":1},{"id":"GO:0006625","count":1}]},{"hash":"374350874261758933","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000395","count":1},{"id":"GO:0000389","count":1},{"id":"GO:0010087","count":1},{"id":"GO:0035196","count":1},{"id":"GO:0030422","count":1}]},{"hash":"1877956585141427675","title":"Neuronal signaling and transcriptional regulation","description":"The terms center on neural function: DNA-templated transcription, glutamatergic synaptic transmission, receptor clustering, and excitatory postsynaptic potential, plus visual learning. A few terms relate to immune signaling or cytotoxic pathways, which may reflect multifunctional proteins or dataset noise. Overall, the dominant theme is neural signaling and transcriptional control.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0010200","count":4},{"id":"GO:0008542","count":3},{"id":"GO:0035249","count":3},{"id":"GO:0043113","count":3}]},{"hash":"1024188604579532855","title":"Cell cycle control and transcription regulation","description":"Most terms cluster around regulation of the cell cycle (G1/S transition, cell division, mitotic cycles) and transcriptional control (negative regulation of transcription by RNA polymerase II), suggesting a cohesive theme of coordinating cell cycle progression with transcription. There are additional signals related to DNA damage sensing and lipid signaling (nucleotide-excision repair recognition, oxylipin biosynthesis) and a few obsolete terms, which introduces some noise but does not override the core theme.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0030182","count":2},{"id":"GO:0000715","count":2},{"id":"GO:0031408","count":2}]},{"hash":"2225100193008152114","title":"Mitochondrial stress response and metabolism","description":"The cluster centers on mitochondrial functions, with terms like regulation of mitochondrial membrane permeability and protein import into the mitochondrial matrix, suggesting a core mitochondrial role. It also includes stress-adaptive and osmoprotectant-related processes (desiccation response, trehalose and glucosylglycerol biosynthesis) and a triglyceride biosynthesis regulator, plus a cell cycle regulatory term, indicating a broader link between mitochondrial function, lipid metabolism, and cellular stress responses. Overall, it points to a cohesive theme of mitochondria-associated stress adaptation and metabolic regulation.","confidence":"Medium","size":11,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":2},{"id":"GO:0010867","count":2},{"id":"GO:1903740","count":2},{"id":"GO:2000134","count":2},{"id":"GO:0070940","count":2}]},{"hash":"2010080952164224895","title":"RNA and protein methylation","description":"The top GO terms cluster around RNA modification (tRNA wobble uridine, tRNA methylation, rRNA modification) and several protein methylation events (peptidyl-lysine dimethylation, N-terminal peptidyl-alanine trimethylation, peptidyl-arginine dimethylation), suggesting a theme of RNA processing and post-translational methylation; a few terms like chlorophyll and vitamin E biosynthesis appear as outliers.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":2},{"id":"GO:0036068","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0018027","count":2}]},{"hash":"954665421176704129","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are dominated by ubiquitin-related protein catabolic processes and ubiquitination linkages (K6, K48), SCF-dependent proteasomal degradation, and autoubiquitination, indicating a cluster centered on ubiquitin-mediated proteolysis. Additional terms on histone turnover and ERAD tie into proteostasis and quality control, supporting a cohesive theme of regulated protein turnover.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:1903265","count":5},{"id":"GO:0036205","count":5},{"id":"GO:0085020","count":5},{"id":"GO:0051865","count":5}]},{"hash":"2083652914137103502","title":"MAPK-Driven Immune Signaling","description":"The presence of ERK1/ERK2 and p38MAPK cascades, together with cellular responses to GM-CSF, phorbol esters, and defense against virus, suggests a coherent theme of MAPK-mediated signaling involved in immune and stress responses. Some terms like face development, Wnt regulation, and symbiont-related host interactions point to broader developmental signaling roles, but the dominant pattern centers on MAPK-driven signaling in immunity and stress.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097011","count":6},{"id":"GO:0070371","count":6},{"id":"GO:0038066","count":6},{"id":"GO:1904628","count":6},{"id":"GO:0048011","count":5}]},{"hash":"1069776507702667390","title":"Unknown","description":"The top terms come from several unrelated biological areas (mitotic cell cycle, plant immune signaling, protein catabolic process, development, and amyloid metabolism). There is no single coherent function linking most terms, so the cluster appears functionally heterogeneous. ","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0080142","count":1},{"id":"GO:0002229","count":1},{"id":"GO:0010112","count":1},{"id":"GO:0030163","count":1}]},{"hash":"262714325039952813","title":"Chromatin remodeling and RNA processing","description":"The cluster\u2019s top GO terms cluster around DNA-templated transcription, chromatin remodeling, and snoRNA/snoRNP assembly and localization, pointing to regulation of gene expression via chromatin state and RNA processing, with supporting signals from histone modification and protein turnover. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0031146","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0000492","count":1},{"id":"GO:0031063","count":1}]},{"hash":"416265910904745881","title":"Unknown","description":"The top GO terms include both plant-specific hormone signaling and metabolism, plus diverse animal developmental processes, with no shared theme or links among proteins; therefore there isn\u2019t a coherent function to name the cluster beyond Unknown.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009742","count":1},{"id":"GO:0019762","count":1},{"id":"GO:0072156","count":1},{"id":"GO:0035914","count":1},{"id":"GO:0036268","count":1}]},{"hash":"546424666974634556","title":"Retinoic acid metabolism and female reproductive development","description":"The cluster centers on retinoic acid biosynthetic and catabolic processes and includes GO terms for uterus development, female gonad development, and female genitalia development, suggesting a link between retinoic acid metabolism and female reproductive development in these proteins.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071615","count":3},{"id":"GO:0042904","count":3},{"id":"GO:0060065","count":3},{"id":"GO:0008585","count":3},{"id":"GO:0034653","count":3}]},{"hash":"446258110897310639","title":"Nervous system development and dendrite morphogenesis","description":"The GO terms show a clear emphasis on neural development and neuron structure, with forebrain development, CNS formation, nervous system development, and dendrite morphogenesis being prominent. The other terms (e.g., methionine cycle, plant defense responses, TGF-beta signaling) appear as outliers, likely due to cross-species annotations or multifunctional roles, but do not override the dominant neural-development theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0033353","count":8},{"id":"GO:0048813","count":8},{"id":"GO:0030900","count":8},{"id":"GO:0021556","count":8},{"id":"GO:0009626","count":8}]},{"hash":"1844620755113931046","title":"Plant Development and Stress Response","description":"The top GO terms point to plant-related developmental and metabolic processes: gibberellin response, chlorophyll biosynthesis regulation, leaf senescence, flavonoid biosynthesis, and general multicellular organism development. There are also stress-related terms (osmotic stress) and chromatin remodeling tied to gene regulation during development. Some terms (e.g., pituitary gland and roof of mouth development) appear noisy, but the dominant signal centers on plant growth and metabolic regulation rather than a single non-plant process.","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":3,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0021983","count":6},{"id":"GO:0060021","count":4},{"id":"GO:0007275","count":4},{"id":"GO:1900056","count":4},{"id":"GO:0010380","count":4}]},{"hash":"2278240590699481476","title":"Cell Division and Innate Immune Response","description":"The top terms show a strong emphasis on cell division and mitotic regulation (cell division, mitotic cell cycle, positive regulation of mitotic metaphase/anaphase transition), alongside innate antiviral defense signals (defense response to virus, innate immune response). This suggests a cluster where cell-cycle control intersects with innate/antiviral responses, with a few peripheral terms hinting at broader stress-related processes (ER stress translation, ciliary regulation). Overall, the label reflects the dominant theme of division coupled with innate immune signaling.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0070389","count":4},{"id":"GO:0051607","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0045087","count":4}]},{"hash":"1570695055638806259","title":"SNARE-Mediated Synaptic Vesicle Trafficking","description":"These proteins cluster around vesicle trafficking through the secretory pathway and delivery of receptors to the synapse. Key GO terms point to ER-to-Golgi and intra-Golgi transport, Golgi ribbon organization, SNARE complex assembly, vesicle fusion with Golgi, and exocytic insertion of neurotransmitter receptors, which together align with synaptic vesicle trafficking and receptor localization underpinning long-term potentiation.","confidence":"High","size":11,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":5},{"id":"GO:0098967","count":5},{"id":"GO:0035493","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0060291","count":5}]},{"hash":"1867745849043258252","title":"Sterol biosynthesis and lipid metabolism","description":"The top GO terms are dominated by sterol and lipid biosynthetic processes, including cholesterol biosynthesis via lathosterol, ergosterol biosynthesis, and specific sterol oxidation steps, along with related ether lipid and fatty acid biosynthesis. Some terms touch on lipid-rich tissues (myelin, sebaceous glands), which aligns with lipid metabolism contexts. Overall, the cluster appears to group proteins involved in sterol/lipid biosynthesis and metabolism.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080065","count":3},{"id":"GO:0046485","count":3},{"id":"GO:0035754","count":3},{"id":"GO:0033490","count":3},{"id":"GO:0006633","count":3}]},{"hash":"246169267625845186","title":"Unknown","description":"These proteins show a broad mix of GO terms spanning chromatin modification (histone methylation), organelle targeting (peroxisome) and transport, developmental processes (forebrain and retina development, single fertilization), cytoskeletal dynamics (actin filament depolymerization), nuclear transport (nuclear pore localization), lipid signaling (SREBP pathway), and DNA damage response. There isn't a single cohesive biological theme tying these terms together, and several entries are obsolete or weakly connected, suggesting diverse or context-dependent roles rather than a shared function.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:2001162","count":5},{"id":"GO:0006625","count":5},{"id":"GO:0030900","count":5},{"id":"GO:0030042","count":5},{"id":"GO:0060041","count":5}]},{"hash":"1503402084376311265","title":"Transmembrane Transport and Metabolic Processes","description":"The Top Terms include several transmembrane transport processes (nitrate, magnesium ion, proton, and transepithelial water transport), indicating a membrane-associated transport function. Also present are metabolic process terms (carbohydrate metabolism) and regulation of iron transport, suggesting a broader theme of transport tied to metabolism. Some terms like import into nucleus or retina development are less connected, but the core signal appears to be membrane transport-related proteins with metabolic roles.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:1902593","count":3},{"id":"GO:0071353","count":3},{"id":"GO:0060041","count":3},{"id":"GO:0015706","count":3},{"id":"GO:0005975","count":3}]},{"hash":"425118219665694156","title":"Organellar RNA editing and processing","description":"Top GO terms point to RNA modification/editing and processing in mitochondria and chloroplasts, plus chloroplast-nucleus signaling, indicating a cohesive organellar RNA metabolism cluster in plants.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":7},{"id":"GO:0016554","count":7},{"id":"GO:0080156","count":7},{"id":"GO:0000961","count":7},{"id":"GO:1905639","count":7}]},{"hash":"98212476463931561","title":"Phospholipid Biosynthesis and Lipid Regulation","description":"The cluster is dominated by GO terms for phospholipid biosynthesis (phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, phosphatidylinositol) and related lipid signaling (platelet activating factor, response to PE), suggesting a lipid metabolism/regulation theme; a few terms about cell-cycle and synaptic regulation appear as secondary associations.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006646","count":1},{"id":"GO:0010512","count":1},{"id":"GO:0006655","count":1},{"id":"GO:0006659","count":1},{"id":"GO:0070317","count":1}]},{"hash":"133189200626400092","title":"Ribosome Biogenesis and RNA Methylation","description":"Top GO terms show strong enrichment for rRNA maturation and various RNA methylation processes (SSU/LSU rRNA, tRNA, and peptidyl-glutamine methylation), pointing to a core function in RNA processing and ribosome assembly. A few outlier terms (defense, lipid transport, small molecule catabolism) are likely ancillary or incidental. Overall, the cluster seems best described by RNA modification linked to ribosome biogenesis.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030490","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0000470","count":1},{"id":"GO:0030488","count":1},{"id":"GO:0018364","count":1}]},{"hash":"1603307465261306689","title":"Cell Cycle and DNA Repair","description":"This cluster is enriched for mitosis-related GO terms (mitotic spindle assembly, mitotic sister chromatid cohesion, cell division) plus DNA maintenance activities (DNA-templated transcription, nucleotide-excision repair preincision complex stabilization), pointing to nuclear processes governing cell-cycle progression and genome integrity. Some other terms about viral processes or symbiont interaction appear to be minor noise in the set.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0007064","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006293","count":1}]},{"hash":"2260473906772125708","title":"Unknown","description":"The GO terms are diverse (chlorophyll catabolic process, menaquinone and biotin biosynthesis, cellulose catabolic process, nitrogen utilization, detoxification, insulin secretion regulation, and response to toxic substances) with no connecting edges, so there is no cohesive function to label confidently.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060244","count":1},{"id":"GO:0015996","count":1},{"id":"GO:0008284","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0098869","count":1}]},{"hash":"1663354207228244046","title":"Renin-Angiotensin Kidney Regulation","description":"The top GO terms cluster around the renin-angiotensin system and kidney development (regulation of blood volume by renin-angiotensin; regulation of aldosterone production; mesonephros development), suggesting a kidney-regulation function for this cluster. Some terms (amyloid-beta metabolism, xylan catabolic process, response to cGMP) are less connected and may be incidental noise. Overall, the strongest signal points to renal and blood-pressure\u2013related regulation.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0030163","count":2},{"id":"GO:0002003","count":2},{"id":"GO:0001823","count":2},{"id":"GO:0070305","count":2}]},{"hash":"2237826316902533459","title":"Unknown","description":"The terms are a mix of plant-related cell wall processes (pectin catabolic process, cell wall organization, flower phyllotactic patterning) with various broad metabolic and catabolic processes (retinol metabolism, isoprenoid biosynthesis, coenzyme A catabolic), and there is no clear, cohesive function tying all proteins together. Given the lack of a consistent theme and no network structure to define a cluster, an Unknown label with no confidence is most appropriate.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0045490","count":2},{"id":"GO:0060773","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0042572","count":2}]},{"hash":"850093565540740889","title":"Hormone-Mediated Plant Defense and Nodulation","description":"The GO terms point to plant hormone signaling (cytokinin, gibberellin, abscisic acid) together with defense responses and nodulation, suggesting a cluster of proteins involved in hormone-regulated biotic interactions, including symbiotic nodulation and immunity. The presence of trafficking and ubiquitin-proteasome terms supports general cellular regulation that underpins these signaling and defense processes.","confidence":"High","size":10,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009607","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0006952","count":2},{"id":"GO:0009740","count":2},{"id":"GO:0009877","count":2}]},{"hash":"552123893660907648","title":"TLR-Mediated Innate Immunity and Cytokine Production","description":"The top GO terms cluster around Toll-like receptor signaling (MyD88-dependent), detection of LPS, and defense responses to Gram-positive bacteria and viruses, with cytokine production, indicating a coherent role in innate immune sensing and signaling; a few peripheral terms (e.g., chromatin and Golgi transport) are likely ancillary or incidental.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":2},{"id":"GO:0045079","count":2},{"id":"GO:0006348","count":2},{"id":"GO:0042127","count":2},{"id":"GO:0006893","count":1}]},{"hash":"1462329181144458453","title":"Flower development and transcriptional regulation","description":"The top GO terms cluster around floral development (floral meristem determinacy, stamen formation, floral whorl structural organization, regulation of double fertilization) and transcriptional regulation (DNA-templated transcription, regulation of RNA Pol II), with a few general cell-cycle terms (spindle assembly, centrosome cycle) and wound response, suggesting a cohesive theme centered on flower formation and its transcriptional control.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0051225","count":1},{"id":"GO:0007098","count":1},{"id":"GO:0010951","count":1},{"id":"GO:0009611","count":1}]},{"hash":"2018387343072502659","title":"Unknown","description":"The top GO terms are spread across vesicle transport (ER-Golgi), development (skeletal system, male gonad), immune defense, translation, and general proliferation, with no single unifying function dominating the cluster. This makes a specific, representative label unclear.","confidence":"","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0051770","count":3},{"id":"GO:0070317","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0001501","count":2}]},{"hash":"1232579816403073797","title":"Plant Growth Regulation and Stress Response","description":"These terms cluster around plant development and metabolism: gibberellin response, regulation of secondary cell wall biogenesis, chlorophyll and flavonoid biosynthesis, and osmotic stress responses. Together they point to a cohesive theme of growth control and stress adaptation in plants, with broader transcriptional regulation terms (chromatin remodeling, snRNA transcription) accompanying them. The occasional peripheral terms (e.g., viral process) may reflect broader annotation context rather than core function of the cluster.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:1901348","count":4},{"id":"GO:1900056","count":3},{"id":"GO:0010380","count":3},{"id":"GO:0009739","count":3},{"id":"GO:0006970","count":3}]},{"hash":"1460443685326293158","title":"Developmental cellular remodeling","description":"The terms span developmental morphogenesis (wing, oogenesis, chaeta), autophagy and apoptosis (cellular remodeling/quality control), and intracellular trafficking (ER\u2013Golgi, intraflagellar transport), suggesting a broad theme of development-linked cellular remodeling rather than a single pathway.","confidence":"Medium","size":10,"edges":29,"triangles":47,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0007476","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0006914","count":2},{"id":"GO:0019886","count":2}]},{"hash":"359994167475937908","title":"Oocyte meiosis I spindle assembly","description":"This cluster is dominated by processes linked to oocyte maturation and meiosis I spindle formation, including spindle assembly in female meiosis I, microtubule polymerization, and SCF-dependent ubiquitin-mediated protein degradation that drives meiotic transitions. A few terms point to neural development, but the strongest recurring themes are meiosis and cytoskeletal dynamics in oocytes.","confidence":"High","size":10,"edges":43,"triangles":104,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":10},{"id":"GO:0006516","count":10},{"id":"GO:0008285","count":10},{"id":"GO:0007057","count":10},{"id":"GO:0051436","count":10}]},{"hash":"1179773191291798962","title":"Developmental Gene Regulation in Muscle, Heart, and Neural Lineages","description":"The cluster centers on transcriptional regulation and differentiation across muscle, heart, and neural lineages (muscle morphogenesis, cardioblast migration, neuron fate commitment, amacrine/astrocyte differentiation) with supporting adhesion and signaling terms, suggesting coordinated gene expression control during development across these tissues.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":8},{"id":"GO:0060415","count":7},{"id":"GO:0060163","count":7},{"id":"GO:0033627","count":7},{"id":"GO:0032922","count":7}]},{"hash":"1147959775691310831","title":"Microtubule-based transport and dynamics","description":"The top GO terms cluster around microtubule-associated activities: regulation of microtubule-based processes, plus-end directed vesicle transport along microtubules, plus-end microtubule depolymerization, spindle dynamics in mitosis, and chloroplast movement, all indicating core involvement in microtubule dynamics and cargo transport. The inclusion of axonemal depolymerization and dendritic transport terms reinforces a general theme of microtubule-driven organization and movement across cellular contexts. Therefore, a label emphasizing microtubule-based transport and dynamics captures the shared function of this cluster.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009904","count":3},{"id":"GO:0032886","count":3},{"id":"GO:0098971","count":3},{"id":"GO:0070462","count":3},{"id":"GO:0000742","count":3}]},{"hash":"609624363974695144","title":"Neural and Muscle Development","description":"The top GO terms emphasize development in neural tissues (substantia nigra development; cerebral cortex radial glia migration) and skeletal muscle fiber development, suggesting a cluster tied to tissue differentiation and growth in brain and muscle. Additional terms point to signaling and regulatory activities (transcription regulation, phosphatase activity, extrinsic apoptotic signaling) that can modulate development and cellular dynamics. Overall, the cluster appears to center on developmental processes in neural and muscular contexts, with accompanying intracellular signaling roles.","confidence":"Medium","size":10,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045945","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0070262","count":2},{"id":"GO:2001241","count":2}]},{"hash":"1858910278841370294","title":"Cell stress, apoptosis, and cell cycle arrest","description":"The top GO terms cluster around apoptotic processes and DNA damage checkpoints, with additional signals for stress responses (nitric oxide, cadmium), hormone-related responses, and transcriptional regulation. This pattern suggests a coherent theme of cellular stress responses that can lead to programmed cell death and halt proliferation, despite some broader terms present (e.g., hormone signaling). Overall, the cluster appears to reflect stress-induced fate decisions and transcriptional changes rather than a single specialized pathway.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006915","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0071375","count":3},{"id":"GO:0048240","count":3},{"id":"GO:0071732","count":3}]},{"hash":"932879010359517131","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0090617","count":2},{"id":"GO:0001889","count":2},{"id":"GO:0009451","count":2}]},{"hash":"792452361943592544","title":"Unknown","description":"TheTop terms are a mix of metabolism and biosynthesis (dephosphorylation, cobalamin and antibiotic biosynthesis, sucrose catabolism) plus unrelated processes (thigmotropism, cell polarity, actin dynamics, karyogamy). With only a single edge and diverse biology, there is no cohesive theme linking these proteins, so the cluster cannot be given a clear label.","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0005987","count":2},{"id":"GO:0009652","count":1}]},{"hash":"520931838489075092","title":"Small GTPase signaling and membrane potential regulation","description":"The cluster is driven by terms centered on small GTPase\u2013mediated signal transduction and negative regulation of Ras signaling, along with regulation of membrane potential and cardiac repolarization. This points to a cohesive theme where GTPase signaling modulates cellular excitability and related processes, with ancillary terms reflecting broader stimulus responses (cAMP, caffeine, cold). Tetramerization is present but likely not the core driver of the cluster\u2019s function.","confidence":"Medium","size":10,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051262","count":5},{"id":"GO:0071320","count":5},{"id":"GO:0009409","count":5},{"id":"GO:0046580","count":4},{"id":"GO:0007264","count":4}]},{"hash":"2173284911132394685","title":"Cofactor biosynthesis and macromolecule modification","description":"This cluster centers on biosynthetic and modification processes: molybdopterin cofactor biosynthesis, iron-sulfur cluster assembly, lipoylation, glycine decarboxylation via the glycine cleavage system, methylation, and tRNA wobble uridine modification. While a few terms touch on protein quality control and cell cycle regulation, the dominant terms point to metabolic cofactor production and molecular modifications, suggesting a cohesive theme around cofactors and related post-translational or post-transcriptional modifications.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006515","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0006777","count":1},{"id":"GO:0019464","count":1},{"id":"GO:0009249","count":1}]},{"hash":"642682125660453967","title":"RNA processing and translation initiation","description":"This cluster combines RNA processing/splicing (spliceosome activity, mRNA export, polyadenylation) with translation initiation/reinitiation (preinitiation complex formation, translation reinitiation), suggesting a shared role in RNA maturation and coordinated control of translation.","confidence":"High","size":10,"edges":42,"triangles":99,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:1901407","count":5},{"id":"GO:1900363","count":4},{"id":"GO:0075525","count":4}]},{"hash":"1378124427080759379","title":"Organellar RNA Editing and Processing","description":"GO terms point to RNA modification and editing in mitochondria and chloroplasts, plus RNA processing and chloroplast\u2013nucleus signaling, suggesting a cohesive role in organellar RNA maturation and inter-organelle communication in plants.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0000961","count":3},{"id":"GO:1905639","count":3}]},{"hash":"934210639545743387","title":"Bacterial cell wall biosynthesis and division","description":"The top terms strongly point to cell envelope biosynthesis and remodeling (peptidoglycan biosynthesis, cell wall organization, regulation of cell shape) and core growth processes (cell cycle, cell division). Additional signals for lipopolysaccharide biosynthesis and related metabolic steps suggest a cohesive set of proteins that build and coordinate the bacterial cell envelope during growth, with some secondary metabolism signals (antibiotic biosynthesis) that can accompany envelope-related pathways. This makes \u201cBacterial cell wall biosynthesis and division\u201d a precise, representative label.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":3},{"id":"GO:0009252","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2}]},{"hash":"885603230538787247","title":"Central carbon metabolism and lipid biosynthesis","description":"This cluster is dominated by core energy pathways: glycolysis, the TCA cycle, gluconeogenesis, and fatty acid biosynthesis (via malonyl-CoA and acetyl-CoA). Amino acid catabolism (leucine, lysine) feeding into acetyl-CoA supports the central carbon flux. A few additional terms (ion transport, nucleoside metabolism) are present but less central to the main theme.","confidence":"High","size":10,"edges":41,"triangles":94,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006552","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0006096","count":4},{"id":"GO:0042759","count":4},{"id":"GO:0006094","count":4}]},{"hash":"2259901233823155690","title":"Terpenoid Biosynthesis","description":"This cluster is dominated by GO terms tied to isoprenoid/terpenoid production: farnesyl diphosphate, geranyl diphosphate, and geranylgeranyl diphosphate biosynthesis, plus monoterpene and cholesterol/quinone biosynthetic processes. These repeatedly point to a shared function in terpenoid/isoprenoid lipid biosynthesis. A couple of terms about translation or protein transport are present but do not define the core theme. Overall, Terpenoid Biosynthesis best captures the common function represented.","confidence":"High","size":10,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":3},{"id":"GO:0045337","count":3},{"id":"GO:0051290","count":3},{"id":"GO:1901663","count":3},{"id":"GO:0033384","count":3}]},{"hash":"1773496479293108558","title":"Photosynthesis-Related Metabolism and tRNA Modification","description":"The strongest signal is photosynthesis, with supporting processes like Mo-molybdopterin cofactor biosynthesis and redox homeostasis, plus tRNA modification pathways that can operate in plastids; while a couple terms are peripheral, the overall theme points to a photosynthesis-linked metabolic module.","confidence":"Medium","size":10,"edges":25,"triangles":27,"max_degree":9,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":4},{"id":"GO:0070329","count":1},{"id":"GO:0006071","count":1},{"id":"GO:0019346","count":1},{"id":"GO:0002143","count":1}]},{"hash":"1792556779033864555","title":"Bacterial LPS and cofactor biosynthesis","description":"This cluster is dominated by GO terms for lipopolysaccharide and O-antigen biosynthesis, as well as biosynthesis of cofactors like cobalamin and protoporphyrinogen. While there are other metabolic and transcription-related terms, the clearest pattern is the emphasis on bacterial surface component and essential cofactor production pathways, justifying a biosynthesis-focused label.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0009103","count":5},{"id":"GO:0009243","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0042853","count":4}]},{"hash":"933282375977931633","title":"RNA Translation and Splicing Machinery","description":"The cluster centers on translation across compartments (cytoplasmic and mitochondrial) with elongation and termination processes, together with spliceosome-associated RNA processing steps and regulatory ncRNA-mediated silencing, indicating a cohesive group of RNA-centric protein synthesis and processing components. A skeletal muscle differentiation term is present but not dominant, so the main theme remains translation and RNA splicing regulation.","confidence":"Medium","size":10,"edges":26,"triangles":28,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0032543","count":1},{"id":"GO:0070125","count":1},{"id":"GO:0035914","count":1}]},{"hash":"91649945522149591","title":"Mitochondrial Metabolite Transport","description":"The cluster centers on mitochondrial metabolite transport and metabolic regulation: multiple terms describe transmembrane transport of metabolites such as citrate, ornithine, CoA, and phosphate, as well as the malate-aspartate shuttle. Additionally, terms for cellular responses to insulin, IGF, amino acid starvation, and fatty acid reflect nutrient- and energy-responsive signaling linked to mitochondrial metabolism. Together, these terms point to a coherent module of mitochondrial transporters coordinating energy production and nutrient sensing.","confidence":"High","size":10,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":9},{"id":"GO:0032869","count":9},{"id":"GO:1990314","count":8},{"id":"GO:0070542","count":8},{"id":"GO:0048250","count":8}]},{"hash":"794793134071030844","title":"ER Protein Folding and Unfolded Protein Response","description":"The set is dominated by ER-related terms: SRP-dependent targeting to membranes, cellular response to unfolded protein, and regulation of ER stress\u2013induced apoptotic signaling, pointing to protein processing in the ER and the unfolded protein response. A few terms (karyogamy, DNA replication) are less aligned and likely incidental. Overall, the cluster reflects ER protein folding and stress response. ","confidence":"Medium","size":10,"edges":20,"triangles":22,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0006616","count":4},{"id":"GO:0016226","count":4},{"id":"GO:1900035","count":4}]},{"hash":"1552545250324281989","title":"RNA processing and ribosome biogenesis","description":"The strongest signals are splicing regulation, ribosome biogenesis, and translation, pointing to a core function in RNA processing and protein synthesis. The presence of DNA repair and SOS response terms suggests additional stress-responsive roles, but the dominant theme seems to be RNA processing and ribosome-related machinery.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048024","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0042274","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2}]},{"hash":"591431628126998798","title":"Cell cycle progression and DNA replication","description":"Dominant GO terms center on DNA-templated transcription, DNA replication, and key cell-cycle transitions (G1/S and G2/M), indicating a core function in cell-cycle entry and progression. Additional terms related to mammary epithelial proliferation and growth signaling (insulin and neurotrophin pathways) likely reflect supporting growth context for proliferating cells. Overall, the cluster is best described as cell cycle progression with DNA replication.","confidence":"High","size":10,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0006260","count":8},{"id":"GO:0033598","count":7},{"id":"GO:0000086","count":7},{"id":"GO:2000775","count":7}]},{"hash":"1414806842387947784","title":"Chromosome maintenance and mitosis","description":"Top GO terms indicate a focus on DNA replication, centromere/chromatin assembly (CENP-A), cell division, and microtubule dynamics, which together underpin chromosome maintenance during mitosis. Some terms (ER transport, ERAD, forebrain development) seem ancillary or noise, but the dominant signal is nuclear genome maintenance during cell division.","confidence":"High","size":10,"edges":12,"triangles":8,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0061641","count":3},{"id":"GO:0051013","count":3}]},{"hash":"132288858602780027","title":"Plant development and cuticle biosynthesis","description":"This cluster mixes terms tied to plant organ formation (bract, seed, floral meristem development) with hormone signaling (ethylene) and epidermal barrier production (cutin and wax biosynthesis). The combination suggests proteins involved in coordinating plant development with epidermal cuticle formation, rather than a single narrow function. Some terms are obsolete, but the underlying theme remains plant development linked to cuticle/wax regulation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0010200","count":2},{"id":"GO:0010432","count":2},{"id":"GO:0048316","count":2},{"id":"GO:0060774","count":2}]},{"hash":"996550720790897421","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":24,"triangles":33,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000462","count":9},{"id":"GO:0042273","count":8},{"id":"GO:0000463","count":8},{"id":"GO:0000398","count":8},{"id":"GO:0000466","count":8}]},{"hash":"798865690465720299","title":"RNA processing and translation initiation","description":"These proteins cluster around mRNA processing (splicing via spliceosome, alternative splicing, polyadenylation, export) and translation initiation (formation of translation preinitiation complex, translation reinitiation), suggesting a shared role in preparing transcripts for translation and assembling initiation machinery.","confidence":"High","size":10,"edges":18,"triangles":7,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":3},{"id":"GO:1900363","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0006378","count":2}]},{"hash":"1597907220317695093","title":"Plant shoot meristem development and stress-responsive translation","description":"This cluster combines plant development signals (axillary shoot meristem initiation, regulation of secondary shoot formation) with cellular stress responses that affect protein synthesis (amino acid starvation response, regulation of translational initiation in response to stress). The ribosome assembly term hints at growth-linked ribosome biogenesis, while telomere maintenance and apoptotic regulation reflect broader cellular stress regulation. Overall, it seems to group proteins involved in shoot development tied to stress-related control of translation.","confidence":"Medium","size":10,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0090506","count":4},{"id":"GO:0034198","count":4},{"id":"GO:2000032","count":4},{"id":"GO:0006407","count":4},{"id":"GO:0000028","count":4}]},{"hash":"988482491056045976","title":"Diverse Metabolic Pathways and Detoxification","description":"The top GO terms point to a range of metabolic processes (chlorophyll catabolism, beta-ketoadipate/aromatic compound degradation, menaquinone and biotin biosynthesis, monoacylglycerol catabolism) along with cellular oxidant detoxification and toxin response. There isn\u2019t a single cohesive pathway linking all proteins, but they cluster around general metabolism of small molecules and detox-related activities. Therefore the label reflects a broad metabolic/detox theme rather than a specific process.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015996","count":6},{"id":"GO:0009234","count":6},{"id":"GO:0098869","count":6},{"id":"GO:0019740","count":6},{"id":"GO:0009102","count":6}]},{"hash":"742891821154752191","title":"Unknown","description":"The top GO terms span lipid translocation, dephosphorylation, serine biosynthesis, multiple transcriptional processes (RNA-templated, RNA Pol II and Pol III), ribosome biogenesis, and diverse N-terminal methylation events, with no single cohesive function uniting these proteins. Consequently, there isn\u2019t a clear, shared theme to name the cluster.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045332","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0001172","count":2},{"id":"GO:0042797","count":2}]},{"hash":"184124564905685413","title":"mRNA processing and translation initiation","description":"The cluster is dominated by mRNA processing and export activities (splicing via the spliceosome, alternative splicing, mRNA polyadenylation/poly(A) regulation, mRNA export) together with translation initiation/reinitiation steps (formation of the translation preinitiation complex, translation reinitiation). This points to a cohesive function in post-transcriptional gene expression control and ribosome recruitment, despite some older annotations.","confidence":"High","size":10,"edges":33,"triangles":51,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":7},{"id":"GO:0045292","count":7},{"id":"GO:1901407","count":7},{"id":"GO:1900363","count":6},{"id":"GO:0002188","count":6}]},{"hash":"295248006508166082","title":"Coenzyme and Lipid Biosynthesis","description":"The top GO terms point to biosynthesis of key cofactors (coenzyme A, NAD+) and lipid/isoprenoid pathways (farnesyl diphosphate, cholesterol) along with related lipid metabolism (carnitine metabolism, beta-oxidation). This suggests a functional module centered on lipid-related metabolism and cofactor biosynthesis, with phosphorylation likely regulating these processes. ","confidence":"Medium","size":10,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":2},{"id":"GO:0046940","count":2},{"id":"GO:0015937","count":2},{"id":"GO:0009435","count":2},{"id":"GO:0046939","count":2}]},{"hash":"1623329802228005256","title":"Retinoic acid signaling in embryonic development","description":"The cluster is enriched for GO terms related to retinoic acid biosynthesis and RA receptor signaling, along with multiple embryonic development processes (forebrain, midgut, inner ear morphogenesis, pituitary development, etc.), suggesting a coherent RA-driven developmental program.","confidence":"High","size":10,"edges":24,"triangles":36,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042904","count":7},{"id":"GO:0021983","count":7},{"id":"GO:0036293","count":7},{"id":"GO:0048384","count":7},{"id":"GO:0048566","count":7}]},{"hash":"2189965896164911659","title":"Central carbon metabolism and stress responses","description":"The cluster shows core energy pathways (TCA cycle, glycolytic process, glyoxylate cycle) alongside diverse stress and signaling responses (response to cAMP, hypoxia, hydrogen peroxide, xenobiotic stimulus, estrogen) and regulation of photorespiration, indicating proteins involved in metabolism linked to environmental and hormonal signaling. ","confidence":"High","size":10,"edges":25,"triangles":34,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":4},{"id":"GO:0006096","count":3},{"id":"GO:0051591","count":3},{"id":"GO:0001666","count":3},{"id":"GO:0080093","count":3}]},{"hash":"1471821072634554792","title":"Negative regulation of signaling and synaptic organization","description":"The cluster shows a strong tilt toward down-regulating signaling pathways (negative regulation of PI3K/AKT signaling, MAPK, T cell receptor signaling) and related dephosphorylation processes, plus components related to synaptic structure (postsynaptic density assembly, synaptic vesicle clustering) and vascular permeability. This pattern suggests a cohesive theme of proteins that dampen signaling while modulating synaptic and endothelial processes.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0097107","count":6},{"id":"GO:0051895","count":6},{"id":"GO:1903984","count":6},{"id":"GO:2000808","count":6},{"id":"GO:0051898","count":6}]},{"hash":"503521547764880904","title":"Cell Cycle and DNA Replication with Proteostasis","description":"Although the cluster has no edges, its GO terms converge on cell division, mitotic cycle, DNA replication, and transcription, plus cytoskeletal organization and ubiquitin-proteasome\u2013mediated quality control. This points to a cohesive role in cell-cycle progression and genome maintenance, coupled with proteostasis mechanisms.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0031122","count":3}]},{"hash":"1964854985741628106","title":"DNA replication and cell cycle control","description":"This cluster is dominated by GO terms related to cell division: centrosome cycle, DNA replication, G2/M transition, and meiotic cell cycle, indicating a cohesive role in cell cycle progression. While terms like embryonic skeletal morphogenesis, sperm capacitation, and signaling pathways appear, they are secondary to the core replication/mitotic themes, so the label best reflects the primary function of the group.","confidence":"High","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007098","count":8},{"id":"GO:0048701","count":8},{"id":"GO:0010571","count":8},{"id":"GO:0006260","count":8},{"id":"GO:0000086","count":8}]},{"hash":"1330573916659542597","title":"Plant abiotic stress response and secondary cell wall biosynthesis","description":"The terms point to plant-specific abiotic stress responses (desiccation, freezing, high light) and ABA biosynthesis regulation, coupled with plant-type secondary cell wall biogenesis, suggesting a cluster of stress signaling and structural cell wall remodeling in plants. Sphingolipid biosynthesis terms may reflect membrane remodeling during stress, reinforcing this theme.","confidence":"High","size":10,"edges":31,"triangles":41,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0001576","count":2},{"id":"GO:0036210","count":2},{"id":"GO:0051999","count":2},{"id":"GO:0009269","count":1},{"id":"GO:0010116","count":1}]},{"hash":"953719872091593425","title":"Unknown","description":"The top terms show a diverse mix of cardiac, immune, transcriptional, developmental, neural signaling, and cell cycle processes, with no clear single function tying the proteins together. This heterogeneity suggests there isn\u2019t a coherent shared role for the cluster, so the label Unknown is appropriate.","confidence":"","size":10,"edges":4,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1903244","count":3},{"id":"GO:0043029","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":3}]},{"hash":"1771508371004239904","title":"RNA processing and translation initiation","description":"The terms point to post-transcriptional RNA processing (splicing, polyadenylation, export) and translation initiation/reinitiation (formation of the preinitiation complex, translation reinitiation). Together, these suggest a cluster of proteins coordinating RNA maturation and the start of translation, possibly linking splicing/export with translational control.","confidence":"High","size":10,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0006406","count":2}]},{"hash":"2247198748978419929","title":"Vesicle trafficking and exocytosis","description":"The cluster is enriched for GO terms describing vesicle targeting, Golgi-associated vesicle fusion, protein transport, exocytic insertion of receptors, and autophagosome docking, pointing to a secretory/recycling machinery theme. Some terms (floral organ abscission, response to freezing) reflect plant stress contexts, but the shared pattern is vesicle trafficking and receptor handling.","confidence":"Medium","size":10,"edges":23,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0010227","count":4},{"id":"GO:0050826","count":4},{"id":"GO:0070254","count":1},{"id":"GO:0001921","count":1},{"id":"GO:0006903","count":1}]},{"hash":"789512462124897637","title":"Plant cell wall remodeling and photosynthesis","description":"The cluster\u2019s top GO terms are dominated by plant-focused processes: pectin catabolic process, polysaccharide catabolic process, and cell wall organization indicate cell wall remodeling, while photosynthesis and the photosynthetic electron transport chain point to chloroplast energy production. Additional terms like floral organ abscission and phyllotactic patterning reinforce a plant developmental context, with a few outliers (e.g., dendritic spine development) likely representing noise.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0060773","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0000272","count":2}]},{"hash":"1169431528575667109","title":"Cell division and vesicle trafficking","description":"The cluster is driven by cell-cycle and growth signals (cell division, mitotic spindle assembly, cell population proliferation, multicellular organism growth) with a strong subset related to intracellular transport (retrograde Golgi-ER transport, COPII vesicle budding). A couple of terms point to chloroplast protein targeting and glucose metabolism, which may be ancillary or organism-specific, but the core pattern links division/growth with vesicle trafficking.","confidence":"Medium","size":10,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006007","count":2},{"id":"GO:0045036","count":2},{"id":"GO:0039707","count":2},{"id":"GO:0090307","count":2}]},{"hash":"1364813069742790777","title":"Ubiquitin-Dependent Protein Degradation and NF-kB Signaling","description":"It centers on ubiquitin-dependent protein turnover (K48-linked and general ubiquitination) and signaling pathways leading to NF-kB activation and TNF-mediated responses, with apoptosis regulation as a core outcome. Some terms touch on receptor turnover and other ubiquitin-associated processes, but ubiquitin-mediated degradation and immune signaling dominate.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0070936","count":3},{"id":"GO:0042981","count":3},{"id":"GO:0033151","count":3},{"id":"GO:0070535","count":3}]},{"hash":"1873108482372317455","title":"RNA Processing and Translation Control","description":"Go terms centered on mRNA processing (polyadenylation, splicing, export) and translation reinitiation/termination, with one item about transcription regulation by RNA Pol I. Although a couple of terms are obsolete or seemingly unrelated, the dominant set reflects RNA maturation and post-transcriptional regulation of gene expression, suggesting these proteins function together in RNA processing and translation control.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":1},{"id":"GO:0003334","count":1},{"id":"GO:0002188","count":1},{"id":"GO:1905000","count":1},{"id":"GO:0075525","count":1}]},{"hash":"668474800111283001","title":"Oxidative stress\u2013driven mitochondrial apoptosis","description":"These terms point to oxidative-stress\u2013driven, mitochondria-mediated apoptosis: intrinsic apoptotic signaling, cytochrome c release, and regulation of mitochondrial membrane potential, with additional hints of mitochondrial outer membrane protein insertion. While ER-Golgi transport and TGF-beta\u2013related responses appear, the strongest signal is oxidative stress\u2013induced mitochondrial apoptosis.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:0010917","count":1},{"id":"GO:0008631","count":1},{"id":"GO:0002037","count":1},{"id":"GO:0090200","count":1}]},{"hash":"343401557286500020","title":"Plant development and patterning (flowers, embryos)","description":"This cluster is enriched for GO terms related to plant organogenesis\u2014meristem development, flower development, axis specification, abaxial cell fate, and somatic embryogenesis\u2014indicating a coherent patterning and developmental program. Auxin signaling and fruit dehiscence further support a focus on organ formation and identity rather than general stress responses, with some cytoskeletal and transcriptional terms providing supporting context.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0001403","count":2},{"id":"GO:0034314","count":2},{"id":"GO:0009942","count":2},{"id":"GO:0010262","count":2}]},{"hash":"1032194268478165401","title":"Plant Cell Wall Biosynthesis & Root Hair Development","description":"The cluster is dominated by plant cell wall biology terms: cell wall organization, RG-II and cellulose biosynthesis, and plant-type secondary cell wall biogenesis, plus root hair cell development. Ethylene biosynthesis also aligns with root hair growth regulation, suggesting these proteins function in wall construction and modification that drive root hair formation. A few minor terms are less related noise. ","confidence":"High","size":10,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":5},{"id":"GO:0010306","count":3},{"id":"GO:0080147","count":3},{"id":"GO:0030244","count":2},{"id":"GO:0009834","count":2}]},{"hash":"243678679087405359","title":"Cell division and chromosome segregation proteins","description":"The strongest signals are GO terms for cell division, microtubule severing, and CENP-A\u2013containing chromatin assembly, which together point to roles in mitotic spindle function and centromere/kinetochore-driven chromosome segregation. Other terms (ER-Golgi transport, LDL receptor regulation) appear ancillary and do not alter the core theme. ","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0006888","count":2}]},{"hash":"1978549820620882051","title":"Neuronal signaling and retina development","description":"This cluster is dominated by neural-related terms: positive regulation of glutamatergic synaptic transmission, acetylcholine catabolic process in the synaptic cleft, and negative regulation of dendritic spine morphogenesis, along with retina development. A few terms about circadian regulation and neuronal metabolism support a brain-centric function theme. Some unrelated GO terms appear as noise (e.g., raffinose family oligosaccharide and cellulose catabolic processes), but the core signals point to neural signaling and eye/retina development.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":4},{"id":"GO:0006695","count":4},{"id":"GO:0009636","count":3},{"id":"GO:0010325","count":3},{"id":"GO:0010841","count":3}]},{"hash":"1439611381767931598","title":"Septin bud neck organization and cytokinesis regulation","description":"This cluster centers on septin ring organization and protein localization to the bud neck, with related processes in septation signaling, actin cable regulation, and mitotic spindle checkpoint signaling\u2014all components of budding yeast cytokinesis. Ubiquitin-dependent protein turnover (K48-linked ubiquitination) aligns with regulated proteolysis during division, reinforcing a theme of cytoskeletal organization and cell division control. Some unrelated terms (e.g., X inactivation, Wnt catabolism) appear as noise, but the dominant signal is bud neck/septin function and cytokinesis.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032186","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0090337","count":4},{"id":"GO:0046621","count":4},{"id":"GO:0070936","count":4}]},{"hash":"1123074186319096510","title":"Glycolysis and Carbohydrate Metabolism","description":"The top GO terms cluster around glycolysis and related carbohydrate pathways (canonical glycolysis, fructose-6-phosphate metabolism, glycogen catabolism, carbohydrate phosphorylation), suggesting these proteins mainly participate in central sugar metabolism. While a couple of biosynthetic terms appear, their signal is weaker, so the main theme is glycolysis/carbohydrate metabolism.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005980","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0006002","count":2},{"id":"GO:0061621","count":2},{"id":"GO:0093001","count":2}]},{"hash":"1492585722823413493","title":"Tubulin Assembly and Protein Folding","description":"The top GO terms point to microtubule/cytoskeleton assembly (tubulin complex assembly, cortical microtubule organization) alongside proteostasis functions (protein folding, chaperone-mediated assembly, ubiquitin-proteasome\u2013mediated quality control), suggesting a cluster of proteins involved in microtubule assembly with concurrent protein quality management. Some terms related to inflammatory regulation and transcription elongation appear incidental rather than core to the theme. ","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050729","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0007021","count":2},{"id":"GO:0043622","count":2},{"id":"GO:0032968","count":2}]},{"hash":"2301120200760220354","title":"Unknown","description":"The top terms show a mix of transcription regulation, development, signaling, and an outlier (symbiont-mediated host transformation), with no single cohesive function tying all proteins together. Because the cluster lacks a unifying theme, a specific, representative label cannot be justified.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0020021","count":1},{"id":"GO:2000753","count":1},{"id":"GO:0035171","count":1}]},{"hash":"1966322870692100647","title":"Plant cell wall biosynthesis and root hair development","description":"The dominant GO terms point to plant-specific processes: cell wall organization (GO:0071555), plant-type secondary cell wall biogenesis (GO:0009834), and rhamnogalacturonan II biosynthesis (GO:0010306), plus root hair cell development (GO:0080147). These strongly suggest proteins involved in plant cell wall formation and root hair growth. A few other terms appear unrelated (e.g., insulin response, leukocyte adhesion), likely annotation noise, but they do not override the main plant cell wall theme.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0009834","count":2},{"id":"GO:0010306","count":1},{"id":"GO:0080147","count":1},{"id":"GO:0034116","count":1}]},{"hash":"475117398269979931","title":"Organelle RNA Editing and Processing","description":"The top GO terms point to RNA modification and editing in mitochondria and chloroplasts, with several terms for mitochondrial and chloroplast mRNA processing/modification and chloroplast-nucleus signaling. This suggests the proteins act in organelle-specific RNA metabolism and inter-organelle communication rather than nuclear/cytosolic RNA processes. A plant-specific context is also implied by the seed dormancy term, but the dominant theme is organellar RNA editing/processing.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":1},{"id":"GO:0016554","count":1},{"id":"GO:0080156","count":1},{"id":"GO:0000961","count":1},{"id":"GO:1905639","count":1}]},{"hash":"1092565970180102574","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009904","count":1},{"id":"GO:0009903","count":1},{"id":"GO:0006621","count":1},{"id":"GO:2000209","count":1},{"id":"GO:0010869","count":1}]},{"hash":"1668096509811643047","title":"Epigenetic Regulation and Chromatin Organization","description":"The cluster\u2019s GO terms cluster around chromatin regulation, including cytosine methylation, histone methylation, and heterochromatin formation, indicating a chromatin-state control module. The developmental terms (uterine gland/uterus morphogenesis, nerve branching) can be mediated by epigenetic regulation during development, suggesting these proteins participate in chromatin-based control of gene expression across tissues. Overall, the group seems to reflect epigenetic regulation of gene expression tied to development, rather than a single signaling pathway.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002674","count":1},{"id":"GO:0048755","count":1},{"id":"GO:0090116","count":1},{"id":"GO:0051571","count":1},{"id":"GO:1903709","count":1}]},{"hash":"184517850679847321","title":"Ubiquitin-Driven Neural Development and Synaptic Regulation","description":"The cluster combines ubiquitin-dependent protein catabolic processes (APC-dependent, K11-linked ubiquitination) with neural development and synaptic functions (nerve branching, postsynaptic density assembly, glutamatergic transmission, corpus callosum development), suggesting proteins that regulate neural development and synapse formation/maintenance via ubiquitin-mediated turnover.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031145","count":1},{"id":"GO:0042787","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0070979","count":1},{"id":"GO:0048755","count":1}]},{"hash":"497323844358136719","title":"Unknown","description":"The GO terms are divergent (plasminogen activation, protein oligomerization, ammonia and nitrogen metabolism, epithelial proliferation, glucose response, insulin secretion, and glutamatergic signaling) with no clear shared function, and there are no edges connecting the proteins. This lacks a cohesive theme to anchor a specific label, so the cluster is best termed Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010756","count":1},{"id":"GO:0051260","count":1},{"id":"GO:0019676","count":1},{"id":"GO:0050679","count":1},{"id":"GO:0009749","count":1}]},{"hash":"1882971451257761344","title":"Unknown","description":"The GO terms are highly diverse (chlorophyll catabolic process, bacterial vitamin biosynthesis, nitrogen utilization, detox and stress responses, and even immune signaling), with no clear common function linking the proteins. This makes a specific, representative label unreliable.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015996","count":1},{"id":"GO:0008284","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0019740","count":1}]},{"hash":"1881954852561166171","title":"Mitotic Regulation and Endosomal Sorting","description":"The cluster centers on cell division and cell cycle control (cell division, exit from mitosis, cell cycle) and a strong signal for multivesicular body sorting/assembly, pointing to a link between mitotic regulation and endosomal trafficking. Additional terms related to autophagy regulation, mitochondrial organization, and fibroblast migration suggest broader cellular remodeling.","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0010458","count":5},{"id":"GO:0071985","count":5},{"id":"GO:0007049","count":5},{"id":"GO:1902902","count":5}]},{"hash":"268189860238738344","title":"Vesicle trafficking and exocytosis","description":"This cluster is centered on vesicle-related processes: regulation of synaptic vesicle exocytosis, regulation of Golgi-to-transport vesicle transport, and regulation of multivesicular body size, with supporting links to lipoprotein particle assembly and podosome-associated actin dynamics. Developmental signaling terms (brain and kidney development, SHH pathway) likely reflect secretory and trafficking roles essential to those processes. Overall, a concise label is vesicle trafficking and exocytosis.","confidence":"Medium","size":9,"edges":28,"triangles":39,"max_degree":8,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:2000300","count":8},{"id":"GO:0031384","count":8},{"id":"GO:0010796","count":8},{"id":"GO:0007420","count":8},{"id":"GO:0055108","count":5}]},{"hash":"1841523893754801414","title":"Cytokinin Signaling and Mitotic Regulation","description":"The cluster is dominated by GO terms for cytokinin-activated signaling and its regulation, plus processes tied to cell division such as spindle microtubule attachment and localization to the cytokinesis site, indicating a theme where cytokinin signaling interfaces with mitotic control. Osmosensory phosphorelay and phosphorylation terms further suggest a broader signaling module that links environmental signals to cell cycle events, with some transcription-related terms likely representing shared regulatory machinery.","confidence":"Medium","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006935","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0007234","count":2},{"id":"GO:0080038","count":2}]},{"hash":"2068378430210408625","title":"Redox homeostasis and detoxification","description":"This cluster is dominated by GO terms related to redox biology, including cellular redox homeostasis, cellular oxidant detoxification, and protein deglutathionylation, suggesting a common function in managing oxidative stress. Other terms like neural crest migration and nucleotide biosynthesis appear less central, but the redox-related functions are the strongest common thread.","confidence":"High","size":9,"edges":10,"triangles":5,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1902236","count":4},{"id":"GO:0003147","count":3},{"id":"GO:1903026","count":3},{"id":"GO:2000651","count":3},{"id":"GO:0098869","count":3}]},{"hash":"836582587759853000","title":"Auxin signaling and organ growth regulation","description":"The dominant GO terms cluster around SCF-dependent ubiquitin-proteasomal protein degradation and auxin-related signaling, including auxin-activated signaling, auxin polar transport, and responses to auxin, which together point to an auxin signaling pathway that governs organ growth. Other terms like peroxisome targeting, actin filament dynamics, and development of forebrain/retina may reflect broader or cross-species annotations and are less central to this theme.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0046620","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0009926","count":1},{"id":"GO:0009733","count":1}]},{"hash":"173880523695516276","title":"TLR-driven innate immune signaling","description":"The GO terms emphasize recognition of bacterial components (detection of LPS) and Toll-like receptor (MyD88-dependent) signaling, along with downstream cytokine production and modulation of pathways such as JNK. This points to proteins coordinating innate immune sensing and cytokine responses rather than a single enzymatic activity.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051770","count":2},{"id":"GO:0002755","count":1},{"id":"GO:0034145","count":1},{"id":"GO:0032497","count":1},{"id":"GO:0051607","count":1}]},{"hash":"1753175968454870757","title":"Endomembrane Trafficking","description":"The proteins are enriched for intracellular vesicle transport processes, especially endosome-to-Golgi retrograde transport, lysosomal and Golgi-to-vacuole trafficking, and endocytic recycling, plus granule transport regulation. This cohesive set points to functions in membrane trafficking and organelle turnover within the endomembrane system, despite one plant ABA signaling term that may be annotation noise.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0090156","count":2},{"id":"GO:0007041","count":2},{"id":"GO:0032456","count":2}]},{"hash":"1095181651135882975","title":"Unknown","description":"The Top Terms include several nervous system development and dendrite morphogenesis terms, but they are mixed with metabolism (L-methionine cycle), plant/defense responses, DNA damage signaling, and other unrelated processes. This diversity suggests there is no single cohesive function linking the proteins, so a specific, representative label cannot be confidently assigned.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0033353","count":7},{"id":"GO:0048813","count":7},{"id":"GO:0030900","count":7},{"id":"GO:0021556","count":7},{"id":"GO:0009626","count":7}]},{"hash":"1294974609854682315","title":"Plant development and hormone signaling","description":"The top GO terms point to plant-specific developmental processes (bract, seed, floral meristem growth) and hormone signaling pathways (auxin, ethylene, ABA), plus transcriptional regulation and cuticle biosynthesis, suggesting a cluster of plant developmental regulators interacting with hormonal signals. This theme best captures the shared function of the proteins in the cluster.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010200","count":2},{"id":"GO:0010432","count":2},{"id":"GO:0048316","count":2},{"id":"GO:0060774","count":2},{"id":"GO:0010451","count":2}]},{"hash":"1962758514651896618","title":"Chromatin remodeling and transcription regulation","description":"Proteins in this cluster are enriched for chromatin remodeling and transcriptional control, including chromatin remodeling (GO:0043044), nucleosome disassembly (GO:0006337), and regulation of transcription from RNA polymerase II promoter (GO:0005987, GO:0000436). While a few terms are non\u2013core or outliers (e.g., sucrose catabolic process, viral RNA replication), the dominant signals point to nuclear chromatin dynamics and transcriptional regulation as the cluster\u2019s shared function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900400","count":1},{"id":"GO:0005987","count":1},{"id":"GO:0000436","count":1},{"id":"GO:0039692","count":1},{"id":"GO:0031055","count":1}]},{"hash":"1155779139824328368","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048354","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0051084","count":2},{"id":"GO:0045041","count":2},{"id":"GO:0033617","count":2}]},{"hash":"1686800715269457730","title":"Organelle protein import","description":"Most terms point to targeting and import of proteins into mitochondria and chloroplasts (stroma/matrix) and membrane insertion, which defines the cluster as related to organelle protein import machinery. Some outliers (viral replication, histone regulation) appear as noise but do not override the core organelle import signal.","confidence":"Medium","size":9,"edges":14,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045037","count":2},{"id":"GO:0045039","count":2},{"id":"GO:0000002","count":2},{"id":"GO:0032094","count":2},{"id":"GO:0030150","count":2}]},{"hash":"1301206654861003403","title":"Central metabolism and heme biosynthesis","description":"The cluster centers on core metabolic processes: TCA cycle, gluconeogenesis, amino acid catabolism (lysine/leucine), and fatty acid biosynthesis, alongside heme/porphyrin biosynthesis. This points to mitochondria-associated energy and cofactor biosynthesis. A couple of immune/stress terms (response to oxidative stress, interleukin-4 response) appear but do not dominate, so the core theme remains metabolic. ","confidence":"High","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":3},{"id":"GO:0006094","count":3},{"id":"GO:0033512","count":3},{"id":"GO:0006783","count":2},{"id":"GO:0071353","count":2}]},{"hash":"131288710276627717","title":"Glycolysis, TCA Cycle, and Acetyl-CoA Metabolism","description":"The top GO terms cluster around central carbon metabolism: glycolysis, the TCA cycle, and pyruvate decarboxylation to acetyl-CoA, with contributions from 2-oxoglutarate metabolism, gluconeogenesis, and amino acid catabolism feeding into acetyl-CoA and fatty acid biosynthesis. A secondary theme involves protein homooligomerization and cell division, suggesting growth-associated metabolic activity. Overall, the proteins appear to form a core energy production and biosynthesis module.","confidence":"High","size":9,"edges":31,"triangles":55,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0006552","count":2}]},{"hash":"865718898260628036","title":"Bacterial Energy Metabolism and Flagellar Motility","description":"This cluster centers on energy-yielding pathways (respiration, TCA, fermentation, photosynthesis, methanogenesis) and contains terms for bacterial flagellum-dependent motility and flagellum assembly, pointing to a prokaryotic energy metabolism module linked to motility.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0022904","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0019516","count":3},{"id":"GO:0015948","count":3}]},{"hash":"458986913061152021","title":"Solute Transport Under Osmotic Stress","description":"The cluster centers on membrane transport of ions and small molecules (sodium-dependent cation transport, nitrite/nitrate/urate transport, glucose/fructose transport, potassium transport) and a related osmotic-stress response, with an additional note on neurotransmitter loading into synaptic vesicles indicating vesicular transport\u2014together signaling a cohesive theme of solute/ion transport and osmotic regulation.","confidence":"High","size":9,"edges":13,"triangles":5,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":2},{"id":"GO:0070715","count":2},{"id":"GO:0044381","count":2},{"id":"GO:0071332","count":2},{"id":"GO:0015707","count":2}]},{"hash":"637606458343946238","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by ribosome-related GO terms (translation, ribosome biogenesis, ribosomal subunit assembly, and tRNA modification), suggesting proteins primarily involved in ribosome production and protein synthesis. Other terms such as cell cycle or amino acid starvation response appear secondary to the ribosome-focused theme.","confidence":"High","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042274","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000027","count":2},{"id":"GO:1903833","count":2}]},{"hash":"1568935381313187193","title":"Bacterial cell wall biosynthesis and envelope organization","description":"The top GO terms point to bacterial envelope-related processes: peptidoglycan biosynthetic process and cell wall organization, alongside phenazine biosynthetic process, all of which are characteristic of bacterial metabolism and cell envelope construction. Some non-bacterial terms (e.g., epithelial maintenance and SMAD signaling) appear, likely representing noise or misannotations, but the strongest recurring theme is bacterial cell wall biosynthesis and envelope remodeling. Confidence in this label is Moderate to Low due to the mixed terms, so I assign Low.","confidence":"Low","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0002047","count":2},{"id":"GO:0030277","count":2},{"id":"GO:0060394","count":2},{"id":"GO:0009405","count":2}]},{"hash":"1110979578306474725","title":"Photosynthesis Light Harvesting and Light Response","description":"The cluster is dominated by GO terms for photosynthesis and light-response processes (light harvesting in PSI and PSII, responses to low and high light, various light wavelengths, and nonphotochemical quenching), suggesting a cohesive group of chloroplast-associated proteins involved in light capture and protection.","confidence":"High","size":9,"edges":23,"triangles":21,"max_degree":7,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":4},{"id":"GO:0009768","count":4},{"id":"GO:0009645","count":4},{"id":"GO:0071486","count":4},{"id":"GO:0018298","count":4}]},{"hash":"711388634227101089","title":"Lignan and phenylpropanoid biosynthesis","description":"This cluster is dominated by GO terms tied to lignan and phenylpropanoid pathways, including lariciresinol and pinoresinol biosynthesis and related anthocyanin/phenylpropanoid biosynthetic processes, suggesting a cohesive role in plant secondary metabolism. The presence of glycolytic and transcription-related terms likely reflects shared cellular processes or annotation background, and a single colanic acid biosynthetic term may be noise or cross-species annotation. Overall, the pattern points to lignan and phenylpropanoid biosynthesis as the core function of this cluster.","confidence":"High","size":9,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006541","count":3},{"id":"GO:0006096","count":2},{"id":"GO:0009242","count":2},{"id":"GO:1902132","count":2}]},{"hash":"2041887547335128647","title":"Unknown","description":"The top GO terms span photosynthesis, cell cycle/division, various metabolic and redox processes, and stress/immune responses, with no single dominant function binding the proteins. This broad and mixed set suggests a heterogeneous or noisy cluster rather than a coherent biological theme, so a concise, representative label cannot be reliably assigned.","confidence":"","size":9,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0033859","count":1}]},{"hash":"534298614573988502","title":"Developmental signaling and mitotic regulation","description":"This cluster mixes developmental and morphogenetic processes (face development, optic nerve morphogenesis, neurotrophin signaling, and Wnt pathway regulation) with mitotic/cell-cycle control (centrosome separation, kinetochore localization, and CDK activity regulation), suggesting proteins involved in coordinating development with cell division. Some terms like symbiont-mediated host cell transformation are less clearly connected but may reflect broader cell\u2013host interactions.","confidence":"Medium","size":9,"edges":14,"triangles":8,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031532","count":8},{"id":"GO:0007100","count":8},{"id":"GO:0045736","count":8},{"id":"GO:0034501","count":8},{"id":"GO:0048011","count":7}]},{"hash":"659514404589991932","title":"Nuclear transcription regulation and chromatin remodeling","description":"This cluster centers on DNA-templated transcription, chromatin remodeling, and transcription initiation-coupled remodeling, with supporting RNA processing (spliceosome) and regulation of RNA Pol II activity. Minor developmental terms appear incidental; the dominant theme is nuclear gene expression control.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0043044","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0045944","count":2},{"id":"GO:2000616","count":2}]},{"hash":"13129906835198595","title":"Ribosome Biogenesis and Translation","description":"Top terms cluster around ribosome assembly and function (ribosome biogenesis, ribosomal small subunit biogenesis, cytoplasmic translation, tRNA modification) with additional signals of cell growth/division, suggesting a coherent role in protein synthesis and ribosome maintenance during proliferation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0042254","count":3},{"id":"GO:1903833","count":2},{"id":"GO:0007049","count":2}]},{"hash":"1030406743462019879","title":"Ribosome Assembly and Translation Control","description":"This cluster mainly features translation-related GO terms (translation, preinitiation complex formation, translation reinitiation, regulation of translation) and ribosome biogenesis/maturation (SSU rRNA processing, rRNA methylation), pointing to proteins involved in ribosome assembly and the protein-synthesis machinery. A couple annotations like neural tube closure and antibiotic response are less representative.","confidence":"High","size":9,"edges":22,"triangles":23,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0001731","count":2},{"id":"GO:0032790","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0000462","count":2}]},{"hash":"468603884351146315","title":"RNA processing and translation initiation","description":"These terms point to RNA maturation steps (splicing, polyadenylation, export) and translation initiation processes (preinitiation complex formation, reinitiation). This indicates a group of proteins involved in post-transcriptional gene expression control, spanning both RNA processing and translation initiation.","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0006378","count":1},{"id":"GO:0006406","count":1}]},{"hash":"1449268858301890314","title":"Ubiquitin-Proteasome Antiviral and Inflammatory Signaling","description":"The top GO terms emphasize ubiquitin-dependent degradation (K48-linked, SCF), viral processes, and inflammatory pathways (TNF signaling, prostaglandin biosynthesis, vitamin D response), suggesting the cluster centers on antiviral responses mediated by the ubiquitin-proteasome system and inflammatory signaling.","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0033209","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0001516","count":2}]},{"hash":"773095359019754912","title":"Ribosome Biogenesis and Translation Initiation","description":"GO terms point to ribosome assembly (ribosome biogenesis, small subunit biogenesis, rRNA maturation) along with initiation steps (preinitiation complex formation, cytoplasmic translation) and tRNA modification, indicating a cohesive group of proteins involved in ribosome production and the start of protein synthesis. The presence of a few cell cycle/division terms likely reflects growth coordination, but the dominant theme is ribosome biogenesis and translation. ","confidence":"High","size":9,"edges":24,"triangles":32,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2}]},{"hash":"29672395650452577","title":"Neural development and axon guidance","description":"This cluster's top GO terms cluster around nervous system development, brain/forebrain development, dendrite morphogenesis, and motor neuron axon guidance, indicating a neural development and connectivity theme. Some terms (DNA replication, ER-stress\u2013related apoptosis) are present but less representative. ","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0008045","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0070059","count":2}]},{"hash":"632508252322132615","title":"N-terminal peptide methyltransferases","description":"The top GO terms are dominated by specific N-terminal peptidyl methylation activities (glycine, alanine, serine) and general methylation, pointing to a shared function as N-terminal methyltransferases; other biosynthetic terms may reflect broader substrate contexts but do not define the core enzymatic role.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018013","count":5},{"id":"GO:0018012","count":5},{"id":"GO:0035572","count":5},{"id":"GO:0035573","count":5},{"id":"GO:0051555","count":4}]},{"hash":"1189270790779739336","title":"Cytokinin signaling and transcriptional regulation in plant growth","description":"This cluster centers on cytokinin-activated signaling and multiple transcription regulation terms (DNA-templated transcription, regulation of transcription by RNA Pol II), with supportive themes of chromatin remodeling and growth processes (secondary cell wall biogenesis, secondary growth). Together these terms point to a group of proteins linking hormone signaling to transcriptional control that drives plant growth. ","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0000122","count":2},{"id":"GO:1901348","count":2}]},{"hash":"2068458954814428954","title":"mRNA Splicing and Export Machinery","description":"The top GO terms emphasize spliceosomal mRNA processing (cis and alternative splicing), mRNA export from the nucleus, and related post-transcriptional regulation (stability, translation reinitiation), pointing to a cohesive module for RNA maturation and export.","confidence":"High","size":9,"edges":11,"triangles":4,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006406","count":5},{"id":"GO:0010610","count":5},{"id":"GO:1900363","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0075525","count":4}]},{"hash":"679701231798911673","title":"Cell Cycle and Mitosis Regulation","description":"Most of the top GO terms point to cell division and mitosis, including cell division, positive regulation of CDK activity, mitotic cell cycle processes, and chromosome condensation. While a few terms touch on autophagy initiation and tissue-specific proliferation (mammary gland), the dominant signal is regulation of the cell cycle and mitotic progression, suggesting this cluster groups proteins involved in cell-cycle control and mitosis.","confidence":"High","size":9,"edges":29,"triangles":43,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0045737","count":7},{"id":"GO:0060153","count":6},{"id":"GO:0010673","count":6},{"id":"GO:0035186","count":6}]},{"hash":"623057610252836123","title":"Amino Acid and Lipid Biosynthesis","description":"This cluster shows a mix of biosynthetic processes for several amino acids (tyrosine, alanine, lysine) along with lipid- and cofactor-related biosynthesis (sphinganine, biotin, heme) and even fatty acid transport, together with a cellular response to insulin stimulus. The common thread is metabolic/biosynthetic activity rather than a single precise pathway, so a general \u201cAmino Acid and Lipid Biosynthesis\u201d label fits best.","confidence":"Medium","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032869","count":5},{"id":"GO:0019878","count":5},{"id":"GO:0015908","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0033585","count":4}]},{"hash":"1239532081899187880","title":"RNA splicing and transcription machinery","description":"The top GO terms are mRNA splicing via spliceosome and DNA-templated transcription, pointing to nuclear RNA processing and transcription roles as the cluster\u2019s core functions. Other terms like stress-related responses appear less central, suggesting they are incidental. This supports a cohesive theme around gene expression at the RNA processing/transcription level.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071291","count":1},{"id":"GO:0003069","count":1},{"id":"GO:0055114","count":1}]},{"hash":"2052836491079599488","title":"Amino acid biosynthesis and catabolism","description":"This cluster is dominated by GO terms related to amino acid metabolism, including biosynthetic processes for beta-alanine, lysine, ornithine, alanine, and biotin, as well as catabolic processes for putrescine and alanine. There\u2019s also a biosynthesis term for protoporphyrinogen IX (a porphyrin pathway) and an antibiotic biosynthesis term, suggesting a broader metabolic rather than signaling role. The presence of both biosynthesis and catabolism of amino acid\u2013derived metabolites points to a cohesive theme around amino acid and cofactor metabolism, despite some outlier or obsolete terms.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048148","count":2},{"id":"GO:0009413","count":1},{"id":"GO:0009447","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0019483","count":1}]},{"hash":"900319102550271090","title":"Multi-organ morphogenesis and differentiation","description":"These proteins cluster around developmental processes across several organs: cardiac vascular smooth muscle differentiation, atrial septum and ventricular septum development, uterus development, and inner ear morphogenesis, with related signals such as estrogen response and calcium ion signaling. While immune-related terms (T-helper 2 differentiation, cellular response to interleukin-4) appear, the dominant theme is morphogenesis and differentiation across multiple tissues, rather than a single pathway. ","confidence":"Medium","size":9,"edges":30,"triangles":50,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045064","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0060947","count":4},{"id":"GO:0071353","count":4},{"id":"GO:0071277","count":3}]},{"hash":"1761862726157824758","title":"Embryonic organogenesis and tissue differentiation","description":"The terms point to broad embryonic organogenesis and tissue differentiation across multiple organs (brain regions, sensory organs, pancreas, teeth, reproductive organs). This cluster likely represents factors involved in general developmental differentiation rather than a single pathway.","confidence":"Medium","size":9,"edges":15,"triangles":7,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060065","count":6},{"id":"GO:0021905","count":6},{"id":"GO:0008585","count":6},{"id":"GO:0030917","count":6},{"id":"GO:0021983","count":6}]},{"hash":"275939927166173540","title":"Heart and neural development","description":"The top GO terms point to developmental programs shaping the heart and nervous system, including heart development, axonogenesis, and Schwann cell development, along with angiogenesis. Additional terms related to transcriptional control, cell cycle, and apoptosis suggest coordinated gene regulation during organogenesis. A plant-specific term appears among the list but the prevalent themes support a vertebrate developmental cluster focused on cardiovascular and neural tissues.","confidence":"Medium","size":9,"edges":12,"triangles":11,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046826","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0001525","count":5},{"id":"GO:0009738","count":5},{"id":"GO:0000086","count":5}]},{"hash":"1962272573349894962","title":"Neural development and growth factor signaling","description":"The cluster is dominated by neural- and development-related signaling terms: neurotrophin TRK receptor signaling, optic nerve morphogenesis, and face development, along with FGF receptor signaling and PI3K/AKT pathway involvement. Negative regulation of Wnt signaling also fits into developmental patterning. While some terms reflect broader stress responses, the prevailing theme is neural development linked to growth factor signaling. ","confidence":"High","size":9,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":4},{"id":"GO:0090090","count":4},{"id":"GO:0020021","count":4},{"id":"GO:0071469","count":4},{"id":"GO:0060324","count":4}]},{"hash":"855748761247169753","title":"Mitosis and spindle assembly","description":"This cluster centers on mitotic processes and microtubule organization. Dominant GO terms include mitotic spindle pole body duplication, mitotic spindle midzone assembly, microtubule nucleation, and general cell cycle/cell division, indicating a core function in mitosis and spindle dynamics. A few terms related to neuron differentiation and mechanosensory signaling suggest additional roles of microtubule dynamics in neuronal development and mechanotransduction, but the prevailing theme remains mitosis and spindle assembly.","confidence":"High","size":9,"edges":24,"triangles":35,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":7},{"id":"GO:0007020","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0051258","count":4},{"id":"GO:0030182","count":4}]},{"hash":"1095095797691193095","title":"Nucleocytoplasmic Transport and Mitosis Regulation","description":"The top GO terms point to nuclear import/export (NLS-bearing protein import into nucleus; mRNA export from nucleus) and mitotic processes (cell division; mitotic sister chromatid separation), suggesting a theme of coordinating nuclear transport with cell cycle progression. Additional signals related to signaling regulation (GTPase activity, serine dephosphorylation) reinforce a regulatory role, while a few terms like viral process or endothelial proliferation appear ancillary. Overall, the cluster seems to represent proteins involved in nucleus-cytoplasm transport tied to mitotic control.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0006607","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0006406","count":4},{"id":"GO:0050790","count":4}]},{"hash":"488505919437920802","title":"Ion and Small Molecule Membrane Transporters","description":"Top GO terms point to transmembrane transport of diverse substrates (potassium, manganese, nitrite, vitamins, xenobiotics) and iron-related homeostasis, suggesting these proteins are membrane transporters handling ions and small molecules rather than a single pathway. This coherent set of transport-related functions justifies a label centered on membrane transporters.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":4},{"id":"GO:0071805","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0042891","count":3},{"id":"GO:0030026","count":2}]},{"hash":"113320736416828732","title":"Post-transcriptional RNA processing and splicing","description":"The proteins are enriched for mRNA maturation processes: spliceosome-mediated and alternative splicing, mRNA polyadenylation regulation, mRNA export, and regulation of mRNA stability, plus translation reinitiation contexts. This points to post-transcriptional gene expression control focused on RNA processing and splicing, despite some obsolete terms. ","confidence":"High","size":9,"edges":17,"triangles":8,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":9},{"id":"GO:0006378","count":8},{"id":"GO:0045292","count":8},{"id":"GO:1900363","count":7},{"id":"GO:0002188","count":7}]},{"hash":"269023060638588186","title":"Synaptic Receptor Trafficking and Membrane Localization","description":"These GO terms cluster around vesicle trafficking from the Golgi to the plasma membrane, exocytic insertion of neurotransmitter receptors into the postsynaptic membrane, and regulation of receptor localization to synapses and membranes. Although a term about cornified envelope assembly appears, the dominant signal is coordinated trafficking and targeting of membrane proteins to synaptic sites, consistent with synaptic receptor localization and Golgi-to-plasma membrane processes.","confidence":"High","size":9,"edges":15,"triangles":7,"max_degree":8,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:1902685","count":7},{"id":"GO:0010811","count":7},{"id":"GO:1903575","count":7},{"id":"GO:0006896","count":7},{"id":"GO:0048280","count":7}]},{"hash":"1900704185532829217","title":"Wnt signaling and developmental processes","description":"The top GO terms point to both positive/negative regulation of canonical Wnt signaling and links to apoptosis, plus several organ-development terms (fungiform papilla formation, superior colliculus development, renal outer medulla development) and cytoskeleton-related processes (GTPase activity, pseudopodium assembly). This suggests a theme around Wnt-mediated signaling influencing cell fate, proliferation, and movement during development, rather than a single, narrow function. Confidence: Medium","confidence":"","size":9,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0008285","count":5},{"id":"GO:0071681","count":4},{"id":"GO:0061380","count":4},{"id":"GO:0000011","count":4}]},{"hash":"824971093701807493","title":"Growth and energy metabolism regulation","description":"The top GO terms point to energy-related processes (positive regulation of oxidative phosphorylation and ATP biosynthesis) and growth-related processes (cell division, centriole elongation). There are also terms related to heat stress response and transcription initiation, suggesting a broader but coherent theme of coordinating cellular growth with energy supply and stress regulation. Overall, the cluster seems to group proteins involved in growth-control processes coupled to metabolism, with some ancillary stress-response signals. ","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070651","count":3},{"id":"GO:1903724","count":2},{"id":"GO:0070370","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0051301","count":2}]},{"hash":"881821307690770767","title":"Bacterial LPS and Capsule Polysaccharide Biosynthesis","description":"The top GO terms cluster around lipopolysaccharide biosynthesis, colanic acid (capsule) biosynthesis, and sugar-nucleotide pathways (GDP-mannose, dTDP-rhamnose, ADP-L-glycero-beta-D-manno-heptose), which together point to synthesis of bacterial cell envelope polysaccharides. Although a few terms seem plant-related or obsolete, the dominant theme is construction of LPS and capsule components. ","confidence":"High","size":9,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0009718","count":5},{"id":"GO:0009103","count":4},{"id":"GO:0009242","count":4},{"id":"GO:0019673","count":4}]},{"hash":"739125815687028079","title":"Carbohydrate metabolism and polysaccharide biosynthesis","description":"The cluster is enriched for pathways tied to carbohydrate metabolism (TCA cycle, glycerol-3-phosphate catabolism) and biosynthesis of carbohydrate-rich macromolecules (UDP-glucuronate, glycosaminoglycans, alginic acid), suggesting a common theme around energy use and polysaccharide production. Some terms related to insulin signaling and xenobiotic response may reflect regulatory or stress-response links to metabolic processes, but carbohydrate metabolism and polysaccharide biosynthesis appear to be the dominant signal.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":3},{"id":"GO:0032868","count":3},{"id":"GO:0042121","count":3},{"id":"GO:0006024","count":3},{"id":"GO:0046168","count":3}]},{"hash":"1899901755047586423","title":"Phytohormone Biosynthesis and Catabolism with Stress Signaling","description":"These proteins show enrichment for phytohormone-related processes (ethylene, gibberellin, auxin, salicylic acid) and stress responses such as hydrogen peroxide\u2013mediated programmed cell death, along with secondary metabolite biosynthesis, implying a cohesive theme of hormone metabolism and stress signaling, despite one outlier term (penicillin biosynthesis).","confidence":"Medium","size":9,"edges":12,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009693","count":7},{"id":"GO:1902835","count":7},{"id":"GO:0042318","count":7},{"id":"GO:0055114","count":7},{"id":"GO:0009686","count":7}]},{"hash":"535798333047003720","title":"Unknown","description":"The top GO terms span diverse and seemingly unrelated areas (plant intercellular transport, various catabolic and biosynthetic processes, and immune/neural regulation), with no single theme that coherently ties the proteins\u2019 functions. This scattered representation suggests the cluster does not reflect one clear biological pathway or process, so a broad, unknown label is appropriate. ","confidence":"","size":9,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1901766","count":1},{"id":"GO:0000256","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0006145","count":1},{"id":"GO:0010497","count":1}]},{"hash":"525227564965457507","title":"Ubiquitin-Dependent Regulation and Vitamin Metabolism","description":"The cluster is driven by ubiquitin-related processes (ubiquitin-dependent ERAD pathway and protein autoubiquitination), suggesting proteostasis regulation. It also includes retinoic acid and calcitriol biosynthesis/catabolism terms, pointing to vitamin A and vitamin D signaling/metabolism. The overlap hints at a theme of ubiquitin-mediated regulation intersecting with vitamin signaling relevant to development. ","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903265","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0071615","count":2},{"id":"GO:0042904","count":2}]},{"hash":"838454864455372763","title":"Plant Hormone Biosynthesis and Metabolism","description":"The GO terms cluster around plant hormone pathways: gibberellin biosynthesis and catabolic processes, auxin catabolic, and ethylene biosynthetic process, suggesting a core theme of hormone production and turnover in plants. The epoxygenase P450 pathway adds a metabolic signaling context. Several items (response to food, hepatocyte differentiation, penicillin biosynthetic process) appear to be noise or cross-species annotations, but the dominant signal is plant hormone metabolism.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0032094","count":2},{"id":"GO:0070365","count":2},{"id":"GO:0019373","count":2},{"id":"GO:0009693","count":1}]},{"hash":"107647811871200313","title":"Plant stress response and chlorophyll regulation","description":"The Top Terms show plant-specific processes tied to growth, stress, and chlorophyll metabolism (leaf senescence, chlorophyll biosynthesis, gibberellin response, osmotic stress, flavonol biosynthesis, secondary cell wall regulation) with additional signals of transcriptional control (chromatin remodeling, snRNA transcription). A few terms (viral process, telomeric D-loop disassembly) hint at broader genome regulation, but the central theme is hormone- and stress-responsive regulation affecting chlorophyll and metabolism in plants.","confidence":"Medium","size":9,"edges":7,"triangles":2,"max_degree":4,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:1900056","count":7},{"id":"GO:0010380","count":7},{"id":"GO:0009739","count":7},{"id":"GO:0006970","count":7},{"id":"GO:0016032","count":7}]},{"hash":"1877843187027312565","title":"Ion transport and membrane potential regulation","description":"This cluster is dominated by GO terms about transmembrane transport of metal and monoatomic cations, sodium export, and stabilization of membrane potential, with supporting notes on T-tubule organization and related signaling (calcineurin-NFAT). A single outlier term about pheromone-triggered conjugation is likely incidental. Taken together, the common theme is membrane ion transport and maintenance of membrane potential, with muscle-related membrane organization aspects.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0014883","count":1},{"id":"GO:0070574","count":1},{"id":"GO:1990938","count":1},{"id":"GO:0099132","count":1},{"id":"GO:0070885","count":1}]},{"hash":"791710741424753612","title":"Neurodevelopmental Growth Signaling","description":"This cluster centers on neural development and morphogenesis, with GO terms such as neurotrophin TRK signaling, optic nerve morphogenesis, and face development, alongside growth-related signaling like FGFR apoptotic signaling and Wnt pathway regulation. DNA replication/transcription terms suggest a proliferative state often associated with development. Some terms (symbiont-mediated host transformation, alkaline pH response, toxic substance response) are less directly connected but do not override the main theme of developmental signaling.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0006351","count":8},{"id":"GO:0048011","count":7},{"id":"GO:0090090","count":7},{"id":"GO:0020021","count":7}]},{"hash":"1962802395075590091","title":"Neural crest development and progenitor proliferation","description":"This cluster centers on neural development signals (neuron development, neurotrophin signaling) and craniofacial morphogenesis (embryonic cranial skeleton morphogenesis), which strongly points to neural crest\u2013driven development. The presence of cell-cycle terms (DNA replication, centrosome cycle, positive regulation of nuclear DNA replication) suggests proliferative progenitors, consistent with neural crest cells expanding before differentiation. Some migration (chemotaxis) and protein turnover (proteasomal regulation) terms further support dynamic developmental processes in this lineage, though the connection is broad.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0006935","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0048666","count":6},{"id":"GO:0032435","count":6}]},{"hash":"630095169632542256","title":"Ubiquitin-Dependent Regulation of Transcription and Proteostasis","description":"These proteins clearly cluster around ubiquitination pathways: multiple GO terms specify different ubiquitin linkages and protein ubiquitination, along with unfolded protein response and histone turnover; transcriptional regulation is also represented. Together they indicate a theme of ubiquitin-dependent regulation of transcription and proteostasis.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0060028","count":2},{"id":"GO:0070936","count":2}]},{"hash":"686841183651191339","title":"Embryonic Development and Organ Morphogenesis","description":"The top GO terms cluster around developmental processes across multiple organs (placenta, heart, pancreas, cartilage, nervous system) and morphogenetic events (left/right patterning, EMT). The common theme is embryonic development and organ formation, so the label captures the cluster\u2019s broad developmental role rather than a single tissue.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":1},{"id":"GO:0060536","count":1},{"id":"GO:0060972","count":1},{"id":"GO:0060806","count":1},{"id":"GO:0003323","count":1}]},{"hash":"115906121511361036","title":"Negative Regulation of Signaling and Trafficking","description":"The cluster shows enrichment for GO terms that describe downregulation across diverse pathways (e.g., TLR3 signaling, clathrin-dependent endocytosis, GPCR internalization, calcium channel activity, autophagy), suggesting these proteins broadly dampen multiple cellular processes rather than a single specific function.","confidence":"Medium","size":9,"edges":12,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0034140","count":3},{"id":"GO:1900186","count":3},{"id":"GO:1901340","count":3},{"id":"GO:0010216","count":3},{"id":"GO:0030474","count":3}]},{"hash":"1500537122168809766","title":"Calcium signaling and ion transport in muscle and synapses","description":"Many top terms converge on calcium homeostasis and transport (mitochondrial and plasma membrane), along with transport of Na+, K+, and Mn2+. Coupled with muscle and heart contraction regulation and long-term synaptic potentiation, the cluster appears to group proteins involved in calcium-dependent signaling that modulates muscle function and synaptic communication.","confidence":"High","size":9,"edges":31,"triangles":54,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":5},{"id":"GO:0007154","count":4},{"id":"GO:0051560","count":4},{"id":"GO:1990034","count":4},{"id":"GO:0014819","count":4}]},{"hash":"1111771875960017841","title":"Plant developmental regulation","description":"This cluster features terms tied to plant development and patterning\u2014longitudinal axis specification, somatic embryogenesis, abaxial fate specification, meristem and flower development\u2014plus auxin signaling and transcription, pointing to a shared role in plant growth and organogenesis. A couple of outliers (spliceosomal assembly and gluconeogenesis) are present but less central. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":2},{"id":"GO:0000387","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0009942","count":1},{"id":"GO:0010262","count":1}]},{"hash":"1308469915088037205","title":"Fungal cell wall remodeling and polysaccharide catabolism","description":"GO terms converge on fungal cell wall remodeling, beta-glucan biosynthesis, and degradation of plant polysaccharides, with biofilm formation and septation indicating a fungal growth-and-structure theme.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044011","count":1},{"id":"GO:1904462","count":1},{"id":"GO:0045493","count":1},{"id":"GO:0044407","count":1},{"id":"GO:0030245","count":1}]},{"hash":"685153625024236589","title":"RNA Splicing and Transcription Regulation","description":"The top terms concentrate on RNA processing (mRNA splice site recognition, Group II intron splicing) and transcription control (regulation of DNA-templated transcription, RNAP II region binding). Obsolete chromatin-related terms appear but do not define a distinct pathway; the core theme is RNA processing coupled with transcription regulation.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006376","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0045843","count":1},{"id":"GO:0000373","count":1},{"id":"GO:0010102","count":1}]},{"hash":"1185645088468113785","title":"Innate Immune Signaling in Dendritic Cells","description":"The top GO terms point to innate immune activation in dendritic cells: MyD88-dependent TLR signaling, detection of lipopolysaccharide, and defense against virus, plus regulation of dendritic cell cytokine production. While a few terms reference transcription or axon guidance, the dominant theme is innate immune signaling and dendritic cell\u2013mediated responses, justifying a label around that function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0002755","count":1},{"id":"GO:0032497","count":1},{"id":"GO:0051607","count":1},{"id":"GO:0048846","count":1}]},{"hash":"2051265004566864923","title":"Unknown","description":"The top terms span energy metabolism, ion transport, phosphorylation signaling, development, and muscle/nerve functions with no single coherent theme tying them together, and there are no edges connecting the proteins. This lack of a unified biological function among the terms suggests the cluster cannot be assigned a specific, representative label.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042777","count":1},{"id":"GO:0099132","count":1},{"id":"GO:0006468","count":1},{"id":"GO:0005980","count":1},{"id":"GO:0072286","count":1}]},{"hash":"905948232336424762","title":"Plant Hormone Signaling and Chromatin Regulation","description":"The top GO terms show strong links to plant hormone signaling (salicylic acid, gibberellin, cytokinin) and to chromatin dynamics (nucleosome assembly, chromatin remodeling), with additional connections to stress responses (osmotic stress, leaf senescence) and metabolic regulation (flavonol biosynthesis), plus a viral process term. This combination suggests a module where hormone signaling and chromatin-mediated transcriptional control coordinate plant stress responses and secondary metabolism. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009751","count":4},{"id":"GO:0009739","count":4},{"id":"GO:0009736","count":4},{"id":"GO:0006334","count":4},{"id":"GO:1900056","count":3}]},{"hash":"1674616696686086820","title":"Nuclear gene expression and genome maintenance","description":"The top GO terms cluster around nuclear processes: chromatin remodeling, DNA-templated transcription, rRNA processing, and double-strand break repair, indicating roles in transcriptional regulation and genome integrity. Although development and signaling terms appear, they seem context-specific rather than defining the core function of the cluster. Thus the label emphasizes the central theme of nuclear gene expression and genome maintenance.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035914","count":3},{"id":"GO:0031018","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000154","count":2}]},{"hash":"1672531267921324301","title":"Retinoic acid and vitamin D metabolism in female reproduction","description":"The terms are dominated by retinoic acid pathways (9-cis-retinoic acid biosynthetic process; retinoic acid catabolic process) and vitamin D pathways (response to vitamin D; calcitriol biosynthetic process from calciol), along with reproductive development terms (uterus development; female gonad development). This points to a core theme of retinoid and vitamin D signaling/metabolism tied to female reproductive development, with some peripheral xenobiotic metabolism terms that may reflect broader metabolic capacity.","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":6},{"id":"GO:0071615","count":4},{"id":"GO:0042904","count":4},{"id":"GO:0060065","count":4},{"id":"GO:0008585","count":4}]},{"hash":"1173432337979964537","title":"Organogenesis and Development","description":"This cluster is enriched for terms related to development across multiple tissues (embryonic organ development, spinal cord development, seminiferous tubule development, skin development) and overall organismal growth (multicellular organism growth, cell population proliferation). Additional terms on DNA-templated transcription and cell-cycle related processes (mitotic sister chromatid cohesion) suggest coordination of gene expression with cell division during developmental programs. Collectively, the proteins likely participate in organogenesis and tissue formation rather than a single tissue-specific function.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007568","count":5},{"id":"GO:0008283","count":5},{"id":"GO:0072520","count":5},{"id":"GO:0048568","count":5},{"id":"GO:0021510","count":5}]},{"hash":"333804758051569046","title":"Female reproductive development and retinoic acid/vitamin D metabolism","description":"The top GO terms center on female reproductive development (uterus, female gonad, female genitalia) and hormone-related biosynthesis/ catabolism (retinoic acid and calcitriol). This points to a module linking female reproductive development with vitamin A and vitamin D related pathways; other terms like xenobiotic metabolism appear less central.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071615","count":7},{"id":"GO:0042904","count":7},{"id":"GO:0060065","count":7},{"id":"GO:0008585","count":7},{"id":"GO:0034653","count":7}]},{"hash":"1804067153316647059","title":"Ras Signaling Regulation","description":"This cluster is characterized by GO terms for positive regulation of GTPase activity and positive regulation of Ras protein signal transduction, pointing to modulation of Ras/other small GTPase signaling pathways. While additional terms cover diverse processes (splicing, development, immune signaling), the shared theme appears to be regulatory control of Ras-related signaling, suggesting a cohesive function around signaling modulation rather than a single static process.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0000373","count":1},{"id":"GO:0010102","count":1},{"id":"GO:0020021","count":1},{"id":"GO:2000753","count":1}]},{"hash":"2195143464039153939","title":"Metal ion transport and detoxification","description":"This cluster centers on transport and homeostasis of various metal ions (cadmium, mercury, copper, zinc, iron) plus detoxification and response to mercury, indicating a shared function in metal ion balance and detox pathways, with an added link to oxidative stress.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":1},{"id":"GO:0050787","count":1},{"id":"GO:0015680","count":1},{"id":"GO:0015694","count":1},{"id":"GO:0060003","count":1}]},{"hash":"969432740166151987","title":"Unknown","description":"The top terms are highly diverse, spanning ribosome biogenesis, histone methylation, peroxisome targeting, forebrain and retina development, actin depolymerization, fertilization, nuclear pore localization, and SREBP signaling. There is no clear single function or pathway linking these terms, so no coherent label can be assigned beyond Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0042273","count":4},{"id":"GO:2001162","count":3},{"id":"GO:0006625","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0030042","count":3}]},{"hash":"121726955898661635","title":"Heterochromatin Formation and Transcription Regulation","description":"This cluster is dominated by chromatin-related terms: rDNA heterochromatin formation, pericentric and subtelomeric heterochromatin formation, and negative regulation of transcription by RNA polymerase II, plus related chromatin maintenance processes like sister chromatid cohesion. A secondary thread includes RNA surveillance (non-stop decay) linked to nuclear gene expression. While a few immune-related terms appear, the central theme is chromatin organization and transcriptional repression, suggesting the proteins function together in establishing or maintaining heterochromatin and gene silencing.","confidence":"Medium","size":9,"edges":13,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0070481","count":3},{"id":"GO:0033128","count":3},{"id":"GO:0034184","count":3}]},{"hash":"202313959722222620","title":"Pollen wall sporopollenin biosynthesis","description":"The top GO terms cluster around sporopollenin and pollen-wall formation (sporopollenin biosynthetic process and cell wall layer assembly) with supporting fatty acid and flavonoid biosynthesis, suggesting a focus on pollen-wall biosynthesis and related plant lipid metabolism.","confidence":"High","size":9,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071770","count":1},{"id":"GO:0006633","count":1},{"id":"GO:0080110","count":1},{"id":"GO:0009715","count":1},{"id":"GO:0009813","count":1}]},{"hash":"1156247794666038054","title":"Embryonic craniofacial and neural development","description":"This cluster centers on embryonic development with a focus on craniofacial structures (face development, cranial skeleton morphogenesis, optic nerve morphogenesis) and neural signaling (neurotrophin pathways). The inclusion of cell cycle-related terms (centrosome cycle, DNA replication) suggests proliferative activity during development, while Wnt signaling regulation aligns with developmental patterning. Although there is one outlier term about symbiont-mediated host transformation, the dominant theme is craniofacial/neuronal development coupled with cell-cycle control.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007098","count":8},{"id":"GO:0048701","count":8},{"id":"GO:0010571","count":8},{"id":"GO:0006260","count":8},{"id":"GO:0048011","count":6}]},{"hash":"1071619884422135459","title":"Plant secondary cell wall biosynthesis and xylan/xyloglucan metabolism","description":"The terms cluster around plant-type secondary cell wall biogenesis and modifications, with specific emphasis on xylan biosynthesis and xyloglucan metabolism, indicating a role in building and remodeling the plant cell wall; a few RNA processing and ER proteolysis terms appear but are likely peripheral.","confidence":"High","size":9,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":2},{"id":"GO:0050826","count":2},{"id":"GO:0009827","count":2},{"id":"GO:0045492","count":2},{"id":"GO:0010411","count":2}]},{"hash":"1256708911381437496","title":"Neurodevelopment and growth-factor signaling","description":"The cluster centers on neural development and growth-factor pathways: neurotrophin TRK signaling, optic nerve morphogenesis, FGFR signaling with PI3K/Akt, and calcium-mediated signaling, along with angiogenesis. Outliers such as alkaline pH response and B cell tolerance induction are present but do not define the main theme.","confidence":"Medium","size":9,"edges":27,"triangles":34,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048011","count":8},{"id":"GO:0020021","count":8},{"id":"GO:0071469","count":8},{"id":"GO:0021631","count":8},{"id":"GO:1902178","count":8}]},{"hash":"1634533373045571105","title":"Antibiotic production and sporulation with metal transport","description":"The cluster is dominated by terms for antibiotic biosynthesis and sporulation, with several metal ion transport processes (arsenate, copper, iron) and nitrogen metabolism (nitrate assimilation, denitrification). This pattern fits a soil or actinobacterial lineage (e.g., Streptomyces/Bacillus) that links secondary metabolism and developmental processes with metal homeostasis, though some terms (like lignin catabolism) add noise. Overall, a cohesive theme is antibiotic production linked to sporulation and metal transport.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0055114","count":9},{"id":"GO:0042128","count":9},{"id":"GO:0019333","count":8},{"id":"GO:0046274","count":8}]},{"hash":"1713593111030630407","title":"Septin ring organization at bud neck","description":"This cluster is dominated by GO terms for septin ring assembly and organization at the bud neck (GO:0032186, GO:0000921) and protein localization to that site (GO:0097271), indicating septin-based scaffolding critical for budding cytokinesis; additional signals related to spindle checkpoint signaling and ubiquitination suggest broader cell-division regulation around this core process.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032186","count":4},{"id":"GO:0051092","count":3},{"id":"GO:0070936","count":3},{"id":"GO:0000921","count":3},{"id":"GO:0090337","count":3}]},{"hash":"884400566859525500","title":"Pol II Transcription Regulation and Chromatin Remodeling","description":"The terms converge on transcriptional control by RNA polymerase II, including negative regulation of Pol II transcription and regulation of Pol II preinitiation complex assembly, complemented by chromatin-related processes such as histone H3 acetylation and nucleosome mobilization, which together modulate gene expression. Some entries touch plant-specific regulatory pathways (photomorphogenesis, flavonoid biosynthesis), but the unifying theme remains transcription regulation and chromatin dynamics.","confidence":"High","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":1},{"id":"GO:1900446","count":1},{"id":"GO:0000436","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0042766","count":1}]},{"hash":"11527154063867804","title":"Telomere maintenance and genome stability","description":"This cluster is dominated by GO terms related to telomere maintenance (telomere lengthening, telomere capping, localization to telomere) together with DNA replication and repair processes (DNA repair, DNA replication, mitotic cell cycle checkpoint signaling), pointing to a coherent theme of preserving chromosome ends and genome integrity. Translation-related tRNA aminoacylation terms appear but are secondary to the telomere/genome stability signals.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0070145","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0010833","count":2},{"id":"GO:0070200","count":2}]},{"hash":"786772685375957396","title":"Lipid catabolism and phospholipid remodeling","description":"The top GO terms cluster around triglyceride catabolic processes (including triglyceride mobilization and acyl-chain remodeling) and phospholipid catabolic processes (phosphatidylethanolamine and phosphatidylcholine), pointing to a cohesive theme of lipid breakdown and membrane lipid remodeling. Additional signaling-related terms exist but are secondary to the lipid metabolism focus.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010898","count":2},{"id":"GO:0010951","count":2},{"id":"GO:0019433","count":1},{"id":"GO:0046338","count":1},{"id":"GO:0034638","count":1}]},{"hash":"2066422405645738149","title":"Plant nitrate/peptide transport with hormone signaling","description":"The terms cluster around transport of oligo- and dipeptides and nitrate, plus plant hormone signaling pathways (auxin and gibberellin) and nitrate responses, indicating a plant-specific function centered on nutrient transport coupled with hormone-mediated responses.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035672","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0080055","count":3},{"id":"GO:0009734","count":3},{"id":"GO:0010167","count":3}]},{"hash":"1586364723363410258","title":"Neural-immune signaling and vesicle trafficking","description":"The terms point to signaling and transport processes across diverse cell types: vesicle fusion, phagocytosis regulation, and immune receptor signaling (B cell), alongside neural development cues such as reelin signaling and neuronal migration. This suggests a theme of signaling coupled with vesicle trafficking in both neural and immune contexts, with additional but related transcription/export regulation components. While diverse, the shared thread is intracellular signaling modulated by vesicle dynamics. Confidence: Medium","confidence":"Medium","size":8,"edges":18,"triangles":21,"max_degree":7,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0050764","count":5},{"id":"GO:0006906","count":5},{"id":"GO:0050861","count":5},{"id":"GO:0021814","count":5},{"id":"GO:0071236","count":5}]},{"hash":"1401537003920872312","title":"Immune Signaling and Stress Response","description":"Top GO terms show immune signaling (Fc-epsilon receptor signaling, inflammatory regulation, viral process) alongside stress responses (hypoxia-related transcription regulation, metal ion responses, proteasome assembly, plant hypersensitive response). The cluster thus reflects signaling tied to immune and general stress responses rather than a single precise function, justifying the label \"Immune Signaling and Stress Response.\" ","confidence":"Medium","size":8,"edges":15,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0038095","count":4},{"id":"GO:0090090","count":4},{"id":"GO:0061418","count":4},{"id":"GO:0010043","count":4},{"id":"GO:0080129","count":4}]},{"hash":"405773954004364517","title":"Bacterial biosynthesis and metabolism","description":"This cluster centers on prokaryotic biosynthetic and metabolic processes: tRNA wobble uridine modification, cobalamin and other biosynthetic pathways (antibiotics, LPS), iron-sulfur cluster assembly, and related metabolic steps, with some indication of cell-cycle regulation. The shared theme appears to be synthesis and assembly of cellular components and cofactors in bacteria.","confidence":"Medium","size":8,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0017000","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0051782","count":2}]},{"hash":"504065875511119992","title":"Oocyte meiosis and spindle assembly","description":"This cluster is dominated by terms about oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization, pointing to proteins involved in oocyte development and meiotic progression, with coordinated proteolysis via the SCF-ubiquitin\u2013proteasome pathway regulating the cell cycle. A few terms related to brain development appear incidental and do not define the main theme. ","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":3},{"id":"GO:0006516","count":3},{"id":"GO:0008285","count":3},{"id":"GO:0007057","count":3},{"id":"GO:0051436","count":3}]},{"hash":"967241140805015629","title":"Ubiquitin-regulated immune signaling","description":"This cluster centers on immune-related functions modulated by ubiquitination, including K48- and K63-linked ubiquitination, adaptive immune processes, RIG-I signaling regulation, NF-kappaB activation, and TNF signaling. The presence of V(D)J recombination and apoptotic regulation further supports a theme of immune signaling and cell fate control governed by ubiquitin pathways, making this a cohesive immune-communication cluster.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070936","count":4},{"id":"GO:0042981","count":4},{"id":"GO:0033151","count":4},{"id":"GO:0070535","count":4},{"id":"GO:1901253","count":4}]},{"hash":"1335574163971922845","title":"Actin-driven dendritic spine morphogenesis and synapse regulation","description":"The terms center on actin cytoskeleton remodeling (actin polymerization, lamellipodium/ruffle assembly, stress fibers) and neuronal development (dendritic spine morphogenesis, hippocampus development) with a role in synaptic vesicle exocytosis. This suggests proteins coordinating actin remodeling during spine formation and synapse maturation, justifying this label.","confidence":"High","size":8,"edges":7,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060999","count":7},{"id":"GO:0016601","count":7},{"id":"GO:0010592","count":7},{"id":"GO:0097178","count":7},{"id":"GO:0045792","count":7}]},{"hash":"1366304551635609074","title":"Neurodevelopment and synaptic signaling","description":"This cluster centers on neural development and synaptic function, highlighted by terms for neural tube closure, cell morphogenesis, and glutamatergic synaptic transmission, along with regulation of synaptic vesicle exocytosis. There are also general cellular processes like DNA replication and transcriptional regulation that may reflect housekeeping roles in these cells, and a few outlier terms (e.g., plant ABA signaling, karyogamy) that are not strongly coherent with the neuronal theme. Overall, the strongest signal ties to neurodevelopment and synaptic activity.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0000902","count":3},{"id":"GO:0001843","count":2},{"id":"GO:2000300","count":2}]},{"hash":"1773654294232735198","title":"Unknown","description":"The GO terms cover diverse domains (animal development: male gonad, brain, neural tube; plant processes: pollen tube growth, phloem transport, nicotianamine biosynthesis) and innate immune signaling (MyD88-dependent TLR, TLR4 regulation, LPS detection) with no clear common function or connectivity, so the proteins do not form a cohesive functional cluster.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0009860","count":1}]},{"hash":"2085585771617944400","title":"Neural development and neurotrophic signaling","description":"These proteins cluster around neural development and neurotrophic signaling. The top GO terms emphasize neural tube closure, face development, and optic nerve morphogenesis, along with neurotrophin TRK receptor signaling and regulation of Wnt signaling, all of which relate to neural patterning and differentiation. While there are some broader or stress-related terms, the dominant theme is neural morphogenesis and neurotrophic signaling, justifying this label.","confidence":"Medium","size":8,"edges":18,"triangles":17,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001843","count":7},{"id":"GO:0046827","count":7},{"id":"GO:0048011","count":6},{"id":"GO:0090090","count":6},{"id":"GO:0020021","count":6}]},{"hash":"766247499408680477","title":"Unknown","description":"The top GO terms are scattered across chromatin regulation, plant hormone signaling, multiple developmental lineages (pituitary, neuron, erythrocyte), apoptosis, and basic metabolism, with no clear shared function linking the proteins. This diversity suggests there is no cohesive theme for a single label.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051572","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0019563","count":1},{"id":"GO:0021983","count":1}]},{"hash":"1371621477365483214","title":"Oocyte maturation and meiotic spindle assembly","description":"The top GO terms cluster around oocyte maturation, spindle assembly in female meiosis I, microtubule polymerization, and ubiquitin-proteasome\u2013mediated protein degradation, all pointing to a shared role in oogenesis and meiosis progression. Some brain development terms are present but appear ancillary to the core meiotic/oogenesis theme.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":8},{"id":"GO:0021678","count":8},{"id":"GO:0006516","count":8},{"id":"GO:0051436","count":8},{"id":"GO:0046785","count":8}]},{"hash":"1358443456750745448","title":"Developmental signaling and morphogenesis","description":"The terms point to broad developmental roles: embryonic patterning, shoot apical meristem maintenance, nervous system development, and morphogenesis, with signaling pathways like PTK signaling and PI3K/AKT involved. Although the specific processes span different organisms (plants and animals) and include some unrelated items, the common theme is involvement in development and signaling for patterning and form, so a label around developmental signaling and morphogenesis fits best.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048354","count":1},{"id":"GO:0048575","count":1},{"id":"GO:0006915","count":1},{"id":"GO:0007169","count":1},{"id":"GO:0009880","count":1}]},{"hash":"1888184826696879704","title":"Extrinsic apoptosis and growth factor signaling","description":"This cluster is dominated by GO terms pointing to extrinsic apoptotic signaling via death receptors (and in absence of ligand) and cellular responses to epidermal growth factor stimulus, indicating a theme of external signal-triggered cell fate decisions and growth-factor\u2013driven signaling. Additional terms about regulation of protein folding, ubiquitination, and mRNA modification suggest broader regulatory context supporting these pathways. Overall, the core pattern is extrinsic apoptosis signaling linked with growth factor\u2013responsive signaling.","confidence":"Medium","size":8,"edges":10,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0090367","count":2},{"id":"GO:0061084","count":2},{"id":"GO:0071364","count":2}]},{"hash":"71789375436643161","title":"Molybdenum cofactor biosynthesis","description":"The cluster shows clear representation of molybdenum cofactor biosynthetic processes, including Mo-molybdopterin cofactor biosynthesis and molybdenum incorporation. These terms point to a shared function in assembling the molybdenum cofactor required by molybdoenzymes, which is the strongest unifying theme among the top terms. The other terms (receptor clustering, vesicle fusion, immune signaling, and neuronal development) appear less central and may reflect broader or incidental associations.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032324","count":1},{"id":"GO:0006777","count":1},{"id":"GO:0072579","count":1},{"id":"GO:0097112","count":1},{"id":"GO:0018315","count":1}]},{"hash":"2214180677068108760","title":"Golgi Vesicle Trafficking and Vacuolar Targeting","description":"The top GO terms cluster around intra-Golgi transport, ER-to-Golgi transport, Golgi-to-vacuole transport, vesicle fusion with Golgi, retrograde transport to the Golgi, and protein targeting to the vacuole\u2014together indicating a cohesive module of Golgi-associated vesicle trafficking and vacuolar targeting (with some autophagy-related transport in the mix).","confidence":"High","size":8,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006891","count":6},{"id":"GO:0090161","count":6},{"id":"GO:0006896","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0048280","count":6}]},{"hash":"882230014177851836","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0050830","count":2}]},{"hash":"282243074818298782","title":"Unknown","description":"The top GO terms span immune signaling (MyD88-dependent and TLR1 pathways), neural development (nerve branching, imaginal disc polarity, multicellular development), intracellular trafficking (endosome-to-Golgi), chromatin localization, dopamine response, and cytoskeleton remodeling (actin severing). With no single cohesive function linking these proteins and no edges connecting them, a concise, representative label cannot be assigned beyond Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0002755","count":6},{"id":"GO:0035751","count":6},{"id":"GO:2000172","count":6},{"id":"GO:1905279","count":6},{"id":"GO:0007275","count":6}]},{"hash":"719628780359659987","title":"Amino acid biosynthesis and catabolism","description":"Based on the top GO terms, the cluster centers on amino acid metabolism, especially serine/threonine/cysteine/homocysteine pathways and transsulfuration, with tryptophan biosynthesis also represented. An outlier term (response to morphine) likely reflects annotation noise rather than a core function. Overall, the label reflects the shared metabolic theme of the proteins.","confidence":"High","size":8,"edges":25,"triangles":40,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000162","count":3},{"id":"GO:0018871","count":2},{"id":"GO:0046360","count":2},{"id":"GO:0043418","count":2},{"id":"GO:0006535","count":2}]},{"hash":"1564103310309662576","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":22,"triangles":29,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0009734","count":2},{"id":"GO:0006417","count":2},{"id":"GO:0046620","count":1},{"id":"GO:0009926","count":1}]},{"hash":"728183504530569693","title":"Plant terpenoid biosynthesis and defense","description":"This cluster features terpenoid biosynthesis signals (sesquiterpene, gibberellin, camphor) and defense-related responses (to herbivore, to amine), suggesting a plant secondary metabolism program tied to defense; other terms like phosphorylation and gluconeogenesis are broader metabolic processes that are less distinctive here.","confidence":"Medium","size":8,"edges":20,"triangles":24,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":3},{"id":"GO:0006094","count":2},{"id":"GO:0014075","count":2},{"id":"GO:0009245","count":2},{"id":"GO:2001289","count":2}]},{"hash":"1843367248383470596","title":"Female reproductive development and retinoic acid metabolism","description":"The top terms cluster around female reproductive development (uterus, female gonad, and female genitalia development) and retinoic acid metabolism (biosynthesis and catabolic processes), suggesting a link between retinoic acid signaling and female reproductive development. Some additional xenobiotic and stress-related processes are present but do not override the dominant theme.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071615","count":7},{"id":"GO:0042904","count":7},{"id":"GO:0060065","count":7},{"id":"GO:0008585","count":7},{"id":"GO:0034653","count":7}]},{"hash":"237335272208752224","title":"Organelle RNA Editing and Processing","description":"The terms cluster around RNA editing/modification in organelles, especially cytidine-to-uridine editing, mitochondrial and chloroplast RNA processing/modification, and chloroplast-nucleus signaling, suggesting proteins involved in organellar RNA editing and processing.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0000961","count":2}]},{"hash":"1023049630309845745","title":"Chloroplast Translation and Photosynthesis","description":"This cluster is dominated by chloroplast-associated processes: translation, photosynthesis, light harvesting in photosystem I, and cytochrome b6f complex assembly, pointing to plastid-encoded protein synthesis and photosynthetic machinery. A few terms like buoyancy regulation and neuromuscular processes seem less directly related and may reflect annotation noise, but the core theme centers on chloroplast function and photosynthetic activity.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0070584","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0031413","count":1},{"id":"GO:0019216","count":1},{"id":"GO:0050881","count":1}]},{"hash":"1908460669804402838","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0032472","count":1},{"id":"GO:0035751","count":1},{"id":"GO:0010270","count":1}]},{"hash":"228124770990541430","title":"Chromatin remodeling and DNA topology","description":"The terms cluster around changes in DNA topology and chromatin structure (DNA topological change, chromatin remodeling, nucleosome positioning) with related chromatin-associated processes; despite some obsolete annotations, the core signals point to proteins that modulate chromatin state and DNA accessibility.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006265","count":2},{"id":"GO:0016584","count":2},{"id":"GO:1990417","count":2},{"id":"GO:0006306","count":2},{"id":"GO:0006605","count":2}]},{"hash":"2080402061520502056","title":"DNA Replication and Repair","description":"Most of the prominent terms point to nuclear DNA metabolism and cell cycle control (DNA repair, DNA replication, transcription, mitotic cell cycle), making \"DNA Replication and Repair\" the best unifying label. The other GO terms (fatty acid biosynthesis, ubiquitin-dependent ERAD, signaling) are less central and may reflect multifunctional proteins or annotation noise.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006633","count":5},{"id":"GO:0006281","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0006260","count":4}]},{"hash":"113137016175348084","title":"Ribosome Biogenesis and Translation Regulation","description":"The cluster shows a strong emphasis on translation (GO:0006412) and ribosome biogenesis (GO:0042254), including maturation of SSU-rRNA, indicating proteins involved in ribosome assembly and protein synthesis. Additional RNA-processing terms (splicing, RNA folding) point to related RNA-processing activities that support translation fidelity and specialized incorporation (e.g., selenocysteine), but the dominant theme remains ribosome assembly and translation control.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0046677","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000372","count":1}]},{"hash":"1926842330596496443","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":14,"triangles":11,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0046677","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0000028","count":2},{"id":"GO:0042273","count":2}]},{"hash":"576081754884068915","title":"Plant Cell Wall Biosynthesis and O-Glycosylation","description":"The terms strongly point to plant cell wall biosynthesis (secondary cell wall, glucuronoxylan, homogalacturonan, cell wall organization) and protein O-glycosylation (via mannose and GalNAc), suggesting these proteins are involved in cell wall polysaccharide production and glycosylated wall proteins. Some unrelated terms appear, but the dominant signal is plant cell wall-related functions.","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0009834","count":3},{"id":"GO:0035269","count":3},{"id":"GO:0010417","count":3},{"id":"GO:0010289","count":3}]},{"hash":"127889959430808557","title":"DNA Damage Response and RNA Processing","description":"The terms indicate a core focus on genome maintenance (SOS response, nucleotide-excision repair, DNA topology changes) and RNA maturation/gene regulation (regulatory ncRNA-mediated gene silencing, snoRNA release from pre-rRNA, positive regulation of mRNA splicing). This blend suggests a cluster of proteins involved in nucleic acid handling and RNA processing.","confidence":"Medium","size":8,"edges":8,"triangles":2,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0009432","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0006289","count":2},{"id":"GO:0006265","count":2}]},{"hash":"636791145651917433","title":"Nuclear mRNA processing and export","description":"The cluster\u2019s top GO terms center on nuclear transport and RNA processing, including import of hnRNPs and splicing factors into the nucleus, mRNA export, ribosomal subunit export, and regulation of nuclear export. Additional terms touch on post-transcriptional RNA silencing, meristem initiation, and responses to xenobiotics, suggesting broader roles tied to RNA handling and nuclear trafficking. Overall, the common thread is nuclear RNA processing and export pathways.","confidence":"High","size":8,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006609","count":4},{"id":"GO:0035048","count":4},{"id":"GO:0006406","count":4},{"id":"GO:0010014","count":4},{"id":"GO:0042176","count":4}]},{"hash":"2246431567504612147","title":"Lipid-GPCR Signaling and Neuronal Modulation","description":"The cluster is dominated by GO terms tying lipid-derived GPCR signaling (sphingosine-1-phosphate receptor signaling, diacylglycerol metabolism, sphingoid catabolic process) to neuronal functions (regulation of glutamatergic synaptic transmission, habituation) and broader signaling including immune pathways. This suggests a cohesive theme around lipid-mediated GPCR signaling influencing neuronal and possibly immune responses, despite a few outliers. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0009236","count":2},{"id":"GO:0071372","count":2},{"id":"GO:0003376","count":2},{"id":"GO:0046521","count":2}]},{"hash":"639086027034543302","title":"RNA and protein methylation","description":"The terms are dominated by methylation/modification processes across RNA (tRNA wobble uridine and tRNA/rRNA methylation) and proteins (peptidyl-arginine methylation, N-terminal methylation, histone methylation), indicating a cohesive theme of methyltransferase activity and post-translational/RNA modifications. A few biosynthesis terms appear, but the central pattern is methylation-related activities.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0018012","count":2},{"id":"GO:0043985","count":2}]},{"hash":"1253860471965979797","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3},{"id":"GO:2001162","count":2},{"id":"GO:0016584","count":2}]},{"hash":"1427336406401654269","title":"Plant development and translation machinery","description":"The cluster is enriched for translation and ribosome biogenesis terms, plus several plant-development GO terms (somatic embryogenesis, abaxial cell fate specification, longitudinal axis specification, meristem development, flower development). This suggests a theme where translation machinery and its regulation intersect with developmental processes in plants. Some antibiotic/cycloheximide response terms reflect stress-related modulation of translation, supporting a core link to translation in development rather than a separate pathway.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0046898","count":1},{"id":"GO:0009942","count":1}]},{"hash":"1901877008473846499","title":"Glycerol Metabolism and Neuronal Development","description":"The cluster shows a clear glycerol metabolism signal with glycerol catabolic and glycerol-3-phosphate catabolic terms, alongside neural development signals such as pituitary gland development, cerebral cortex development, and neuron maturation. There are also broader terms like apoptotic process and cell proliferation, and some obsolete terms, but they do not dominate. Overall, the cluster seems enriched for glycerol metabolism and neuronal development functions.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0019563","count":2},{"id":"GO:0016575","count":2},{"id":"GO:0021983","count":2},{"id":"GO:0046168","count":2}]},{"hash":"277174059061630725","title":"Retinoic acid and vitamin D metabolism","description":"The most represented terms are retinoic acid biosynthesis/catabolism and calcitriol biosynthesis, pointing to vitamin A and vitamin D metabolic pathways. This cluster also includes related developmental terms, suggesting roles in differentiation. Therefore, a concise label \"Retinoic acid and vitamin D metabolism\" captures the core theme. However, given the diversity of terms and lack of network connectivity, confidence is Medium.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035902","count":3},{"id":"GO:0032259","count":3},{"id":"GO:0071615","count":2},{"id":"GO:0042904","count":2},{"id":"GO:0060065","count":2}]},{"hash":"1550905581461312419","title":"RNA processing and rRNA maturation","description":"These proteins cluster around RNA processing and ribosomal RNA maturation. Dominant terms include transcription termination by RNA Pol II, rRNA processing steps (ITS1 cleavage, snoRNA release), and spliceosome-associated mRNA splicing and exon ligation, pointing to RNA maturation and processing as the core function. Some terms like DNA topology changes and viral genome replication may be ancillary connections to genome maintenance or infection contexts but are not central to the main theme.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006369","count":6},{"id":"GO:0000464","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0000378","count":5}]},{"hash":"1865635718646010812","title":"Retroviral Life Cycle and Latency","description":"The top GO terms point to stages of viral infection and proviral maintenance: proviral latency establishment, uncoating, RNA-templated DNA synthesis (reverse transcription), and the viral life cycle, plus host-driven activation of viral genome replication; together they describe steps of retroviral entry, integration, and replication inside the host. There is also a term for leukocyte migration reflecting host immune response, and a couple of unrelated terms likely from annotation noise (sepal formation, protein folding). Overall, the pattern best fits a viral infection/replication module, especially retroviral latency.","confidence":"High","size":8,"edges":10,"triangles":4,"max_degree":6,"top_function":"protein folding","top_go_terms":[{"id":"GO:1901407","count":6},{"id":"GO:0075713","count":4},{"id":"GO:0048453","count":4},{"id":"GO:0044829","count":4},{"id":"GO:0006278","count":4}]},{"hash":"1591532776936932508","title":"MVB Trafficking and Mitotic Exit","description":"Based on the top GO terms, the cluster centers on vesicle trafficking involving multivesicular bodies (MVBs) and the regulation of mitosis exit, suggesting a coherent theme around vesicle sorting/assembly and cell division control. Additional terms point to related processes in vesicle exocytosis and autophagy, with a few more general terms like ribosome biogenesis. Overall, the dominant signals align with MVB trafficking and mitotic regulation, with some peripheral terms. ","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0010458","count":3},{"id":"GO:0071985","count":3},{"id":"GO:2000300","count":3},{"id":"GO:1902902","count":3}]},{"hash":"1177462548994396404","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":5,"triangles":1,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000398","count":4},{"id":"GO:0009432","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0002188","count":3}]},{"hash":"596758303639731105","title":"Cellular stress response and protein homeostasis","description":"The top GO terms cluster around cellular stress responses (gamma radiation, heat), stress signaling (MAPK cascade), and proteostasis (protein stabilization, ROS regulation). Negative regulation of intracellular transport and cell growth further tie into coordinating stress responses with trafficking and growth control. Lens fiber morphogenesis and anterograde axonal transport may reflect tissue-specific roles, but the prevailing theme is stress response and protein homeostasis.","confidence":"Medium","size":8,"edges":21,"triangles":25,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":5},{"id":"GO:0007568","count":4},{"id":"GO:0032387","count":4},{"id":"GO:0030308","count":4},{"id":"GO:0050821","count":4}]},{"hash":"1626817452946221784","title":"Ubiquitin-Proteasome Regulation of Mitosis","description":"This cluster is dominated by ubiquitin-dependent degradation pathways (SCF-dependent proteasomal proteolysis, K11 and K48 linkages) and protein modification by neddylation, in the context of cell-cycle control (G2/M transition, exit from mitosis, and cell division). These terms together suggest a cohesive role in regulating mitosis through targeted proteolysis and ubiquitin-related signaling.","confidence":"High","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0000086","count":7},{"id":"GO:0016032","count":7},{"id":"GO:0070911","count":7},{"id":"GO:0070979","count":7}]},{"hash":"1703175269676752070","title":"Oxidative Stress and Energy Metabolism","description":"The strongest terms point to cellular response to oxidative stress and redox homeostasis, coupled with positive regulation of oxidative phosphorylation and ATP biosynthesis, suggesting a core theme of managing redox balance while boosting energy production. Some terms about ER-Golgi vesicle transport and cell cycle-related processes (centriole elongation, cell division) appear as peripheral associations, possibly reflecting broader cellular stress responses or annotation overlap. Overall, the cluster seems centered on redox regulation linked to energy metabolism rather than a single narrow function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034599","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0045454","count":2},{"id":"GO:1903724","count":1},{"id":"GO:0070370","count":1}]},{"hash":"1116164222946263762","title":"RNA processing and translation initiation","description":"This cluster is dominated by GO terms for mRNA maturation and splicing (spliceosome, alternative/cis splicing), mRNA export, and translation initiation/reinitiation (preinitiation complex formation), suggesting proteins involved in RNA processing and the initiation of translation, despite some obsolete annotations.","confidence":"High","size":8,"edges":8,"triangles":3,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1900363","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0006406","count":3}]},{"hash":"2302443709270381770","title":"Carbohydrate metabolism and mitochondrial energy production","description":"The cluster is dominated by carbohydrate metabolism terms (glycolysis, gluconeogenesis, fructose and ethanol metabolism) and includes mitochondrial-related processes (mitochondrial ribosome assembly), suggesting a focus on energy generation and metabolic regulation, with autophagy as a related stress-response link.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006067","count":2},{"id":"GO:0061668","count":2},{"id":"GO:0006003","count":1},{"id":"GO:1902153","count":1},{"id":"GO:0006094","count":1}]},{"hash":"665128921391124323","title":"Organelle gene expression and ribosome biogenesis","description":"The cluster is dominated by terms related to transcription in mitochondria and plastids and to ribosome assembly within mitochondria and chloroplasts, indicating a shared role in organelle gene expression and translation machinery. Some metabolic terms appear but do not disrupt the prevailing theme of organelle transcription/translation processes.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0009658","count":1},{"id":"GO:0042794","count":1},{"id":"GO:0061668","count":1},{"id":"GO:0006393","count":1}]},{"hash":"857148616437040320","title":"Unknown","description":"The top GO terms span very different processes (nitrogen fixation, iron-sulfur cluster assembly, protein maturation, mitochondrial translation, ER organization, and several catabolic pathways) with no single cohesive function tying the proteins together. This mixed set suggests no clear, unified theme, so a precise functional label is not confidently assignable.","confidence":"","size":8,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009399","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0051604","count":1},{"id":"GO:0070681","count":1}]},{"hash":"1006333211977557278","title":"Diverse Developmental Pathways","description":"Top GO terms point to a range of developmental and differentiation processes across plants, insects, and vertebrates (meristem transition, eye morphogenesis, organ development, gametogenesis, and immune differentiation). The common thread is broad developmental regulation rather than a single pathway, so a wide label capturing multispecies development is appropriate.","confidence":"Medium","size":8,"edges":9,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010228","count":4},{"id":"GO:0071277","count":3},{"id":"GO:0006366","count":3},{"id":"GO:0034670","count":2},{"id":"GO:0016330","count":2}]},{"hash":"2300317237208816417","title":"Autophagy and cellular quality control","description":"The top GO terms show macroautophagy and nucleophagy prominently, plus post-translational modification pathways (neddylation/ufmylation) that regulate protein turnover and autophagy. There are additional stress-response and metabolic terms, but the dominant theme centers on autophagy and proteostasis. Confidence: Medium","confidence":"","size":8,"edges":17,"triangles":16,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":4},{"id":"GO:2000220","count":4},{"id":"GO:0045116","count":4},{"id":"GO:1990592","count":4},{"id":"GO:0044805","count":4}]},{"hash":"799255089250147677","title":"Chromatin Remodeling and Heterochromatin Formation","description":"This cluster is enriched for GO terms centered on heterochromatin formation across multiple genomic contexts (rDNA, pericentric, subtelomeric) and on chromatin remodeling, as well as replication-dependent chromatin assembly, pointing to a cohesive group of proteins involved in establishing and maintaining chromatin structure and transcriptional silencing. A couple of peripheral terms (mRNA decay, Rho signaling regulation) are present but do not change the dominant chromatin-focused theme.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":8},{"id":"GO:0045815","count":8},{"id":"GO:0051290","count":8},{"id":"GO:0006335","count":8},{"id":"GO:0070481","count":7}]},{"hash":"1444090543294016478","title":"Plant hormone-driven stress response with chromatin remodeling","description":"The GO terms center on plant hormone responses (salicylic acid, gibberellin), abiotic stress (osmotic), and developmental/biochemical processes (leaf senescence, chlorophyll and flavonol biosynthesis), along with chromatin remodeling and heterochromatin formation, and even viral processes. Taken together, this suggests a cohesive plant-specific program where hormone signaling governs stress responses and development, modulated at the chromatin level.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009751","count":3},{"id":"GO:0009739","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0008584","count":2},{"id":"GO:1900056","count":2}]},{"hash":"1688838865601073644","title":"Plant metabolism and intercellular transport","description":"The GO terms cluster around plant-specific processes: plasmodesmata-mediated intercellular transport, various nitrogen and purine catabolic pathways (oxalate, allantoin/ureide, purine nucleobase), and defense/stress responses (hypoxia and salicylic acid). While a few terms like antibiotic biosynthesis appear, the dominant signals point to plant metabolism and intercellular communication, suggesting a cohesive plant-focused cluster.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010497","count":2},{"id":"GO:0033609","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0006508","count":2},{"id":"GO:1901766","count":1}]},{"hash":"2271781048353844977","title":"Embryonic and neural morphogenesis","description":"Most enriched GO terms cluster around tissue morphogenesis and development (face, optic nerve morphogenesis, thymus and placenta development) and are complemented by signaling pathways (neurotrophin TRK signaling, Wnt regulation) and contextual stress responses (cadmium, alkaline pH). This suggests a cohesive theme of embryonic tissue morphogenesis with neural development and related signaling.","confidence":"Medium","size":8,"edges":22,"triangles":29,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048538","count":8},{"id":"GO:0071276","count":8},{"id":"GO:0000187","count":8},{"id":"GO:0001890","count":8},{"id":"GO:0048011","count":7}]},{"hash":"1221600149092154162","title":"Developmental transcription and signaling regulators","description":"These proteins show enrichment for DNA-templated transcription and multicellular development, suggesting roles as transcriptional regulators during development. They also include regulators of signaling and cytoskeletal dynamics (positive regulation of GTPase activity, Arp2/3-mediated actin nucleation, tyrosine phosphorylation) and processes like mRNA transport and pigmentation, which often co-occur in developmental contexts and cell movement. Overall, they seem to comprise a broad set of development- and signaling-related regulators rather than a single pathway, hence a label focused on developmental transcription and signaling is appropriate.","confidence":"Medium","size":8,"edges":8,"triangles":4,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000742","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0031954","count":2}]},{"hash":"676847296958905146","title":"Neuronal mitochondrial calcium and autophagy","description":"The GO terms mix neural functions (fear response, learning, synaptic transmission) with mitochondrial processes (calcium import into mitochondrion, mitophagy/autophagy, protein import into mitochondrial matrix) and ROS regulation. This suggests a cohesive module where neuronal activity depends on mitochondrial calcium handling and mitochondrial quality control, justifying a label that highlights both neuronal and mitochondrial-autophagy aspects.","confidence":"High","size":8,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001662","count":3},{"id":"GO:2000378","count":3},{"id":"GO:1903959","count":3},{"id":"GO:0006820","count":3},{"id":"GO:1903146","count":3}]},{"hash":"1622956984291614503","title":"Mitochondrial transport and energy metabolism","description":"The top GO terms are dominated by transmembrane transport of metabolites into and out of mitochondria (citrate, ornithine, CoA, phosphate), plus the malate-aspartate shuttle and adaptive thermogenesis, pointing to a mitochondria-centered theme for transport and energy production. Other terms about fatty acid response and IGF signaling fit into overall metabolic regulation but do not override the mitochondrial transport/metabolism pattern.","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990314","count":3},{"id":"GO:0070542","count":3},{"id":"GO:0048250","count":3},{"id":"GO:0034198","count":3},{"id":"GO:0035349","count":3}]},{"hash":"1625503116828746391","title":"RNA splicing and mRNA export","description":"The top GO terms cluster around RNA processing activities: alternative and cis splicing via spliceosome, mRNA splicing, and mRNA export from the nucleus, with a weaker thread toward translation reinitiation. While a few terms are unrelated or obsolete, the dominant pattern is RNA maturation and nuclear handling of transcripts, justifying a label focused on RNA processing and export.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0042307","count":1},{"id":"GO:0016037","count":1}]},{"hash":"891352200114397308","title":"RNA processing and translation initiation regulation","description":"The terms center on RNA processing (mRNA splicing, polyadenylation) and translation control (initiation, reinitiation, preinitiation complex formation, IRES-driven initiation), with additional links to transcription and development, suggesting a cluster of proteins involved in regulating gene expression at both RNA processing and translational levels rather than a single specialized function.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0075525","count":3}]},{"hash":"1557295264329238354","title":"Ribosome Biogenesis and Spliceosome Assembly","description":"The top GO terms are dominated by 90S preribosome and pre-catalytic spliceosome assembly, plus rRNA processing steps (ITS1 cleavage, preribosome assembly), indicating a module of RNA processing machinery involved in ribosome biogenesis and pre-mRNA splicing. Although a couple terms are obsolete, the central theme clearly points to RNA maturation pathways. ","confidence":"High","size":8,"edges":16,"triangles":14,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000354","count":1},{"id":"GO:0000464","count":1},{"id":"GO:0034463","count":1},{"id":"GO:0072423","count":1},{"id":"GO:0006378","count":1}]},{"hash":"1302235908939758066","title":"Ubiquitin-Dependent Proteolysis and Signaling Regulators","description":"The top GO terms cluster around ubiquitin-dependent protein degradation (K48- and general ubiquitination) and regulation of major signaling pathways (NF-\u03baB activation, TNF signaling), with additional links to receptor turnover (Wnt receptor catabolic process) and apoptosis. This suggests a cohesive group of proteins that modulate proteostasis and signaling via ubiquitination, despite some outlying terms like V(D)J recombination and septin ring organization.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0070936","count":4},{"id":"GO:0042981","count":4},{"id":"GO:0033151","count":4},{"id":"GO:0070535","count":4}]},{"hash":"417483625045527047","title":"Female reproductive development and retinoic acid metabolism","description":"This cluster is dominated by GO terms for female gonad/uterus/female genitalia development and retinoic acid biosynthesis/catabolism, indicating a cohesive theme around female reproductive development and vitamin A signaling; a few xenobiotic metabolism terms appear incidental but do not define the cluster.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":3},{"id":"GO:0071615","count":2},{"id":"GO:0042904","count":2},{"id":"GO:0008585","count":2},{"id":"GO:0034653","count":2}]},{"hash":"400485416696611736","title":"Protein acetylation and related metabolism","description":"The top terms are largely centered on acetylation processes (spermidine and putrescine acetylation, N-terminal acetylation, histone H4 acetylation), suggesting an acetylation-focused theme. Additional terms point to various metabolic pathways (arginine biosynthesis, N-acetylglucosamine metabolism, mycothiol biosynthesis) and some outliers (rRNA processing, centromeric cohesion). The strongest cohesive signal is acetylation, but the cluster shows broad, diverse functions with no interaction evidence, so the label reflects a dominant theme rather than a tightly connected function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0032918","count":1},{"id":"GO:0043967","count":1},{"id":"GO:0006526","count":1},{"id":"GO:0032920","count":1}]},{"hash":"1927499360530817385","title":"SNARE-driven vesicle trafficking and exocytosis","description":"This cluster centers on membrane trafficking and exocytosis, with GO terms for SNARE complex assembly, vesicle fusion with the Golgi, and exocytic insertion of receptors, plus endosome-to-Golgi transport and vacuole fusion. The presence of mucus secretion and eosinophil degranulation supports a theme of regulated vesicle docking and fusion in secretory and immune contexts, consistent with SNARE-mediated trafficking.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":2},{"id":"GO:0070254","count":2},{"id":"GO:0001921","count":2},{"id":"GO:0016240","count":2},{"id":"GO:0048280","count":2}]},{"hash":"1215671101691766789","title":"Broad Developmental Morphogenesis","description":"The top GO terms cluster around diverse developmental processes, including neuron differentiation and migration, axon guidance, and organ morphogenesis across tissues and species (animal and plant). Actin filament depolymerization supports cytoskeletal remodeling essential for morphogenesis, reinforcing a overarching theme of developmental programs rather than a single pathway.","confidence":"Medium","size":8,"edges":13,"triangles":10,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:2000691","count":8},{"id":"GO:0097477","count":8},{"id":"GO:0008585","count":8},{"id":"GO:0048482","count":8},{"id":"GO:0008045","count":8}]},{"hash":"2250190975587299599","title":"Plant Hormone Biosynthesis and Metabolism","description":"The top GO terms indicate multiple hormone biosynthesis and catabolic pathways (ethylene, gibberellin, auxin, salicylic acid) and related secondary metabolism (proanthocyanidin) as well as ROS-associated defense signaling (hydrogen peroxide-mediated programmed cell death). This suggests the cluster centers on plant hormone production and metabolism, plus defense-related metabolic processes; an outlier term like penicillin biosynthesis likely reflects annotation noise rather than a core function.","confidence":"High","size":8,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009693","count":3},{"id":"GO:1902835","count":3},{"id":"GO:0042318","count":3},{"id":"GO:0009686","count":3}]},{"hash":"593072475810382254","title":"Female reproductive development and lipid hormone biosynthesis","description":"This cluster centers on lipid- and vitamin-derived signaling pathways, including prostaglandin biosynthesis, retinoic acid biosynthesis/catabolism, and calcitriol biosynthesis, which are key in development and reproductive biology. The presence of uterus development and female gonad development terms supports a link to reproductive processes governed by lipid and vitamin signals. Some other terms (e.g., xenobiotic metabolism) are present but appear ancillary to this core theme.","confidence":"High","size":8,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":5},{"id":"GO:0071615","count":4},{"id":"GO:0042904","count":4},{"id":"GO:0060065","count":4},{"id":"GO:0008585","count":4}]},{"hash":"41146948992995300","title":"Cation Transport and Synaptic Potentiation","description":"The top GO terms are dominated by ion transport across membranes (sodium, potassium, and other cations) and by long-term synaptic potentiation, pointing to proteins involved in membrane transport that can modulate neuronal signaling and plasticity. While a few terms touch on other processes (lipopolysaccharide biosynthesis, muscle fiber type transitions), the core signal is consistent with ion transport linked to synaptic function.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0036376","count":2},{"id":"GO:0030007","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0009103","count":1}]},{"hash":"153767781536399301","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072089","count":3},{"id":"GO:0061158","count":2},{"id":"GO:1903265","count":2},{"id":"GO:0001519","count":2},{"id":"GO:0010586","count":2}]},{"hash":"1093235623123713068","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036205","count":2},{"id":"GO:0042981","count":2},{"id":"GO:0060395","count":1},{"id":"GO:0060261","count":1},{"id":"GO:0075297","count":1}]},{"hash":"361588531426502422","title":"Mitochondrial and membrane signaling in neurons","description":"The top GO terms point to mitochondrial processes (mitochondrion inheritance; cardiolipin metabolism) alongside signaling and membrane-associated activities (PKC signaling, protein localization to membrane rafts, dopaminergic synaptic transmission, TLR3 signaling, ECM remodeling, and cell adhesion molecule production). This suggests a cohesive theme of signaling events coordinated at mitochondrial lipids and membrane microdomains in neuronal contexts, rather than a single specific pathway. Therefore, a label emphasizing neuronal membrane-signaling with mitochondrial lipid involvement seems appropriate.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0060355","count":5},{"id":"GO:0070528","count":5},{"id":"GO:0045861","count":5},{"id":"GO:0000001","count":5},{"id":"GO:0032226","count":5}]},{"hash":"1989811747017382831","title":"Floral development and hormone signaling in plants","description":"The cluster centers on floral organ and seed development (bract, floral meristem, seed) with multiple hormone signaling pathways (ethylene, ABA, and auxin-related patterning) and regulation of cuticle components, suggesting a cohesive module coordinating flower development with surface protection.","confidence":"Medium","size":8,"edges":11,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010200","count":1},{"id":"GO:0010432","count":1},{"id":"GO:0048316","count":1},{"id":"GO:0060774","count":1},{"id":"GO:0010451","count":1}]},{"hash":"2097376128910894078","title":"Osmotic Stress-Linked Solute Transport","description":"The cluster\u2019s top GO terms converge on transport activities for a variety of solutes (glucose/fructose import, nitrite and urate transport, sodium-dependent cation transport, potassium ion transport) and a response to osmotic stress, suggesting a cohesive group of membrane transporters involved in osmoregulation and nutrient/ion uptake. The presence of a transcription regulation term is less central but could reflect regulatory control of transport genes under stress, so the label emphasizes transport and osmotic response as the core theme.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006970","count":2},{"id":"GO:0070715","count":2},{"id":"GO:0044381","count":2},{"id":"GO:0071332","count":2}]},{"hash":"1592323737593593938","title":"Amino acid and nucleobase transport","description":"GO terms indicate transport across the plasma membrane for diverse substrates (adenine, guanine, uracil, urate, xanthine, hypoxanthine, glutamine, asparagine) and positive regulation of glutamine transport. Despite no edges, the shared function is membrane transport of small molecules, especially amino acids and nucleobases, pointing to transport-related proteins as a coherent cluster.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098702","count":1},{"id":"GO:0015747","count":1},{"id":"GO:0098710","count":1},{"id":"GO:0070904","count":1},{"id":"GO:0098721","count":1}]},{"hash":"2184710644595637025","title":"Prostaglandin and retinoid biosynthesis in female reproduction","description":"The cluster is dominated by GO terms for prostaglandin biosynthesis and retinoic acid biosynthesis, plus reproductive-development terms such as uterus and female gonad development, pointing to a theme around lipid/retinoid metabolism in female reproductive biology. Some terms (e.g., calcitriol biosynthesis, xenobiotic/alkaloid metabolism) are less coherent with this core theme, indicating a mix of associations or secondary connections. ","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":8},{"id":"GO:0071615","count":7},{"id":"GO:0042904","count":7},{"id":"GO:0060065","count":7},{"id":"GO:0008585","count":7}]},{"hash":"985181910661222026","title":"Prostaglandin and Retinoid Biosynthesis","description":"The top GO terms are dominated by prostaglandin biosynthesis and retinoic acid biosynthesis, with supporting entries for retinoid catabolism and calcitriol biosynthesis, indicating a cluster focused on lipid mediator production and vitamin A/D metabolism. Redox-related terms are present but secondary, and a few reproduction-related terms may reflect tissue-specific contexts rather than core function.","confidence":"High","size":8,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":5},{"id":"GO:0098869","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0071615","count":3},{"id":"GO:0042904","count":3}]},{"hash":"1417120250579875886","title":"Plant hormone signaling and transcription regulation","description":"These proteins are enriched for plant hormone responses (salicylic acid, gibberellin, cytokinin) and transcriptional regulation (RNA polymerase II\u2013mediated transcription), indicating a cluster tied to hormone signaling and hormone-responsive gene expression. A viral process term appears incidental and does not dominate the theme. Confidence: High.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009751","count":2},{"id":"GO:0009739","count":2},{"id":"GO:0009938","count":2}]},{"hash":"535733483417542282","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":2},{"id":"GO:0090617","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0000961","count":2}]},{"hash":"603557909039637219","title":"Unknown","description":"There are no GO terms listed for this cluster (no Top Terms provided), so no shared function or process can be inferred from the data. Without functional annotations, a precise label cannot be assigned.","confidence":"","size":8,"edges":12,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[]},{"hash":"1159492081036076891","title":"Vesicle trafficking and signaling in neural-immune contexts","description":"Based on the top GO terms, the core of the cluster centers on intracellular protein transport and vesicle fusion, with several immune-related (regulation of phagocytosis, B cell receptor signaling) and neural development signals (reelin signaling, radial glia migration). While some terms are more peripheral (antibiotic response, aging-related stress, transcription regulation, insulin secretion), the dominant pattern points to vesicle-mediated trafficking and signaling shared by neural and immune systems. This cohesive theme supports a label focused on vesicle trafficking and signaling in neural-immune contexts.","confidence":"Medium","size":8,"edges":3,"triangles":1,"max_degree":2,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":4},{"id":"GO:0050764","count":3},{"id":"GO:0006906","count":3},{"id":"GO:0050861","count":3},{"id":"GO:0021814","count":3}]},{"hash":"1429386388583476762","title":"DNA damage response to xenobiotic stress","description":"The top GO terms point to cellular responses to xenobiotic stimuli and DNA repair processes (base-excision repair and translesion synthesis), with supporting signals for apoptosis regulation and inflammatory response. This suggests proteins in the cluster participate in managing DNA damage and stress responses triggered by chemical exposures, including xenobiotics and metals like cadmium, rather than a single developmental or metabolic pathway. Thus, the label reflects the dominant theme of DNA damage repair under xenobiotic stress. ","confidence":"Medium","size":8,"edges":24,"triangles":35,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0001541","count":2},{"id":"GO:0007568","count":1},{"id":"GO:0071276","count":1},{"id":"GO:0045008","count":1}]},{"hash":"217312565795357493","title":"Bacterial metabolite biosynthesis","description":"This cluster\u2019s top GO terms are dominated by biosynthetic processes for metabolites and cofactors (biotin, menaquinone, poly-hydroxybutyrate, antibiotic), plus related catabolic activities. While there are some outliers (chlorophyll catabolic, glucuronoside catabolic, transcription), the strongest signal is biosynthesis of small molecules in bacteria, suggesting a metabolism-focused theme rather than a specific signaling or interaction module.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0019391","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0006351","count":3}]},{"hash":"349923384426153281","title":"Plant growth and immune signaling","description":"The cluster centers on intracellular signal transduction and transcription, with plant-specific processes like pollen tube guidance and growth, indicating signaling roles in development. It also includes immune-related terms (defense response to virus, innate immune response) and ubiquitin-related protein turnover, suggesting a module where signaling coordinates growth with stress and defense, regulated by ubiquitination.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":2},{"id":"GO:0010183","count":2},{"id":"GO:0080092","count":2},{"id":"GO:0035520","count":2},{"id":"GO:1903070","count":2}]},{"hash":"920944286116937751","title":"Immune signaling and transcription regulation","description":"These proteins show enrichment for regulatory GO terms related to immune signaling (negative regulation of TLR3 signaling; positive regulation of TNF-mediated signaling), endocytosis control, proteasomal turnover, calcium channel activity, as well as transcription and translation processes. The common thread appears to be modulation of signaling pathways and gene expression rather than a single concrete function, making the label suggestive but not definitive. ","confidence":"Medium","size":8,"edges":22,"triangles":35,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0034140","count":6},{"id":"GO:0045648","count":6},{"id":"GO:1900186","count":6},{"id":"GO:0006412","count":6},{"id":"GO:1901799","count":6}]},{"hash":"499315440871360160","title":"Unknown","description":"Top terms are a mix of plant-specific cell wall biosynthesis and glucuronoxylan formation with diverse animal cellular processes (transcription, mRNA processing, development, telomere regulation, nuclear export, migration, muscle regeneration, CDK activity). This lack of a single cohesive function implies no clear functional theme for the cluster. ","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":3},{"id":"GO:0010417","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1991547443871784611","title":"Oocyte Maturation and Female Meiosis","description":"Most terms point to oocyte biology: oocyte maturation and spindle assembly in female meiosis I are explicit, supported by regulation of cell proliferation and ubiquitin-protein ligase\u2013dependent protein turnover, which are key in meiotic control. While other terms touch on circadian rhythm and early neural development, those are less central to the cluster's core function, so the label emphasizes oocyte maturation and meiosis.","confidence":"Medium","size":8,"edges":13,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":6},{"id":"GO:0001556","count":5},{"id":"GO:0006516","count":5},{"id":"GO:0007057","count":5},{"id":"GO:0051436","count":5}]},{"hash":"956628015612532345","title":"Wnt-regulated organ development","description":"Top terms show canonical Wnt signaling and its negative regulation, alongside multiple tissue development processes (superior colliculus, fungiform papilla, hair follicle placode, renal outer medulla). This pattern suggests a core theme of Wnt-mediated organogenesis, with ancillary cellular processes like proton transmembrane transport present but not defining the cluster.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":8},{"id":"GO:0071681","count":7},{"id":"GO:0061380","count":7},{"id":"GO:0000011","count":7},{"id":"GO:0044336","count":7}]},{"hash":"1173754711694248533","title":"RNA Pol II Transcription Regulation","description":"The top GO terms are dominated by transcriptional control involving RNA polymerase II, including negative regulation of Pol II transcription and regulation of preinitiation complex assembly, with related chromatin-associated processes (histone acetylation, nucleosome mobilization). Additional terms hint at downstream growth and metabolic responses (photomorphogenesis, cellular respiration), supporting a cohesive theme of Pol II transcription regulation and its regulation by chromatin and signaling pathways.","confidence":"High","size":8,"edges":10,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":3},{"id":"GO:0043966","count":3},{"id":"GO:1900446","count":3},{"id":"GO:0000436","count":3},{"id":"GO:0000122","count":3}]},{"hash":"2086270541133133023","title":"Ubiquitination-Regulated TNF/JNK Signaling","description":"The top GO terms cluster around protein ubiquitination (autoubiquitination, K6-linked) and regulation of TNF-mediated signaling and the JNK cascade, with supporting references to ERAD-related ubiquitination. This suggests a cohesive role for ubiquitin modification in controlling inflammatory signaling pathways.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":7},{"id":"GO:0070535","count":6},{"id":"GO:1901253","count":6},{"id":"GO:2000620","count":6},{"id":"GO:0033209","count":6}]},{"hash":"1641685232853491363","title":"Insect cuticle development and molting","description":"This cluster is dominated by GO terms for chitin catabolic process, chitin-based cuticle development, and ecdysis, pointing to proteins involved in insect cuticle formation and molting. Although there are immune signaling terms (NF-kappaB activation, interleukin responses) present, the strongest and most cohesive signal is cuticle biology and molting, justifying a label centered on insect cuticle development and molt processes.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006032","count":3},{"id":"GO:0051216","count":3},{"id":"GO:0070741","count":3},{"id":"GO:0040003","count":3},{"id":"GO:0007250","count":3}]},{"hash":"1689373419204783269","title":"Plant Hormone Signaling and Chloroplast Regulation","description":"The top GO terms emphasize plant hormone signaling (cytokinin, gibberellin), regulation of chlorophyll biosynthesis, leaf senescence, osmotic stress response, and transcriptional control (chromatin remodeling, snRNA transcription), suggesting these proteins act as plant growth and stress regulators tied to chloroplast function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":4},{"id":"GO:1900056","count":2},{"id":"GO:0010380","count":2},{"id":"GO:0009739","count":2},{"id":"GO:0006970","count":2}]},{"hash":"1509523262162175283","title":"Plant cell wall remodeling and pollen tube growth","description":"Dominant GO terms are plant-related: pectin catabolic/metabolic processes, mucilage pectin biosynthesis, pollen tube growth, and cell wall modification, along with general carbohydrate metabolism. This pattern points to a cluster of proteins involved in plant cell wall construction/remodeling and pollen tube development, consistent with processes required for plant reproduction and cell wall dynamics. A few terms like neuroblast proliferation and lung morphogenesis appear but with low representation and do not define the cluster; thus a plant-centered function label is appropriate.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007405","count":2},{"id":"GO:0060441","count":2},{"id":"GO:0005975","count":2},{"id":"GO:0045490","count":1},{"id":"GO:0048358","count":1}]},{"hash":"1037866668867717971","title":"Mitotic Progression and Cytokinesis with ER-Golgi Trafficking","description":"This cluster centers on mitosis and cytokinesis, including mitotic spindle assembly, exiting mitosis, and abscission, plus vesicle trafficking between the ER and Golgi essential for membrane remodeling during cell division. While a couple of terms touch on stress responses, the dominant signal ties to mitotic progression and cytokinesis with concurrent vesicle transport.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071454","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000920","count":3},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2}]},{"hash":"2179878045047173497","title":"Fungal cell wall biosynthesis and remodeling","description":"Dominant signals are fungal-type cell wall assembly, organization, and beta-D-glucan biosynthesis/catabolism, indicating a module focused on fungal cell wall biogenesis and remodeling. A couple of terms (rRNA methylation, peroxisome targeting) are less representative but do not override the core theme.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070475","count":1},{"id":"GO:1902609","count":1},{"id":"GO:0031408","count":1},{"id":"GO:0000917","count":1},{"id":"GO:0006076","count":1}]},{"hash":"264113393692318782","title":"RNA processing and mRNA decay regulation","description":"These proteins show enrichment for processes related to RNA metabolism and control of gene expression at the RNA level, including negative regulation of translation, deadenylation-dependent mRNA decay, poly(A) tail shortening, and mRNA processing body assembly, as well as regulation of transcription elongation by RNA Pol II. The pattern suggests a cohesive theme of post-transcriptional regulation rather than a single enzymatic pathway, though a few terms are less connected. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901001","count":1},{"id":"GO:0051245","count":1},{"id":"GO:0000289","count":1},{"id":"GO:0006368","count":1},{"id":"GO:0017148","count":1}]},{"hash":"1346298024735715221","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009088","count":1},{"id":"GO:0009089","count":1},{"id":"GO:0019877","count":1},{"id":"GO:0044210","count":1},{"id":"GO:0006526","count":1}]},{"hash":"1513630709322994350","title":"Regulation of cell proliferation, migration, and differentiation","description":"The terms cluster around growth signaling (Ras pathway regulation), cytoskeletal/motility processes (pseudopodium assembly, fibroblast migration), lineage differentiation (osteoblast, macrophage, neuroblast differentiation), and synaptic/modification regulation, plus ECM remodeling via collagen biosynthesis. Together they point to coordinated regulation of cell fate decisions, movement, and tissue remodeling rather than a single pathway.","confidence":"Medium","size":7,"edges":13,"triangles":9,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032966","count":5},{"id":"GO:0046579","count":5},{"id":"GO:0010821","count":5},{"id":"GO:0010762","count":5},{"id":"GO:0055108","count":5}]},{"hash":"1253797223811541128","title":"Vesicle trafficking and neuronal signaling","description":"This cluster centers on membrane trafficking and signaling: vesicle fusion and regulation of phosphoinositides point to endomembrane dynamics; ribophagy and phagocytosis relate to autophagic/endocytic processes; reelin signaling and radial glia migration reflect neural development cues, with B cell receptor signaling providing an immune-vesicle signaling context. Together, these terms suggest a core function in intracellular membrane dynamics and associated signaling in neural development and immune-related processes.","confidence":"Medium","size":7,"edges":12,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0034517","count":4},{"id":"GO:0060304","count":3},{"id":"GO:0050764","count":2},{"id":"GO:0006906","count":2},{"id":"GO:0050861","count":2}]},{"hash":"213950161271208298","title":"Plant defense and hormone signaling (nodulation)","description":"The terms show strong signals for defense and biotic response, plus hormone signaling pathways (cytokinin, gibberellin, ABA) and nodulation, suggesting a cluster of proteins involved in plant immune responses and nodulation-related signaling.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009607","count":3},{"id":"GO:0009736","count":3},{"id":"GO:0009877","count":3},{"id":"GO:0006952","count":3},{"id":"GO:0009740","count":3}]},{"hash":"880905626095382868","title":"Ubiquitin-dependent endocytosis and MVB sorting","description":"The GO terms strongly point to ubiquitin-regulated endocytic pathways and multivesicular body sorting (e.g., positive regulation of ubiquitin-dependent endocytosis, ubiquitin-dependent protein catabolic process via the MVB pathway, and protein transport to vacuole via MVB sorting). Although a couple of reproduction-related terms are present, the unifying theme is endocytic trafficking and proteolysis via the ubiquitin/MVB system.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007293","count":2},{"id":"GO:1904669","count":2},{"id":"GO:0010796","count":2},{"id":"GO:0007291","count":2}]},{"hash":"1976375266382349598","title":"Retinoic Acid Metabolism and Female Reproductive Development","description":"This cluster is dominated by GO terms for retinoic acid biosynthesis and catabolism, and includes multiple terms on uterus/female gonad/genitalia development, indicating RA-regulated pathways in female reproductive development.","confidence":"High","size":7,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071615","count":5},{"id":"GO:0042904","count":5},{"id":"GO:0060065","count":5},{"id":"GO:0008585","count":5},{"id":"GO:0034653","count":5}]},{"hash":"779989757543099981","title":"Neuronal synapse formation and cytoskeletal remodeling","description":"The GO terms cluster around neuronal development and synaptic function\u2014regulation of synaptic vesicle exocytosis, brain development, dendritic spine growth, and Rac-driven cytoskeletal remodeling (lamellipodium/ruffle assembly)\u2014as well as Golgi-to-plasma-membrane trafficking. This suggests a common theme of assembling synapses through vesicle regulation and actin dynamics.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000300","count":3},{"id":"GO:0031384","count":3},{"id":"GO:0010796","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0060999","count":3}]},{"hash":"816420050820307365","title":"Neuronal vesicle exocytosis and receptor trafficking","description":"Dominant GO terms point to neurotransmitter release and vesicle handling in neurons, including calcium-regulated exocytosis, exocytic insertion of receptors at the postsynaptic membrane, and regulation of synaptic vesicle recycling, plus neuron cellular homeostasis. A secretory process related to insulin secretion appears but does not overshadow the synaptic vesicle theme, so the label reflects the core function of the cluster.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035774","count":2},{"id":"GO:0030154","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0070050","count":2},{"id":"GO:0090502","count":2}]},{"hash":"754936765260745914","title":"Ubiquitin-Proteasome Proteolysis and Vesicle Trafficking","description":"The terms point to proteasome- and ubiquitin-dependent protein degradation, together with endosome/lysosome localization and vesicle fusion, indicating a cluster centered on proteolysis and vesicular trafficking pathways that handle protein turnover and cargo sorting, with phagocytosis regulation as a related facet. A minor note is the enucleate erythrocyte development term, which may reflect membrane remodeling processes rather than a primary erythroid role.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0045721","count":1},{"id":"GO:0033033","count":1},{"id":"GO:0048822","count":1},{"id":"GO:0043161","count":1}]},{"hash":"1951428479486089384","title":"Neural and cardiac development with transcriptional regulation","description":"This cluster features multiple terms linking transcriptional regulation (RNA Pol II transcription, circadian regulation of gene expression, SREBP signaling) with differentiation and morphogenesis in neural and muscular lineages (subpallium neuron fate commitment, amacrine cell differentiation, astrocyte differentiation regulation, muscle tissue morphogenesis, cardioblast migration). The combination suggests proteins involved in coordinating gene expression with neural and cardiac/muscular development.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":4},{"id":"GO:0060415","count":3},{"id":"GO:0060163","count":3},{"id":"GO:0033627","count":3},{"id":"GO:0032922","count":3}]},{"hash":"2259089038827728500","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":8,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0071787","count":4},{"id":"GO:1905869","count":4},{"id":"GO:0034145","count":4}]},{"hash":"164439504799127655","title":"Innate Immune Sensing and Defense","description":"Proteins in this cluster show enrichment for immune recognition and signaling, including detection of lipopolysaccharide, MyD88-dependent Toll-like receptor signaling, and defense responses to virus, plus related signaling pathways like salicylic acid and hydrogen peroxide signaling. These immune-related terms dominate, supporting a label centered on innate immune sensing and defense; other terms reflect general stress/transcriptional regulation but do not outweigh the immune theme.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045429","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0009863","count":1}]},{"hash":"1365150210157799393","title":"Polyol and aldehyde metabolism under stress","description":"This cluster\u2019s top GO terms cluster around metabolism of sugar alcohols (D-sorbitol, xylitol) and aldehydes (furfural) with fermentation to ethanol, alongside stress responses (nitrosative stress, lipopolysaccharide response). This points to a theme of carbohydrate/alcohol metabolism coupled with cellular stress or defense processes. Some terms (prostaglandin metabolism, blood pressure regulation) are less central and may reflect broader organismal context, but the core signals fit a metabolism-with-stress theme.","confidence":"Medium","size":7,"edges":14,"triangles":10,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0033859","count":2},{"id":"GO:0006062","count":2},{"id":"GO:0043458","count":2},{"id":"GO:0051409","count":2}]},{"hash":"2230421364136422636","title":"Translation machinery and regulation","description":"The top terms cluster around core translation processes\u2014initiation, elongation, termination, cytoplasmic translation, and ribosome biogenesis, including selenocysteine incorporation. Deadenylation-dependent mRNA decay also ties into gene expression control linked to translation. A couple of peripheral terms (glial proliferation, antibiotic response) exist but do not override the main theme. ","confidence":"High","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0042254","count":3},{"id":"GO:0000288","count":2},{"id":"GO:0006415","count":2},{"id":"GO:0001514","count":2}]},{"hash":"1368792552343068103","title":"Methylation and lipid biosynthesis","description":"The cluster\u2019s top GO terms are dominated by methylation-related processes, including tRNA methylation, wobble uridine modification, N-terminal peptidyl-alanine trimethylation, and arginine methylation. In addition, there are biosynthetic processes for sterol, ubiquinone, and vitamin E, pointing to lipid/quinone metabolism. A transcription-related term appears but is not central to the cluster\u2019s core functions, so the label highlights the primary themes of methylation and lipid biosynthesis.","confidence":"Medium","size":7,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016126","count":2},{"id":"GO:0006744","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0002098","count":1},{"id":"GO:0016049","count":1}]},{"hash":"1957266290495532692","title":"Cell Growth and Energy Metabolism","description":"The cluster centers on core cellular production and growth: energy-related processes (positive regulation of oxidative phosphorylation, positive regulation of ATP biosynthetic process) alongside cell cycle activities (cell division, centriole elongation) and gene expression machinery (RNA polymerase II transcription preinitiation complex assembly, mRNA export). Some outlier terms (viral replication, obsolete stress-related terms) exist, but the dominant theme ties growth with energy metabolism and transcriptional activity.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1903724","count":1},{"id":"GO:0070370","count":1},{"id":"GO:0019079","count":1},{"id":"GO:0051301","count":1},{"id":"GO:1903862","count":1}]},{"hash":"1420030243165756767","title":"Transcription Regulation & Oxidative Stress","description":"These proteins show GO terms centering on transcriptional control (DNA-templated transcription, regulation of DNA binding, and related regulatory activities) and oxidative stress responses (cellular response to oxidative stress, cellular oxidant detoxification). There are a few outliers (photoreceptor maintenance, viral process, cytochrome complex assembly), but the dominant theme links transcription regulation with oxidative stress defense. This suggests a cluster of proteins involved in gene regulation under stress conditions, rather than a single, cohesive complex. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903026","count":1},{"id":"GO:0045494","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0017004","count":1},{"id":"GO:0098869","count":1}]},{"hash":"936121611539177778","title":"Unknown","description":"The GO terms are highly diverse and sparse, spanning development, cell cycle and apoptosis regulation, RNA processing, protein deubiquitination, stress responses, circadian regulation, and metabolism. There is no dominant shared function, so a specific, representative label isn\u2019t well-supported. ","confidence":"","size":7,"edges":16,"triangles":15,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0071600","count":1},{"id":"GO:0045023","count":1},{"id":"GO:0043066","count":1},{"id":"GO:1904404","count":1},{"id":"GO:0071301","count":1}]},{"hash":"413894358505221313","title":"DNA Transcription Regulation & Oxidative Stress Response","description":"The strongest GO signals are for DNA-templated transcription and regulation of DNA binding, suggesting a core set of transcription regulators. Additional terms point to modulation of nuclear processes and oxidative stress/detoxification, with supporting metabolic functions (FAD biosynthesis, sulfate assimilation) that often accompany stress-responsive transcriptional networks. This hints at a cluster centered on transcription regulation with ancillary stress and metabolic roles.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:1903026","count":2},{"id":"GO:0018401","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0016032","count":2}]},{"hash":"360548832191986546","title":"Neural development and glutamate biosynthesis","description":"This cluster is dominated by neural development terms (neuron maturation, neural precursor proliferation, in utero embryonic development) and includes neurotransmitter-related metabolism (L-glutamate biosynthetic process), with supportive signals for stem cell proliferation and broader developmental contexts such as pituitary development; redox homeostasis suggests general cellular maintenance during development.","confidence":"Medium","size":7,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0021983","count":5},{"id":"GO:0045648","count":5},{"id":"GO:0042551","count":5},{"id":"GO:2000179","count":5},{"id":"GO:0097054","count":5}]},{"hash":"2010293872538469775","title":"Mitochondrial calcium signaling and insulin secretion","description":"This cluster is driven by GO terms for calcium import into the mitochondrion and positive regulation of mitochondrial calcium concentration, plus a term linking calcium signaling to insulin secretion. Together these suggest a core theme of mitochondrial calcium handling that modulates insulin release. Additional terms like protein folding in the ER and redox homeostasis indicate broader cellular maintenance but are not as central to the main mitochondrial-calcium-insulin axis.","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035786","count":2},{"id":"GO:0036444","count":2},{"id":"GO:0051561","count":2},{"id":"GO:0032024","count":2},{"id":"GO:0000122","count":2}]},{"hash":"515347224600183185","title":"ER Stress and Redox Homeostasis","description":"This cluster is enriched for oxidative detoxification and redox homeostasis, alongside ER-specific processes like response to ER stress and protein folding in the ER, indicating a shared function in managing oxidative stress and protein quality control within the secretory pathway.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0055114","count":3},{"id":"GO:1903026","count":2},{"id":"GO:0034976","count":2}]},{"hash":"2283985384094333596","title":"Chloroplast Photosynthesis and Complex Assembly","description":"The top GO terms strongly center on photosynthesis and photosystem I assembly, indicating proteins involved in chloroplast light reactions and assembly of photosynthetic complexes (with supporting terms like cytochrome complex assembly). While some terms relate to broader regulatory or non-photosynthetic processes, the dominant signal is chloroplast photosynthesis machinery.","confidence":"High","size":7,"edges":18,"triangles":23,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0048564","count":2},{"id":"GO:0015979","count":2},{"id":"GO:1903026","count":1},{"id":"GO:0045494","count":1},{"id":"GO:0018401","count":1}]},{"hash":"1892408924806219988","title":"Unknown","description":"The top GO terms are very diverse (oxidant detoxification, metal ion response, auxin signaling, light-response, DNA damage response, growth regulation, translation), with no single coherent function linking the proteins. This suggests the cluster lacks a clear shared biological process, so an Unknown label is appropriate.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0055119","count":1},{"id":"GO:2000030","count":1},{"id":"GO:0043517","count":1},{"id":"GO:0010043","count":1}]},{"hash":"1740268453373709577","title":"Diverse Metabolite Biosynthesis","description":"The GO terms indicate multiple distinct biosynthetic processes (antibiotics, porphyrin, biotin, lysine, LPS, serine, glycolate, phospholipids) across different metabolites, suggesting a cluster focused on diverse metabolic biosynthesis rather than a single pathway. A transport term appears but is peripheral to the core theme. ","confidence":"Medium","size":7,"edges":7,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0006782","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0019878","count":2},{"id":"GO:0009103","count":2}]},{"hash":"456140123438916089","title":"Plant defense and hormone signaling responses","description":"This cluster is characterized by GO terms pointing to plant immune and growth hormone pathways, including responses to salicylic acid and chitin (pathogen-associated signals), regulation of antifungal innate immunity, gibberellin and ethylene-related signaling, and developmental processes like atrichoblast and sclerenchyma differentiation. Although translation is a broad term present, the overarching theme centers on plant defense and hormone-regulated development, suggesting a cohesive, though not perfectly uniform, functional theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0009751","count":1},{"id":"GO:0010200","count":1},{"id":"GO:0009739","count":1},{"id":"GO:0009938","count":1}]},{"hash":"923871340658483924","title":"RNA processing and splicing machinery","description":"This cluster is enriched for RNA metabolism activities: spliceosome assembly, mRNA splicing, snRNP assembly, tRNA processing, and rRNA maturation, suggesting a core role in RNA processing complexes. A few terms about chromatin and transcription are present but secondary to the dominant RNA processing signals.","confidence":"High","size":7,"edges":9,"triangles":5,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006605","count":3},{"id":"GO:0006369","count":3},{"id":"GO:0033962","count":2},{"id":"GO:0008334","count":2},{"id":"GO:1990141","count":2}]},{"hash":"1913580195337745161","title":"Unknown","description":"The terms are a diverse mix (nuclear RNA processing in Cajal bodies, telomerase RNA localization, cell division, host protein translocation, toxin transport, cytokine production, immune signaling, cocaine response, and sperm binding) with no clear common function or network connectivity, so there isn't a coherent single function to label the cluster.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904871","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0044053","count":1},{"id":"GO:1901998","count":1},{"id":"GO:1904874","count":1}]},{"hash":"513235709553999919","title":"Plant innate immunity and hormone cross-talk","description":"This cluster centers on plant defense signaling (response to salicylic acid and chitin) and hormone interactions (gibberellin and ethylene precursor ACC), suggesting how immune responses interlink with growth-related pathways. Additional terms on antifungal defense and tissue differentiation (sclerenchyma, atrichoblast) fit the developmental/defense context, while a single unrelated term (uterus development) likely represents noise. Overall, a cohesive theme of plant immune signaling intertwined with hormonal regulation.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009751","count":6},{"id":"GO:0010200","count":6},{"id":"GO:0009739","count":6},{"id":"GO:0009938","count":6},{"id":"GO:0080169","count":6}]},{"hash":"1063784129735718099","title":"Hypusine-Linked Translation Regulation","description":"The cluster shows a strong enrichment for translation-related GO terms (translation, translational initiation, elongation, termination, and frameshifting) and the specific process of peptidyl-hypusine biosynthesis, which is essential for eIF5A function in translation. While other terms touch on defense or vesicle processes, the dominant signal is the translation machinery and its regulation via hypusination, justifying a translation-centered label.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903272","count":1},{"id":"GO:0008612","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006452","count":1},{"id":"GO:0034050","count":1}]},{"hash":"554460277216062538","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":14,"triangles":16,"max_degree":5,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":5},{"id":"GO:0006412","count":4},{"id":"GO:0000463","count":3},{"id":"GO:0035073","count":2},{"id":"GO:0042273","count":2}]},{"hash":"1226589151685659062","title":"mRNA Splicing and Export Regulation","description":"The top GO terms point to post-transcriptional RNA processing, especially mRNA export from the nucleus and spliceosome-mediated (including alternative) splicing, with some ncRNA-mediated gene silencing and translational reinitiation themes. A few terms about polyadenylation and DNA replication appear tangential, suggesting the cluster centers on RNA maturation and regulation of gene expression at the RNA level.","confidence":"Medium","size":7,"edges":9,"triangles":5,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":4},{"id":"GO:0006406","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0006260","count":3}]},{"hash":"2102199550497154778","title":"Viral modulation of host RNA processing","description":"The cluster features host RNA processing activities (pre-miRNA processing, mRNA splicing, miRNA catabolism) and transcription Regulation (DNA-templated transcription, antitermination) together with viral-related processes (establishment of integrated proviral latency, viral budding via ESCRT), suggesting a theme where viruses interact with and modulate host RNA metabolism and transcription. ","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070934","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0031054","count":2},{"id":"GO:0031564","count":2},{"id":"GO:0000398","count":2}]},{"hash":"1612684213529884163","title":"Plant Hormone Biosynthesis and Fruit Ripening","description":"Top GO terms cluster around biosynthesis of plant hormones (ethylene, gibberellin, auxin) and related regulatory processes, plus biosynthesis of secondary metabolites (proanthocyanidin), with supporting processes like hydrogen peroxide\u2013mediated programmed cell death and fruit ripening. Although there are a few odd terms (penicillin biosynthesis, obsolete oxidation-reduction process), the majority point to hormone-driven metabolic pathways and maturation in plants, suggesting a cohesive theme of hormone production linked to ripening and defense.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009693","count":2},{"id":"GO:0042318","count":2},{"id":"GO:0009686","count":2},{"id":"GO:0045487","count":2}]},{"hash":"1446560524482828191","title":"Mitochondrial and Cytoplasmic Translation Machinery","description":"The top GO terms are dominated by translation processes, including mitochondrial translation, mitochondrial translational elongation, cytoplasmic translation, translational termination, and regulation of elongation, indicating the cluster primarily reflects components of the protein synthesis machinery across both mitochondrial and cytosolic contexts. A few terms related to splicing or signaling (spliceosome-related) appear less central, and muscle differentiation or BDNF response may reflect context-specific regulation but do not override the core translation theme.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0032543","count":2},{"id":"GO:0070125","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0045901","count":2}]},{"hash":"1988011000755102960","title":"Eye and craniofacial development","description":"Top terms show a clear emphasis on eye/visual system development (visual perception, optic nerve morphogenesis) and craniofacial patterning (face development). Neurotrophin signaling and Wnt pathway modulation are well-known contributors to neural and craniofacial development, supporting this theme. Some terms concern general cell-cycle control or stress responses, which may reflect background cellular processes rather than the core function of the cluster; those do not outweigh the visual/face development signal. Thus, the name Eye and craniofacial development reflects the predominant pattern in this cluster.","confidence":"Medium","size":7,"edges":5,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045736","count":6},{"id":"GO:0034501","count":6},{"id":"GO:0007601","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0048011","count":5}]},{"hash":"566240561647470994","title":"Ribosome Biogenesis and Nuclear Export","description":"The top GO terms cluster around ribosome assembly and processing (ribosome biogenesis, maturation of LSU-rRNA, and large subunit export from the nucleus), suggesting a shared function in ribosome production and transport; the remaining terms are more peripheral, though they may reflect broader cellular housekeeping and trafficking activities.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901857","count":1},{"id":"GO:0010971","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0000055","count":1}]},{"hash":"720748228420592679","title":"Arginine and Histone Methylation (Epigenetic Regulation)","description":"The top GO terms include both peptidyl-arginine methylation and histone H4-R3 methylation, pointing to methylation-based chromatin modification as the core shared function. The presence of cell growth and cellular senescence terms supports an epigenetic influence on the cell cycle, even though other terms (metabolic or transport-related) may reflect broader annotations in the dataset.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0090398","count":2},{"id":"GO:0019919","count":2},{"id":"GO:0043985","count":2},{"id":"GO:0009236","count":2}]},{"hash":"303894422966630600","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006470","count":2},{"id":"GO:0006541","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0019379","count":1},{"id":"GO:0009970","count":1}]},{"hash":"619716009797989769","title":"Malate and Pyruvate Metabolism","description":"This cluster is dominated by GO terms for malate and pyruvate metabolism (malate catabolic/metabolic; pyruvate metabolic), indicating a core central carbon metabolism theme. Other terms like NADP regulation and growth-related processes appear less prominently, suggesting secondary links to biosynthesis and cell growth, but the primary signal is malate/pyruvate metabolism.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043464","count":3},{"id":"GO:0051262","count":3},{"id":"GO:0006108","count":3},{"id":"GO:1902031","count":3},{"id":"GO:0006090","count":3}]},{"hash":"2104198656367174370","title":"Diverse Developmental Processes","description":"This cluster\u2019s GO terms span development and differentiation across plants, invertebrates, and vertebrates (e.g., meristem transitions, eye morphogenesis, ring gland and organ development, macrophage/exocrine pancreas differentiation, vitellogenesis, seed maturation). The common theme is broad involvement in developmental programs and cell fate decisions rather than a single pathway, justifying a label around diverse developmental processes.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009737","count":3},{"id":"GO:0010228","count":2},{"id":"GO:0034670","count":2},{"id":"GO:0016330","count":2},{"id":"GO:0045671","count":2}]},{"hash":"793655498061854483","title":"Transsulfuration and sulfur amino acid metabolism","description":"The terms cluster around sulfur-containing amino acid metabolism, including serine and homocysteine catabolism, cysteine biosynthesis via transsulfuration, and hydrogen sulfide production, indicating a cohesive pathway group for sulfur amino acid metabolism.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0018871","count":2},{"id":"GO:0046360","count":2},{"id":"GO:0043418","count":2},{"id":"GO:0006535","count":2},{"id":"GO:0009088","count":2}]},{"hash":"263613209211379372","title":"Unknown","description":"The GO terms are highly diverse, including mitosis-related processes (spindle-kinetochore attachment, cytokinesis localization), transcription termination, neuron differentiation, metabolic and signaling regulation, apoptosis signaling, DNA repeat maintenance, and lead ion response. This lack of a cohesive functional theme suggests no single, representative label can capture the cluster's biology. ","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0098609","count":7},{"id":"GO:0005979","count":7},{"id":"GO:0030846","count":7},{"id":"GO:1901901","count":7},{"id":"GO:0051315","count":7}]},{"hash":"1600306328193082635","title":"DNA replication and centrosome cycle","description":"The top GO terms are dominated by DNA replication (GO:0006260), centrosome cycle (GO:0007098), and positive regulation of nuclear cell cycle DNA replication (GO:0010571), with supporting signals from DNA topology and chromatin-related processes (e.g., nucleosome positioning, heterochromatin formation). While embryonic cranial skeleton morphogenesis appears among terms, the strongest and most consistent theme links to replication and centrosome-associated cell cycle control and chromatin dynamics, justifying this label.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":4},{"id":"GO:0007098","count":3},{"id":"GO:0010571","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006265","count":2}]},{"hash":"531567899146365512","title":"Neuronal development and signaling","description":"This cluster\u2019s top terms emphasize neuronal functions (visual perception, excitatory postsynaptic potential) and signaling pathways (GPCR signaling, GTPase activity regulation), along with broader development processes like multicellular development and angiogenesis. The mix suggests a theme centered on neuronal development and cell signaling, despite some outliers related to cell cycle and plant signaling. Confidence: Medium","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0007275","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0007205","count":3}]},{"hash":"1347497717352572095","title":"Unknown","description":"The terms span diverse functions: lipid and membrane lipid metabolism (unsaturated fatty acid biosynthesis, ergosterol regulation, and sphingolipid metabolism) alongside nitrogen metabolism and unrelated tissue-specific processes (myelin maintenance, sebaceous gland differentiation) and mitochondrial inheritance. This lack of a consistent, single functional theme makes a coherent label unreliable.","confidence":"","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006636","count":7},{"id":"GO:0006809","count":7},{"id":"GO:0042128","count":7},{"id":"GO:0032286","count":7},{"id":"GO:0032443","count":7}]},{"hash":"1167798346748997990","title":"Steroid and Vitamin Metabolism with Xenobiotic Stress","description":"The top GO terms include retinol and retinal metabolism (vitamin A), testosterone biosynthesis and androgen metabolism (steroids), and fructose biosynthesis, plus regulation of urine volume, indicating broad metabolic roles. They also feature xenobiotic-related processes such as naphthalene catabolic process and cellular response to cadmium ion, suggesting a cluster that centers on metabolic pathways with detox/chemical-stress responses. The combination of vitamin A and steroid metabolism with xenobiotic stress signals justifies this label over a more specific one, though the diversity implies a broad metabolic/detox theme; hence the \"Medium\" confidence.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0042572","count":7},{"id":"GO:0042574","count":6},{"id":"GO:0061370","count":6},{"id":"GO:0008209","count":5}]},{"hash":"136628002021670628","title":"Craniofacial neural development signaling","description":"The GO terms cluster around neural and craniofacial development and signaling, including face development and optic nerve morphogenesis, supported by neurotrophin signaling, Wnt pathway regulation, and FGFR-related apoptotic signaling. A DNA replication term and stress/toxic response entries appear as broader cellular context or incidental associations. Overall, the dominant theme is signaling pathways guiding craniofacial and neural development.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0048011","count":5},{"id":"GO:0090090","count":5},{"id":"GO:0020021","count":5},{"id":"GO:0071469","count":5}]},{"hash":"510476004593005785","title":"RNA and protein methyltransferases","description":"The top GO terms cluster around various methylation and RNA modification processes (tRNA methylation, tRNA wobble uridine modification, rRNA modification, N-terminal peptidyl-alanine trimethylation, and peptidyl-arginine methylation), indicating enzymes that transfer methyl groups to RNA and proteins. A few hormone-response terms appear, but the dominant signal is methylation/modification activity, making this an appropriate, cohesive label.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009751","count":2},{"id":"GO:0009739","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0016049","count":2}]},{"hash":"2226701626851721390","title":"Peroxisomal lipid metabolism and organ development","description":"The top GO terms converge on peroxisome-associated fatty acid and amino acid catabolism (acetyl-CoA and propionyl-CoA pathways, glyoxysome organization) and on development of metabolically active organs (liver, adipose tissue, brain) plus lipid transport. This suggests a cluster of proteins involved in peroxisomal lipid metabolism with links to organ development.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0046356","count":5},{"id":"GO:0010111","count":5},{"id":"GO:0001889","count":5},{"id":"GO:1902860","count":5},{"id":"GO:0006550","count":5}]},{"hash":"1283725366802764023","title":"Gene Expression and Cellular Stress Responses","description":"The cluster\u2019s top GO terms highlight regulation of translation initiation and DNA-templated transcription, together with stress-related processes (ER-stress\u2013induced apoptotic signaling, cellular response to cadmium, defense against Gram-positive bacteria). While a few terms touch development, the dominant theme is gene expression control coupled with cellular stress responses, justifying a label centered on expression regulation and stress response.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0050830","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0001403","count":2}]},{"hash":"545938627772999665","title":"Redox Homeostasis and Detoxification","description":"This cluster is dominated by GO terms tied to oxidation-reduction activity and detoxification (oxidation-reduction process; cellular oxidant detoxification; cell redox homeostasis; protein deglutathionylation), indicating a shared function in maintaining redox balance. While a few terms touch on unrelated areas like methylamine metabolism or neural crest\u2013related heart formation, these appear peripheral and do not override the redox-focused signature. Therefore, \"Redox Homeostasis and Detoxification\" best captures the core theme of this protein group.","confidence":"High","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0098869","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0030416","count":3},{"id":"GO:0003147","count":2}]},{"hash":"47939847019909906","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":8,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":3},{"id":"GO:0097171","count":2},{"id":"GO:0071548","count":2},{"id":"GO:0044210","count":2},{"id":"GO:0006207","count":2}]},{"hash":"1915271937331394189","title":"Chromatin Remodeling and Transcription Regulation","description":"The cluster is dominated by GO terms related to chromatin state and transcription control (chromatin remodeling, heterochromatin formation, and regulation of transcription by RNA polymerase II), suggesting a cohesive role in epigenetic regulation. A few terms pertain to development or stress responses that are less directly tied to chromatin, but the prevailing theme points to epigenetic regulation of gene expression.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0045648","count":2},{"id":"GO:0051572","count":2},{"id":"GO:0045471","count":2}]},{"hash":"81287342927969858","title":"Unknown","description":"The GO terms are highly heterogeneous (oogenesis, endochondral ossification, cartilage development, ethanol metabolism, mitochondrial ribosome assembly, innate immune regulation, spore germination, peptidoglycan turnover), with no single shared pathway or function and no edges linking the proteins. This prevents a coherent, specific cluster label beyond Unknown.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048477","count":2},{"id":"GO:0006067","count":1},{"id":"GO:0061668","count":1},{"id":"GO:0045089","count":1},{"id":"GO:0001958","count":1}]},{"hash":"1026426270767003077","title":"Unknown","description":"The terms span retinoid metabolism, vitamin D biosynthesis, reproductive development, xenobiotic and aromatic compound metabolism, protein quality control, and stress response, with no single cohesive function tying all proteins together. Because of this disparate set, a specific, intuitive label is not apparent.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0071615","count":3},{"id":"GO:0042904","count":3},{"id":"GO:0060065","count":3},{"id":"GO:0008585","count":3}]},{"hash":"1958057104122791472","title":"Bacterial envelope and thiol-metabolite biosynthesis","description":"The GO terms cluster around biosynthetic pathways for envelope components (lipopolysaccharide) and thiol-based metabolites (bacillithiol, mycothiol), with related metabolism activities (glucose) and antibiotic biosynthesis (kanamycin). This suggests a cohesive theme of envelope component synthesis coupled with redox-related metabolite biosynthesis in bacteria, even though several stress- or obsolete-related terms are also present.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":1},{"id":"GO:0009413","count":1},{"id":"GO:0033577","count":1},{"id":"GO:0010555","count":1},{"id":"GO:0071793","count":1}]},{"hash":"1263862110094701102","title":"Mitotic Chromosome Segregation Machinery","description":"The GO terms point to mitosis-focused processes: spindle assembly, sister chromatid cohesion and segregation, and overall cell division, with supporting references to mitotic DNA replication. While a few other terms touch on trafficking or proteostasis, the dominant signal is involvement in mitotic chromosome handling and division.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0030042","count":4},{"id":"GO:0031081","count":4},{"id":"GO:1903461","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0007064","count":4}]},{"hash":"1720020599217831082","title":"Heavy metal transport and detoxification","description":"The proteins are enriched for transport and detoxification of multiple metal ions (cadmium, mercury, copper, zinc, iron) and for copper homeostasis, plus a mercury-response and oxidative-stress related term, suggesting a cohesive function in metal ion handling and detoxification.","confidence":"High","size":7,"edges":12,"triangles":9,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":3},{"id":"GO:0050787","count":3},{"id":"GO:0015680","count":3},{"id":"GO:0015694","count":3},{"id":"GO:0060003","count":3}]},{"hash":"1491690549393917436","title":"Neuronal synapse signaling and spine morphogenesis","description":"The top GO terms cluster around neural synaptic functions: Rho-mediated signaling at synapses, dendritic spine morphogenesis, receptor clustering, and protein localization to the synapse, with neurotrophin/TRK signaling and visual perception suggesting neuronal/retinal synaptic activity. A few terms (symmetric Wnt regulation, symbiont-mediated transformation, alkaline pH response) may be peripheral noise relative to the core neural synapse theme.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007266","count":5},{"id":"GO:0060997","count":5},{"id":"GO:0007601","count":5},{"id":"GO:0043113","count":5},{"id":"GO:0008285","count":5}]},{"hash":"1303018072314455420","title":"Membrane Solute Transport","description":"The proteins cluster around diverse membrane transport activities: sugar import (glucose, fructose) and sugar-related responses, sodium-dependent cation transport, nitrite/nitrate/urate transport, and even neurotransmitter loading into synaptic vesicles, all pointing to moving various solutes across membranes and contributing to osmotic balance.","confidence":"High","size":7,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":6},{"id":"GO:0070715","count":6},{"id":"GO:0044381","count":6},{"id":"GO:0071332","count":6},{"id":"GO:0015707","count":6}]},{"hash":"2253205154070744777","title":"Female reproductive development and retinoic acid/vitamin D metabolism","description":"The top GO terms include uterine and female genitalia development, plus retinoic acid biosynthesis/catabolic processes and calcitriol (vitamin D) biosynthesis. This suggests a cluster tied to female reproductive tissue development with shared metabolism of retinoic acid and vitamin D, even though some xenobiotic/metabolic terms are also present.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071615","count":2},{"id":"GO:0042904","count":2},{"id":"GO:0060065","count":2},{"id":"GO:0008585","count":2},{"id":"GO:0034653","count":2}]},{"hash":"1312337048467567398","title":"Stress and Immune Signaling","description":"The terms include DNA-templated transcription, ABA signaling, development, dopamine response, dsRNA response, LPS response, defense against Gram-positive bacteria, innate immune response, and a pain-related behavioral response. This mix points to regulation of transcription in response to stress and engagement of immune/defense pathways, spanning both plant and animal contexts. Since there isn\u2019t a single tightly shared function across all terms, the label reflects a broad cluster of stress- and immune-signaling processes.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0009738","count":4},{"id":"GO:0007275","count":4},{"id":"GO:1903351","count":3},{"id":"GO:0043330","count":3}]},{"hash":"2294087097069886286","title":"Nutrient and Ion Transport with Stress Response","description":"GO terms indicate diverse membrane transport activities (sodium-dependent organic cation transport, nitrite/urate transport, potassium transport, fructose and glucose import) alongside stress responses (osmotic stress response, defense-related callose regulation). The common thread appears to be transport of nutrients and ions across membranes coupled to stress signaling, rather than a single cohesive function. An outlier term about neurotransmitter loading into synaptic vesicles is present but does not override the overall transport/meta-metabolic theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000071","count":1},{"id":"GO:0006970","count":1},{"id":"GO:0070715","count":1},{"id":"GO:0044381","count":1},{"id":"GO:0071332","count":1}]},{"hash":"1170314502388268518","title":"Nucleobase Transport Across Membrane","description":"The cluster is dominated by GO terms for import/transport of nucleobases (adenine, guanine, uracil, xanthine, hypoxanthine, urate) across the plasma membrane, indicating a shared function as nucleobase transporters. Some unrelated development terms appear but do not define the core theme.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098702","count":1},{"id":"GO:0015747","count":1},{"id":"GO:0098710","count":1},{"id":"GO:0070904","count":1},{"id":"GO:0098721","count":1}]},{"hash":"1507723316571085823","title":"Developmental signaling and morphogenesis","description":"This cluster centers on embryonic development and tissue patterning, with terms like mesoderm formation, face development, optic nerve morphogenesis, and neural tube patterning via Wnt and Hedgehog (Smoothened) signaling. The inclusion of DNA replication suggests proliferative phases common in development, while parathyroid hormone response adds endocrine signaling context. Overall, the common theme is developmental signaling and morphogenesis.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071374","count":4},{"id":"GO:1901621","count":4},{"id":"GO:0001707","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0048011","count":3}]},{"hash":"194908763167367010","title":"Chromatin organization and heterochromatin formation","description":"The top GO terms are dominated by heterochromatin formation (pericentric and subtelomeric) and broader chromatin organization, with supporting hints from histone modification processes. A couple of terms touch on RNA decay and immune cell functions, but the strongest, recurring theme across the cluster is chromatin structure and heterochromatin formation. Confidence: Medium","confidence":"","size":7,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":2},{"id":"GO:0070481","count":1},{"id":"GO:0033128","count":1},{"id":"GO:0034184","count":1},{"id":"GO:0031508","count":1}]},{"hash":"1176068847459291339","title":"Plant floral/seed development and cuticle biosynthesis","description":"This cluster centers on plant developmental processes (bract/seed/flower meristem growth) and transcriptional activity, together with cuticle-related pathways (cutin and wax biosynthesis). The presence of hormone signaling terms (ethylene, ABA, auxin) suggests coordinated development regulated by hormones. Overall, the terms point to reproductive development linked with cuticle formation in plants.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010200","count":2},{"id":"GO:0010432","count":2},{"id":"GO:0048316","count":2},{"id":"GO:0060774","count":2},{"id":"GO:0010451","count":2}]},{"hash":"2263609800579272458","title":"Flowering-time transcriptional regulation","description":"The top GO terms indicate strong enrichment for transcriptional regulation, especially regulation of DNA-templated transcription and transcription initiation at RNA polymerase II promoter, paired with plant-specific terms like regulation of flower development and photoperiodism. This points to a cluster of transcriptional regulators that coordinate flowering time in response to day length, rather than a general metabolic or structural function. Some unrelated terms (viral process, rRNA maturation) appear, but the dominant theme is plant transcription control linked to flowering.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0016032","count":1},{"id":"GO:0006367","count":1},{"id":"GO:0001113","count":1}]},{"hash":"1494126522040706433","title":"TGF-beta/BMP Signaling Regulation","description":"The top GO terms cluster around modulation of TGF-beta/BMP signaling, including negative regulation of BMP signaling and negative regulation of TGF-beta receptor signaling, plus cellular responses to TGF-beta stimulus. The recurring hint of peptidyl-threonine dephosphorylation suggests phosphatases modulating SMAD activity, reinforcing a theme of signaling regulation. A couple of terms (meristem identity, vacuole fusion) seem peripheral or context-specific but do not outweigh the central link to TGF-beta/BMP pathway control.","confidence":"High","size":7,"edges":11,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030514","count":3},{"id":"GO:0042347","count":3},{"id":"GO:0061191","count":3},{"id":"GO:0000173","count":3},{"id":"GO:0046827","count":3}]},{"hash":"698152029637490509","title":"ER stress\u2013related proteostasis and QC","description":"This cluster centers on protein quality control and proteostasis: ER-stress\u2013driven translation initiation, misfolded protein transport, ubiquitin-proteasome QC in the nucleus, and related targeting/transport processes, indicating maintenance of protein folding and turnover.","confidence":"Medium","size":7,"edges":9,"triangles":3,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0036494","count":3},{"id":"GO:0070843","count":3},{"id":"GO:0006626","count":3},{"id":"GO:0071630","count":3}]},{"hash":"770535079503926109","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0052889","count":2},{"id":"GO:2000344","count":2},{"id":"GO:0016042","count":2},{"id":"GO:0006402","count":1},{"id":"GO:0010738","count":1}]},{"hash":"36698178863564044","title":"Cell Cycle Regulation and Mitosis","description":"Cluster shows strong enrichment for cell cycle and mitosis-related terms (cell cycle, cell division, positive regulation of G2/M, centriole elongation), indicating a coherent theme of cell cycle control and mitotic machinery. Spliceosome-related terms are present but do not override the dominant cell-cycle signal.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0000387","count":1},{"id":"GO:2000825","count":1},{"id":"GO:0000398","count":1},{"id":"GO:1902188","count":1}]},{"hash":"1434202271698029006","title":"Chromatin modification and nucleosome assembly","description":"This cluster\u2019s top GO terms are dominated by chromatin-related processes: nucleosome assembly and histone modification/methylation regulation (including H3-K4 and H3-K27 methylation categories). Although several terms are marked obsolete and a couple outliers touch on estradiol secretion or T cell tolerance, the strongest, recurrent signal is chromatin remodeling and nucleosome organization, suggesting these proteins share chromatin-associated functions rather than a single cohesive signaling pathway.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000791","count":1},{"id":"GO:0044648","count":1},{"id":"GO:0006334","count":1},{"id":"GO:0002458","count":1},{"id":"GO:0061087","count":1}]},{"hash":"280862886389657810","title":"Actin Cytoskeleton Remodeling during Cell Division","description":"This cluster is driven by actin-related terms: negative regulation of Arp2/3 complex-mediated actin nucleation and actin filament depolymerization, plus cell division. These collectively point to cytoskeletal remodeling essential for mitosis/cytokinesis. Other terms (peroxisome targeting, development of forebrain/retina, nuclear pore localization, SREBP signaling) are more diverse and may reflect broader roles or annotation noise, but the dominant theme is actin dynamics linked to cell division.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0034316","count":2},{"id":"GO:2001162","count":1},{"id":"GO:0006625","count":1},{"id":"GO:0030900","count":1}]},{"hash":"2089222236838461581","title":"Regulation of protein quality control and intracellular trafficking","description":"The proteins show enrichment for several negative regulatory GO terms related to trafficking and protein handling, including negative regulation of clathrin-dependent endocytosis, GPCR internalization, and autophagosome maturation, as well as proteolysis, deglycosylation, and ERAD-related processes. This points to a common theme of modulating protein turnover and intracellular trafficking quality control, even though some terms (like xenobiotic response) are broader.","confidence":"Medium","size":7,"edges":10,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0034140","count":2},{"id":"GO:1900186","count":2},{"id":"GO:1901340","count":2}]},{"hash":"2050538790456147010","title":"Unknown","description":"This cluster's top terms are two obsolete GO annotations related to conjugation and mitochondrial protein targeting, each with only a single instance and no observed interactions between proteins. Because the terms are outdated and there is no cohesive, current functional signal linking the proteins, there isn\u2019t a reliable theme to assign a descriptive label.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000746","count":1},{"id":"GO:0006627","count":1}]},{"hash":"1540745992516171383","title":"Unknown","description":"The listed GO terms cover diverse biological processes across different kingdoms (mammary gland proliferation, plant floral abscission, copper response, transcription regulation, neuronal spine development, ion transport, endosome trafficking, podosome assembly, cytokinesis, and immune cell apoptosis). This lack of a common theme suggests there isn't a cohesive function tying these proteins together, so the cluster can't be confidently named beyond Unknown.","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033601","count":2},{"id":"GO:0071280","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0010227","count":1},{"id":"GO:0060999","count":1}]},{"hash":"1384998859152829713","title":"Unknown","description":"There is no clear common function among the proteins: the only top term is an obsolete GO term (RNA phosphodiester bond hydrolysis, endonucleolytic) with frequency 1, and there are no edges or connections to suggest a shared pathway or role.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":1}]},{"hash":"1580594655381311480","title":"Oocyte maturation and meiotic spindle assembly","description":"The cluster is dominated by GO terms related to oocyte maturation, female meiosis I spindle assembly, and microtubule dynamics, plus proteasomal protein turnover (SCF-dependent ubiquitin-proteasome pathway). A couple of development terms are present but secondary. This suggests a cohesive theme around meiotic progression in oocytes and associated cytoskeletal remodeling.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":7},{"id":"GO:0006516","count":7},{"id":"GO:0008285","count":7},{"id":"GO:0007057","count":7},{"id":"GO:0051436","count":7}]},{"hash":"2022400762295746379","title":"Wnt signaling in development","description":"This cluster centers on canonical Wnt signaling and its regulation, with terms for both positive and negative regulation of the pathway, and several development-related processes (hair follicle placode formation, fungiform papilla formation, renal outer medulla development). The recurring emphasis on Wnt signaling and its role in organogenesis suggests a cohesive theme around Wnt-mediated developmental processes, despite a few outlier terms. ","confidence":"Medium","size":7,"edges":16,"triangles":16,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071681","count":4},{"id":"GO:0061380","count":4},{"id":"GO:0000011","count":4},{"id":"GO:0044336","count":4},{"id":"GO:0090090","count":4}]},{"hash":"2267826639639382288","title":"Retinoic acid and lipid metabolism in development","description":"The top GO terms point to retinoic acid biosynthesis and catabolic processes, triglyceride and other lipid metabolic activities, and reproductive development terms (uterus/female gonad development), suggesting a theme centered on lipid-based metabolic signaling, particularly retinoic acid (and related vitamin D pathways) in development. Some terms (like ozone response) may be less directly related noise. ","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":2},{"id":"GO:0006641","count":2},{"id":"GO:0071615","count":1},{"id":"GO:0042904","count":1},{"id":"GO:0060065","count":1}]},{"hash":"676413663170586535","title":"Amyloid metabolism and neural signaling","description":"This cluster centers on amyloid-beta metabolic processes and APP-related regulatory steps, with accompanying neural signaling terms (GPCR-related adenylate cyclase inhibition and cGMP response) and membrane lipid metabolism (sphingolipids). The presence of drinking behavior and neuroimmune/antigen presentation hints at brain-related functions, while protein processing/degradation terms support neuronal protein turnover. Overall, the dominant theme ties amyloid metabolism to neural signaling.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0050435","count":2},{"id":"GO:0042756","count":2},{"id":"GO:0019886","count":2},{"id":"GO:0007193","count":2},{"id":"GO:0001823","count":2}]},{"hash":"1112068131241404145","title":"Plant root and phloem development","description":"The top GO terms include root development and phloem development, with related terms like hair cell differentiation, pointing to a plant-specific developmental program in vascular tissues. Other terms (DNA replication, transcription initiation, UV protection, hypoxia response) are general cellular processes that may be co-expressed but do not define the cluster\u2019s main theme. Thus, the leading theme is plant tissue development, especially roots and phloem, with some housekeeping processes accompanying it.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0048364","count":2},{"id":"GO:0010088","count":2},{"id":"GO:0006265","count":1},{"id":"GO:0006306","count":1},{"id":"GO:0006269","count":1}]},{"hash":"1256900777440645994","title":"Ubiquitin-mediated protein degradation","description":"This cluster centers on ubiquitination processes (autoubiquitination, ubiquitin-dependent ERAD, K63-linked ubiquitination) and related protein turnover, with some stress/hormone signaling terms. The dominant pattern ties proteins to ubiquitin-dependent proteolysis and quality control, suggesting a coherent group of ubiquitination machinery and degradation pathways.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0070534","count":3},{"id":"GO:0008626","count":2},{"id":"GO:0010200","count":2}]},{"hash":"609427384461551269","title":"Neural and Cardiac Signaling and Transcription","description":"The top GO terms span transcription and nuclear export (gene regulation) alongside neural and cardiac signaling features, including sensory perception, responses to caffeine and clozapine, and cardiac electrical activity (Purkinje depolarization, ventricular repolarization). This suggests a cluster of proteins involved in gene regulation and diverse signaling pathways that integrate neural and cardiac function, rather than a single, cohesive pathway. ","confidence":"Medium","size":7,"edges":8,"triangles":3,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0007275","count":7},{"id":"GO:0019233","count":7},{"id":"GO:0071313","count":5}]},{"hash":"2269771097541081388","title":"Developmental Differentiation and Morphogenesis","description":"Top GO terms center on multicellular development (gastrulation, organ differentiation) and tissue formation processes (cardiac muscle differentiation, endochondral ossification), with supporting signs of cell proliferation and cytoskeletal remodeling (actin depolymerization) and transcriptional regulation. Although some terms are older/obsolete, the cluster as a whole points to developmental programs driving tissue specification and morphogenesis.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0030042","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0016575","count":2}]},{"hash":"1189084430902083518","title":"Diverse sugar catabolic pathways","description":"Proteins in this cluster are linked to the metabolism and breakdown of a variety of carbohydrates, including N-acetylglucosamine, tagatose-6-phosphate/lactose pathways, ribose, fructose, sulfoquinovose, and related carbohydrate phosphorylation and salvage steps. The common theme is utilization and processing of multiple sugars rather than a single substrate, justifying a label of diverse sugar catabolic pathways.","confidence":"High","size":7,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006044","count":2},{"id":"GO:0009750","count":1},{"id":"GO:1902777","count":1},{"id":"GO:2001059","count":1},{"id":"GO:0097171","count":1}]},{"hash":"432113936378688160","title":"Wnt-Dependent Development","description":"Most of the top GO terms point to Wnt signaling and its regulation (canonical Wnt pathway, both activation and inhibition) as well as diverse developmental processes (taste papilla/fungiform papilla formation, hair follicle placode formation, superior colliculus and renal medulla development). This suggests the cluster is enriched for genes participating in Wnt-mediated developmental programs across tissues. While a few terms (vacuole inheritance, pseudopodium assembly, indole-3-methanol response) are less directly linked to Wnt signaling, they may reflect broader cellular roles or annotation noise. Therefore, the cluster is best characterized as Wnt-dependent developmental processes.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0071681","count":7},{"id":"GO:0061380","count":7},{"id":"GO:0000011","count":7},{"id":"GO:0044336","count":7},{"id":"GO:0090090","count":7}]},{"hash":"879579559699480440","title":"Plant cell wall polysaccharide biosynthesis","description":"The cluster shows strong enrichment for biosynthetic processes that build plant cell wall polysaccharides (xyloglucan, xylogalacturonan, glucuronoxylan, arabinan, plant-type secondary cell wall biogenesis), with related sugar biosynthesis terms like fucose. Collectively these indicate a function in assembling plant cell wall polymers, despite a few non-plant terms appearing as annotations.","confidence":"High","size":7,"edges":18,"triangles":23,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035118","count":1},{"id":"GO:0010398","count":1},{"id":"GO:0009834","count":1},{"id":"GO:0042353","count":1},{"id":"GO:0009969","count":1}]},{"hash":"1261711071429435650","title":"Autophagy and Vacuolar Targeting","description":"The proteins are strongly associated with autophagy-related processes (nucleophagy, piecemeal microautophagy of the nucleus, Cvt pathway, mitophagy, and targeting to the vacuole), plus components like C-terminal lipidation linked to autophagy machinery and stress responses that can intersect with apoptosis and cytoskeletal dynamics. This combination points to a cohesive theme of autophagy and vacuolar degradation pathways.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0044805","count":5},{"id":"GO:0034727","count":5},{"id":"GO:0032258","count":5},{"id":"GO:0000422","count":5},{"id":"GO:0006501","count":5}]},{"hash":"1523109656043849150","title":"Chromatin assembly and histone modification","description":"The dominant GO terms point to chromatin biology, including nucleosome assembly and histone methylation (H3-K4/K27), indicating epigenetic regulation of gene expression. While a few terms relate to broader cell-cycle or immune processes, the core theme across the cluster is chromatin remodeling and histone modification.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":4},{"id":"GO:2000791","count":3},{"id":"GO:0044648","count":3},{"id":"GO:0002458","count":3},{"id":"GO:0061087","count":3}]},{"hash":"2013103658628944290","title":"Pollen-pistil fertilization signaling in plants","description":"The cluster is enriched for GO terms related to pollen-pistil interaction and double fertilization, with calcium-mediated signaling and sperm-related processes linked to fertilization, suggesting roles in pollen tube signaling and fertilization events in plants.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009567","count":2},{"id":"GO:2000008","count":2},{"id":"GO:0080155","count":2},{"id":"GO:0048240","count":2},{"id":"GO:0019722","count":2}]},{"hash":"555389841344116735","title":"Cell Migration and Cytoskeleton Regulation","description":"These proteins are linked by GO terms governing cell movement and cytoskeleton dynamics (fibroblast migration, pseudopodium assembly), signaling (Ras pathway), and tissue remodeling processes (collagen biosynthesis, exosomal secretion), as well as differentiation and organelle organization. Together, they suggest a theme of coordinated regulation of cell shape, motility, and associated signaling.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032966","count":2},{"id":"GO:0046579","count":2},{"id":"GO:0010821","count":2},{"id":"GO:0010762","count":2},{"id":"GO:0031274","count":2}]},{"hash":"1851602648407371813","title":"Epithelial Polarity and Tight Junction Assembly","description":"The top GO terms strongly point to establishing and maintaining epithelial cell apical/basal polarity and bicellular tight junction assembly, indicating a core role in epithelial polarity and junction formation. Nearby terms touch on related polarity regulation, cytoskeletal dynamics (pseudopodium assembly, migration), and signaling, which fits with polarized cell architecture coordinating movement and signaling. Overall, the cluster seems centered on epithelial polarity and junctional organization, with some ancillary regulatory processes.","confidence":"Medium","size":6,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045197","count":2},{"id":"GO:0070830","count":2},{"id":"GO:0035641","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0032966","count":1}]},{"hash":"1562970964065306379","title":"mRNA processing: splicing, export, and stability regulation","description":"This cluster centers on post-transcriptional RNA processing and regulation, with strong signals for spliceosome-mediated splicing (cis and alternative), mRNA export from the nucleus, polyadenylation, and regulation of mRNA stability (including stress responses), plus elements related to translation reinitiation. The cohesive theme is mRNA maturation and control of its fate from processing to translation.","confidence":"High","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":5},{"id":"GO:0045292","count":4},{"id":"GO:0010610","count":4},{"id":"GO:1900363","count":3},{"id":"GO:0002188","count":3}]},{"hash":"2161608899097006433","title":"Nucleotide Biosynthesis and Salvage","description":"The cluster\u2019s GO terms are dominated by nucleotide metabolism: ADP and CDP biosynthesis, AMP salvage, and various phosphate transfer and nucleotide interconversion processes (purine ribonucleotide interconversion, nucleoside monophosphate phosphorylation). These indicate a coherent theme around synthesis and salvage of nucleotides. While there are some unrelated terms like liver/brain development and mitotic spindle assembly appearing, they are less represented and likely reflect broader or context-specific annotations. Overall, the strongest common function ties to nucleotide metabolism.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001889","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0015951","count":1},{"id":"GO:0006172","count":1}]},{"hash":"263968759720788532","title":"Unknown","description":"The top GO terms are diverse and largely unrelated (male gonad development, NF-kappaB signaling, vitamin biosynthesis, various dephosphorylation reactions, toxin response, and a P450 pathway). With no edges or coherent shared function among the proteins, there isn\u2019t a clear theme to name this cluster, so it\u2019s best labeled Unknown to reflect the lack of a unifying function.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":2},{"id":"GO:0007252","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0016311","count":2}]},{"hash":"2252155384961572841","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"This cluster has GO terms centered on oocyte maturation (GO:0001556) and spindle assembly in female meiosis I (GO:0007057), plus microtubule polymerization (GO:0046785) and SCF-dependent ubiquitin-proteasomal degradation (GO:0031146). Together these suggest a functional module focused on meiosis initiation and meiotic spindle regulation in oocytes, with related cell-cycle and degradation processes. Some neural development terms appear but are likely secondary to the dominant meiosis-related signals.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":5},{"id":"GO:0006516","count":5},{"id":"GO:0008285","count":5},{"id":"GO:0007057","count":5},{"id":"GO:0051436","count":5}]},{"hash":"156632190560296420","title":"Golgi-to-synapse vesicle trafficking and receptor localization","description":"This cluster centers on proteins involved in Golgi-associated vesicle transport, including Golgi-to-vacuole pathways, general intracellular transport, and exocytic insertion of neurotransmitter receptors at the synapse, as well as receptor localization to the synapse and related trafficking dynamics. While a couple terms touch on other processes, the dominant signal is Golgi-mediated vesicle trafficking linked to synaptic receptor positioning.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":3},{"id":"GO:0006886","count":2},{"id":"GO:1902685","count":2},{"id":"GO:0010811","count":2},{"id":"GO:1903575","count":2}]},{"hash":"1023347068276454007","title":"Ubiquitin-proteasome\u2013mediated proteolysis (cell cycle)","description":"The strongest signals are SCF-dependent proteasomal ubiquitin-dependent protein catabolic process and APC/C-dependent catabolic process, indicating degradation of cell-cycle regulators by the ubiquitin-proteasome system. Other terms reflect broader stress-response and detoxification processes (glutathione metabolism, redox homeostasis, UV response, antibiotic response) but are less central to the cluster\u2019s core function. Overall, the cluster seems focused on regulated protein degradation linked to cell-cycle control, with some ancillary stress-context signals.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0031145","count":2},{"id":"GO:1901170","count":1},{"id":"GO:0006749","count":1},{"id":"GO:0009411","count":1}]},{"hash":"1628523513547018068","title":"Ubiquitin-regulated antiviral NF-\u03baB immunity","description":"GO terms emphasize antiviral defense, innate immunity, and canonical NF-\u03baB signaling, coupled with ubiquitin-dependent protein turnover (K48-linked ubiquitination). This supports a cluster whose function centers on ubiquitin-modulated NF-\u03baB\u2013driven antiviral immune responses, with a few peripheral terms related to broader immune processes.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090073","count":5},{"id":"GO:0051607","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0043123","count":4},{"id":"GO:0042787","count":4}]},{"hash":"2052999330457988538","title":"Microtubule dynamics and intracellular transport","description":"The cluster is dominated by GO terms related to microtubule regulation and dynamics (spindle separation, centrosome functions, kinetochore attachment, plus-end depolymerization) and motor-driven transport (anterograde dendritic transport, chloroplast movement). These collectively point to cytoskeletal (microtubule-based) processes coordinating division, movement, and intracellular trafficking, across diverse systems.","confidence":"High","size":6,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":5},{"id":"GO:0007100","count":4},{"id":"GO:0009904","count":3},{"id":"GO:0032886","count":3},{"id":"GO:0098971","count":3}]},{"hash":"2090644634310470626","title":"Developmental signaling and stress responses","description":"These proteins collectively touch on developmental processes (placenta development, thymus development, spermatogenesis) and various signaling pathways (neurotrophin TRK signaling, negative regulation of canonical Wnt signaling), alongside cellular responses to cadmium ion and hydrogen peroxide. This pattern suggests a cluster of genes involved in developmental signaling that is modulated by oxidative/metal stress, rather than a single tissue-specific function.","confidence":"Medium","size":6,"edges":8,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0000187","count":3},{"id":"GO:0001890","count":3},{"id":"GO:0048538","count":3},{"id":"GO:0046827","count":3}]},{"hash":"1181102230960469674","title":"Photosynthesis light harvesting and photoprotection","description":"GO terms emphasize photosynthesis, light harvesting in photosystem I, nonphotochemical quenching, and responses to light intensity, pointing to chloroplast-associated energy capture and photoprotection mechanisms; occasional mitochondrial electron transport terms appear incidental rather than defining the cluster.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0022904","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0006122","count":1},{"id":"GO:0009768","count":1}]},{"hash":"1326326003190171351","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":1},{"id":"GO:0006461","count":1},{"id":"GO:1990180","count":1},{"id":"GO:0042245","count":1},{"id":"GO:0001680","count":1}]},{"hash":"1220399201239511485","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":2},{"id":"GO:0009089","count":2},{"id":"GO:0042823","count":2},{"id":"GO:0006006","count":2},{"id":"GO:0008615","count":2}]},{"hash":"2007080974709041635","title":"Stress-Responsive Translation and Proteostasis","description":"The cluster centers on translation, including mitochondrial translational initiation, and includes functions related to protein stability and ubiquitin-mediated degradation, along with cell cycle regulation and p53-mediated signaling in response to stress (e.g., actinomycin D). This points to a cohesive module where protein synthesis, degradation control, and stress-induced cell cycle responses are coordinated.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0070124","count":1},{"id":"GO:1904667","count":1},{"id":"GO:0032986","count":1},{"id":"GO:0071157","count":1}]},{"hash":"345163877128484765","title":"Diverse Metabolite Catabolism and Detoxification","description":"The top GO terms point to catabolic processing of a variety of metabolites (uracil, chlorophyll, menaquinone, biotin, monoacylglycerol) and detoxification, plus general oxidation-reduction processes and responses to toxic substances. This suggests a shared theme of metabolizing diverse small molecules and handling toxins, rather than a single specific pathway. Confidence: Medium","confidence":"","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006212","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0015996","count":2},{"id":"GO:0009234","count":2}]},{"hash":"1812796262972152481","title":"Unknown","description":"There are no GO terms shown to bind the proteins into a common function, so a reliable label cannot be inferred. With only network metrics and no functional signals, the cluster remains unidentified.","confidence":"","size":6,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[]},{"hash":"402078452435347093","title":"Bacterial energy and nucleotide metabolism","description":"The top GO terms cluster around metabolic activities: glycolytic process, nicotinamide/nicotinate metabolism and salvage, nucleotide salvage (nicotinate nucleotide), uracil catabolism, and nitrogen utilization, indicating a cohesive theme of energy production and nucleotide/vitamin metabolism in bacteria. Some terms like phenazine biosynthesis appear as minor outliers, but the dominant pattern supports a metabolism-focused cluster.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0002047","count":2},{"id":"GO:1904524","count":2},{"id":"GO:0006602","count":2},{"id":"GO:0019740","count":2}]},{"hash":"1855233220660992791","title":"RNA processing and translational control","description":"The top GO terms cluster around RNA metabolism and translation, including mRNA splicing regulation via spliceosome, rRNA maturation, and regulatory polyadenylation, plus translation initiation/reinitiation and viral-like translation termination-reinitiation. This points to a coherent RNA processing/translation-control module. Some terms (cocaine response, cranial skeleton morphogenesis) appear unrelated and may be incidental. ","confidence":"Medium","size":6,"edges":12,"triangles":10,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0042220","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0006260","count":2}]},{"hash":"650394338838667287","title":"Nucleotide metabolism and RNA modification","description":"The top GO terms cluster around nucleotide biosynthesis, salvage, and interconversion (AMP salvage, ADP biosynthetic, CDP biosynthetic, purine ribonucleotide interconversion, ITP metabolism, nucleoside monophosphate phosphorylation), with an additional link to RNA modification (tRNA pseudouridine synthesis). The liver/brain development terms may reflect broader or pleiotropic roles of these proteins or annotation noise, but the dominant theme is nucleotide metabolism and RNA processing.","confidence":"Medium","size":6,"edges":11,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0044209","count":3},{"id":"GO:0001889","count":2},{"id":"GO:0015951","count":2},{"id":"GO:0006172","count":2},{"id":"GO:0046041","count":2}]},{"hash":"567074289332882137","title":"Organelle RNA Processing and Editing","description":"The top GO terms cluster around RNA maturation in organelles: mitochondrial and chloroplast mRNA processing/modification, including C to U editing, polysistronic processing in chloroplasts, and regulation of organellar RNA catabolic processes. This consistent theme across mitochondria and chloroplasts suggests a cohesive function in organelle RNA processing/editing, hence the label.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031426","count":3},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0000961","count":2}]},{"hash":"1664807211184718438","title":"RNA processing and translation","description":"The cluster is dominated by RNA metabolism and protein synthesis terms, with strong signals for translation (including cytoplasmic translation) and mRNA processing, plus ribosomal RNA maturation. A few terms (e.g., dexamethasone response, DNA repair, oenocyte development) are less central, but the core theme centers on RNA processing and translation machinery.","confidence":"High","size":6,"edges":9,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006378","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0002181","count":1},{"id":"GO:0000462","count":1}]},{"hash":"494573336173953407","title":"Photosynthesis-Linked Central Metabolism","description":"The cluster shows strong representation of GO terms related to photosynthesis, the TCA cycle, NADPH regeneration, and oxidative stress response, pointing to proteins involved in energy capture and redox homeostasis in photosynthetic organisms. Other terms appear more tangential (transcription, development, lipid regulation), suggesting some annotation noise, but the dominant signal supports a metabolism/energy-production theme rooted in photosynthetic contexts.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0060696","count":1},{"id":"GO:0006099","count":1}]},{"hash":"1145077573818240614","title":"Cell Stress Signaling and Gene Regulation","description":"The top GO terms span ER-stress\u2013triggered intrinsic apoptotic signaling, Hippo signaling, transcription and translation regulation, antiviral response, CD40 signaling, and post-translational modification (phosphorylation and deubiquitination). This mix suggests a broad regulatory theme where cells sense stress and coordinate gene expression and signaling, rather than a single cohesive pathway; plus the absence of edges indicates the proteins may act in diverse contexts, supporting a high-level label rather than a specific pathway.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070059","count":2},{"id":"GO:0035329","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006417","count":1},{"id":"GO:0009615","count":1}]},{"hash":"1178174065384629038","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071548","count":6},{"id":"GO:0044210","count":6},{"id":"GO:0006207","count":6},{"id":"GO:0006526","count":6},{"id":"GO:0007494","count":6}]},{"hash":"1776719550689984379","title":"Neuronal development and synaptic signaling","description":"The prominent GO terms point to nervous system development, dopamine responsiveness, excitatory synaptic activity, and calcium-dependent neurotransmitter exocytosis, indicating a coherent theme of neuronal signaling and synaptic function. A few unrelated terms (immune response, starvation) may reflect broader annotations in the cluster but do not define the core function.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007399","count":4},{"id":"GO:1903351","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0000186","count":4}]},{"hash":"428286380224700454","title":"Unknown","description":"The top GO terms cover a wide range of unrelated processes\u2014from nuclear import and microtubule nucleation to phosphorylation, proteolysis, stress responses, and tissue-specific development\u2014without a clear, single shared function. This suggests the cluster may reflect diverse, possibly pleiotropic roles rather than a cohesive, well-defined module. ","confidence":"","size":6,"edges":8,"triangles":5,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006607","count":5},{"id":"GO:0007020","count":4},{"id":"GO:0006468","count":4},{"id":"GO:0097264","count":4},{"id":"GO:0071313","count":4}]},{"hash":"265092420581730584","title":"Cellular stress response and energy metabolism","description":"The cluster centers on GO terms for oxidative stress response, heat acclimation, and energy production (oxidative phosphorylation and ATP biosynthesis), pointing to a theme of cellular stress adaptation linked with metabolic regulation. It also includes growth-related processes (centriole elongation, cell division) and transcription initiation, suggesting a broader overlap between stress response and basic cellular growth and transcriptional control. A few terms (e.g., viral genome replication) are less cohesive with the main theme, but the dominant signals point to stress response and energy/growth coupling.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034599","count":3},{"id":"GO:0055114","count":2},{"id":"GO:1903724","count":2},{"id":"GO:0070370","count":2},{"id":"GO:0019079","count":2}]},{"hash":"977105757582342443","title":"RNA processing and splicing machinery","description":"The cluster is centered on RNA maturation and turnover, with strong signals for tRNA processing, spliceosome assembly and mRNA splicing, and maturation of SSU-rRNA, plus deadenylation-dependent decapping of nuclear-transcribed mRNA. Additional terms like P-body assembly and histone mRNA metabolism extend to RNA turnover and RNA metabolism, supporting a cohesive theme of RNA processing and RNA-guided regulation. Overall, the cluster represents RNA processing and metabolism.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":6},{"id":"GO:0033962","count":5},{"id":"GO:0008334","count":5},{"id":"GO:1990141","count":5},{"id":"GO:0000387","count":5}]},{"hash":"588950331447494416","title":"mRNA processing and translation initiation","description":"The top GO terms cluster around mRNA maturation steps (splicing via spliceosome, mRNA export, polyadenylation) and translation initiation (translation reinitiation, preinitiation complex formation), indicating proteins coordinating mRNA processing with initiation of translation (including viral reinitiation contexts). Some terms are obsolete, but the core signal is coherent around these functions.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1900363","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0075525","count":5},{"id":"GO:0006378","count":5},{"id":"GO:0006406","count":5}]},{"hash":"883367889992101622","title":"mRNA processing and translation initiation","description":"Top GO terms indicate mRNA maturation (splicing, polyadenylation, export) together with translation initiation and reinitiation (preinitiation complex formation, reinitiation), suggesting a cluster of proteins coordinating mRNA processing and initiation of translation, including potential viral-like reinitiation mechanisms.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1900363","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0006406","count":3}]},{"hash":"1490853946070235317","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms tied to ribosome production and function\u2014ribosome biogenesis, small subunit assembly/biogenesis, maturation of SSU rRNA, and translation\u2014pointing to a group involved in assembling and using ribosomes for protein synthesis. Additional terms like DNA-templated transcription and innate immune response appear, but the ribosome-related terms are the strongest common thread, making ribosome biogenesis and translation the most representative label.","confidence":"High","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0045087","count":2}]},{"hash":"1859742824260828127","title":"Post-transcriptional RNA processing and regulation","description":"The terms emphasize spliceosome-driven splicing (including alternative splicing) and mRNA export, plus ncRNA-mediated gene silencing and translation reinitiation, indicating a cluster focused on RNA maturation and post-transcriptional control.","confidence":"High","size":6,"edges":12,"triangles":10,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":5},{"id":"GO:0048026","count":5},{"id":"GO:1900363","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0075525","count":3}]},{"hash":"143965863888920665","title":"RNA and protein methylation","description":"The top GO terms are dominated by methylation-related processes, including tRNA wobble uridine modification, rRNA modification, and various N-terminal methylations/dimethylations/trimethylations of peptides, with an additional note for related histone methylation. While a couple terms touch on unrelated biosynthetic pathways, the strongest shared function across the cluster is RNA and protein methylation activity, suggesting a group of methyltransferases or modification-related proteins. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002098","count":3},{"id":"GO:0036068","count":3},{"id":"GO:0000154","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0009234","count":3}]},{"hash":"1677660195096801731","title":"Organelle RNA editing and processing in plants","description":"The terms cluster around RNA modification and processing in plant organelles (mitochondria and chloroplasts), including cytidine-to-uridine editing, chloroplast-nucleus signaling, and regulation of organellar RNA catabolic processes. This points to RNA maturation and regulation within plant organelles as the common theme.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":4},{"id":"GO:0009451","count":4},{"id":"GO:0016554","count":4},{"id":"GO:0080156","count":4},{"id":"GO:0000961","count":4}]},{"hash":"1862218580624987472","title":"Auxin signaling and organ growth regulation","description":"The top terms are dominated by auxin-related processes (auxin-activated signaling pathway, response to auxin, auxin polar transport) and regulation of organ growth, pointing to a common theme of auxin-mediated growth control. A handful of RNA modification terms appear but seem ancillary to the main signal, which remains auxin signaling as the cluster\u2019s core function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046620","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0009926","count":1},{"id":"GO:0009733","count":1},{"id":"GO:0090305","count":1}]},{"hash":"1096111848234128975","title":"Pectin metabolism and pollen tube growth","description":"The strongest signals are plant-specific: pectin biosynthesis and catabolism, mucus/pollen tube\u2013related cell wall remodeling, and pollen tube growth, suggesting a cluster tied to plant cell wall dynamics during reproductive development. Some unrelated terms (base-excision repair, nucleobase transport) appear but do not drive the theme.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":1},{"id":"GO:0045490","count":1},{"id":"GO:0048358","count":1},{"id":"GO:0009860","count":1},{"id":"GO:0043086","count":1}]},{"hash":"548561500306950166","title":"Multitissue Development and Differentiation","description":"GO terms here span development and differentiation across multiple tissues (uterus, atrial/ventricular septa, inner ear, erythroid lineages, pancreas) and include an estrogen response. This lack of a single organ-specific function suggests a general role in developmental morphogenesis and lineage specification rather than a specific pathway, hence a broad developmental/differentiation label.","confidence":"Medium","size":6,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":4},{"id":"GO:0003290","count":3},{"id":"GO:0003281","count":3},{"id":"GO:0043627","count":3},{"id":"GO:0042472","count":3}]},{"hash":"489863428529480807","title":"Spliceosome and mRNA Processing","description":"The top GO terms cluster around spliceosome assembly, various forms of mRNA splicing (alternative and cis), mRNA export, and regulation of mRNA polyadenylation, indicating a coherent module of RNA processing. A few terms touch on translation reinitiation, but the dominant signal is RNA processing machinery.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0000387","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0045787","count":2},{"id":"GO:0075525","count":2}]},{"hash":"73027540413497790","title":"Plant organelle RNA editing and processing","description":"It centers on RNA editing and processing in plant mitochondria and chloroplasts (cytidine-to-uridine editing, organelle RNA modification/processing) and chloroplast-nucleus signaling, with a hint of plant development.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":3},{"id":"GO:1905639","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0000961","count":3},{"id":"GO:0016554","count":3}]},{"hash":"630527284101049702","title":"Unknown","description":"The terms span cytoskeletal assembly, signaling, diverse tissue development (glial, cardiac, renal), metabolism, and stress responses, with no single coherent function tying all proteins together. This heterogeneity suggests no clear cluster-level function can be confidently assigned.","confidence":"","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007020","count":5},{"id":"GO:0006468","count":5},{"id":"GO:0097264","count":5},{"id":"GO:0071313","count":5},{"id":"GO:0048708","count":5}]},{"hash":"1193161607192294984","title":"Ribosome biogenesis and translation initiation","description":"The top GO terms are dominated by ribosome assembly and translation-related processes: ribosome biogenesis, maturation of SSU-rRNA, formation of the translation preinitiation complex, translation reinitiation, and RNA guanine-N7-methylation. These points strongly suggest a cluster focused on ribosome production and the start/reinitiation of translation, with only minor related terms appearing as secondary cellular growth contexts. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1565457529499229768","title":"Flavonoid and pigment biosynthesis","description":"Most terms center on biosynthesis and modification of plant secondary metabolites, especially flavonoids and anthocyanins (kaempferol O-glucoside, cyanidin glucoside, anthocyanin-containing compounds) and related phenylpropanoid derivatives (lignin), suggesting a theme around plant pigment/secondary metabolite production. Some terms appear out of place (e.g., lipoteichoic acid biosynthesis, obsolete GO terms), likely reflecting annotation noise. Overall, a plant flavonoid/pigment biosynthesis theme is the best unifying label.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030259","count":3},{"id":"GO:0016999","count":3},{"id":"GO:0070395","count":2},{"id":"GO:0002175","count":2},{"id":"GO:0009808","count":2}]},{"hash":"1430993068568603276","title":"Ethylene-driven fruit ripening and hormone biosynthesis","description":"The cluster shows multiple plant-hormone related terms (ethylene biosynthesis, gibberellin and auxin metabolism, salicylic acid catabolism) and fruit ripening, plus related secondary metabolism and stress responses, indicating a cohesive module of hormonal control and maturation processes in fruit.","confidence":"High","size":6,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009693","count":4},{"id":"GO:0042318","count":4},{"id":"GO:0009686","count":4},{"id":"GO:0045487","count":4}]},{"hash":"895662447961226593","title":"Amino Acid, Heme, and Lipid Biosynthesis","description":"These proteins show a pattern of several biosynthetic pathways: amino acid biosynthesis (tyrosine, phenylalanine, and lysine-related terms), heme biosynthesis, sphinganine (sphingolipid) biosynthesis, and biotin biosynthesis, plus fatty acid transport. The common thread is involvement in assembling core metabolites and cofactors, with lipid-related processes tying the theme together, supporting a metabolic biosynthesis cluster.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0015908","count":2},{"id":"GO:0042853","count":2},{"id":"GO:0033585","count":2},{"id":"GO:0006783","count":2}]},{"hash":"2210359399934482511","title":"Chlorophyll and Quinone Cofactor Biosynthesis","description":"Most of the top GO terms point to biosynthetic pathways for pigments and electron-transport cofactors: chlorophyll, phylloquinone (vitamin K), plastoquinone, menaquinone, ubiquinone, and heme O. This suggests the cluster comprises proteins involved in producing cofactors essential for photosynthesis and respiration. A few unrelated terms (like some signaling or RNA processing annotations) likely reflect noise or broader gene annotations, but the dominant theme is cofactor biosynthesis, justifying this label.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048034","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0010236","count":2},{"id":"GO:0042371","count":2},{"id":"GO:0042372","count":2}]},{"hash":"1657282423114469472","title":"Bacterial exopolysaccharide biosynthesis","description":"The Top Terms are dominated by biosynthetic processes for polysaccharides and surface polymers (lipopolysaccharide, colanic acid, UDP-sugars, GDP-mannose/rhamnose, UDP-xylose) with an additional polymer like polyhydroxybutyrate. This points to a coherent theme of producing extracellular or cell-surface polysaccharides and related carbohydrate metabolism in bacteria, despite no reported edges in the cluster. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042619","count":3},{"id":"GO:0030245","count":3},{"id":"GO:0009103","count":2},{"id":"GO:0033499","count":2}]},{"hash":"1696728460090657218","title":"Epigenetic transcriptional repression and heterochromatin formation","description":"The cluster is dominated by GO terms pointing to transcriptional silencing and chromatin organization, including negative regulation of transcription by RNA polymerase II, negative regulation of histone methylation (H3K4), and formation of pericentric and subtelomeric heterochromatin. A related term on nuclear mRNA decay suggests coupling between transcriptional control and RNA surveillance. Some immune/migration terms appear less central to the core theme but may reflect broader regulatory roles. ","confidence":"Medium","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051572","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0070481","count":3},{"id":"GO:0033128","count":3},{"id":"GO:0034184","count":3}]},{"hash":"949759609550954326","title":"Plant hormone signaling and chlorophyll biosynthesis regulation","description":"This cluster centers on plant-specific processes: gibberellin response, regulation of chlorophyll biosynthesis, leaf senescence, and flavonol biosynthesis, plus osmotic stress response, suggesting a module coordinating growth hormones with chloroplast metabolism under stress. While there are more general terms like chromatin remodeling and viral process, the core theme points to plant growth regulation and chlorophyll-related biosynthesis. Confidence: Medium","confidence":"","size":6,"edges":7,"triangles":4,"max_degree":4,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:1900056","count":4},{"id":"GO:0010380","count":4},{"id":"GO:0009739","count":4},{"id":"GO:0006970","count":4},{"id":"GO:0016032","count":4}]},{"hash":"1775700338500359380","title":"Neural and vascular development","description":"The set of GO terms centers on angiogenesis, heart development, axonogenesis, Schwann cell development, visual processing, and excitatory synaptic activity, all hallmark processes of neural and cardiovascular morphogenesis and function. Additional terms about the G2/M cell cycle transition and apoptosis reflect general developmental control during tissue formation. The combination points to a neurovascular development theme; the abscisic acid-activated signaling pathway term is plant-specific and likely incidental, but does not outweigh the neural/vascular pattern.","confidence":"Medium","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001525","count":6},{"id":"GO:0009738","count":6},{"id":"GO:0000086","count":6},{"id":"GO:0043065","count":6},{"id":"GO:0014850","count":6}]},{"hash":"83937158415976695","title":"Unknown","description":"The set of GO terms includes transcription regulation, development and differentiation, phosphorylation dynamics, metabolism, and cytoskeletal processes, with only a single observed interaction among six proteins. This scattered functional spectrum provides no single cohesive function to label the cluster; best to mark it Unknown.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045944","count":5},{"id":"GO:0001824","count":4},{"id":"GO:0006470","count":4},{"id":"GO:0007586","count":4},{"id":"GO:0007020","count":3}]},{"hash":"1561166301118971434","title":"Neural development and growth factor signaling","description":"The cluster contains terms for neurotrophin TRK receptor signaling, FGFR signaling, PI3K/AKT, optic nerve morphogenesis, and face development, all pointing to neural development guided by growth factor receptor pathways. Additional terms like Wnt regulation and cellular responses fit within broad developmental signaling networks, supporting a cohesive theme of growth-factor\u2013driven neural development. Confidence: High","confidence":"","size":6,"edges":10,"triangles":6,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":6},{"id":"GO:0090090","count":6},{"id":"GO:0020021","count":6},{"id":"GO:0071469","count":6},{"id":"GO:0060324","count":6}]},{"hash":"1807440185650061364","title":"Oxidative Stress Response and Redox Homeostasis","description":"Dominant representation of redox and oxidative stress processes: detoxification of oxidants, hydrogen peroxide catabolism, and removal of superoxide radicals are prominent GO terms, with supporting links to mitochondrial cytochrome complex assembly and redox-regulated signaling via I-kappaB phosphorylation. Erythrocyte homeostasis also suggests systems maintaining redox balance in blood cells. While extracellular matrix organization and germ cell proliferation terms are present, they appear less central to the cluster's core function, so the redox-focused theme best explains the set.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0030198","count":4},{"id":"GO:0034101","count":2},{"id":"GO:0007252","count":2},{"id":"GO:0017004","count":2},{"id":"GO:0098869","count":2}]},{"hash":"829723773863862711","title":"Cellular Stress Signaling and Energy Metabolism","description":"The top GO terms cluster around responses to various stimuli (insulin, lithium, heat, hypoxia, epinephrine, cAMP) and energy-related processes (ATP biosynthesis, response to ATP) along with programmed cell death. This points to a common theme of stress- and signaling-driven regulation of metabolism and survival, rather than a single specific pathway. The seed maturation term is less central but may reflect broader developmental signaling contexts; overall, the theme is stress response linked to energy management.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"programmed cell death","top_go_terms":[{"id":"GO:0032869","count":6},{"id":"GO:0010226","count":5},{"id":"GO:0012501","count":5},{"id":"GO:0009408","count":5},{"id":"GO:0001666","count":5}]},{"hash":"816425252946898991","title":"Skin development and pigmentation signaling","description":"The cluster shows multiple terms tied to epidermal development and pigmentation (skin development, pigmentation, multicellular organism development), suggesting a cohesive role in skin-related differentiation and pigment pathways. While additional processes (GTPase signaling, calcium transport, hypoxia response) appear, the most coherent theme centers on skin development and pigmentation.","confidence":"Medium","size":6,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0031954","count":2},{"id":"GO:0071456","count":2}]},{"hash":"2241290130897361816","title":"Unknown","description":"The terms span ear vascular development, transcription, synaptic potentiation, calcium-dependent exocytosis, and a variety of biosynthetic processes (sugars, lipids, and bacterial cell components) with no clear shared function. This spread suggests annotation noise or a mixture of proteins with diverse roles rather than a cohesive biological theme. Therefore, there isn\u2019t a coherent label beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060716","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0060291","count":3},{"id":"GO:0045956","count":3},{"id":"GO:0009103","count":2}]},{"hash":"2007022897562305676","title":"Yeast DNA replication and protein quality control","description":"This cluster brings together core genome maintenance (DNA replication) with widespread proteostasis and trafficking themes (unfolded protein response, chaperone activity, SRP targeting to membranes, ER stress), plus yeast-specific processes like karyogamy and morphogenesis. The co-occurrence suggests a cohesive program in budding yeast that links DNA replication and cell growth with protein maturation and membrane targeting during development and mating.","confidence":"Medium","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0000742","count":3},{"id":"GO:0006616","count":2},{"id":"GO:0016226","count":2}]},{"hash":"1944118137773765815","title":"Viral life cycle proteins","description":"These proteins cluster around viral life cycle processes: proviral latency establishment, host-mediated activation of viral genome replication, RNA-templated DNA biosynthesis, and uncoating, indicating a shared function in viral propagation. Some terms like sepal formation and leukocyte migration appear as incidental annotations, but the dominant theme is virus-host interaction and genome replication steps typical of viruses.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075713","count":1},{"id":"GO:0048453","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0006278","count":1},{"id":"GO:0019061","count":1}]},{"hash":"2262714668066345246","title":"mRNA Splicing and Translation Initiation","description":"The proteins here show a coherent link between RNA processing (spliceosome-mediated splicing and mRNA export) and translation initiation/reinitiation (formation of the preinitiation complex and related translational control), suggesting a cluster of factors involved in coordinating mRNA maturation with the start of translation.","confidence":"High","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:1900363","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0006406","count":1}]},{"hash":"1320220552634323033","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":11,"triangles":10,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0071031","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0006369","count":3}]},{"hash":"1932772095170488674","title":"mRNA processing and translation initiation","description":"Proteins in this cluster are linked to RNA processing (splicing, polyadenylation, and export) and to the initiation/termination phases of translation (formation of the preinitiation complex and reinitiation events). The GO terms cluster around mRNA maturation and translation initiation, indicating a coherent role in processing transcripts and preparing them for translation.","confidence":"High","size":6,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:1900363","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0006406","count":2}]},{"hash":"2150910494418151881","title":"Plant Hormone Signaling and Nutrient Transport","description":"The list centers on plant hormone signaling (auxin-activated pathway and gibberellin homeostasis) and nutrient transport/response (nitrate transport/assimilation, peptide transport) with related responses, suggesting a cluster of proteins involved in hormone-regulated nutrient uptake and transport.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009734","count":2},{"id":"GO:0035672","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0080055","count":2},{"id":"GO:0010167","count":2}]},{"hash":"819017884469608696","title":"Osmotic stress and solute transport","description":"This cluster is best described as osmotic stress response coupled with membrane transport of various solutes (sugars, ions, and anions), reflected by terms for osmotic response and multiple transporter activities (glucose/fructose import, nitrate/nitrite/urate transport, sodium-dependent cation transport, potassium ion transport).","confidence":"Medium","size":6,"edges":5,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":3},{"id":"GO:0070715","count":3},{"id":"GO:0044381","count":3},{"id":"GO:0071332","count":3},{"id":"GO:0015707","count":3}]},{"hash":"1962375854440549156","title":"Plant flavonoid pigment biosynthesis and detoxification","description":"The top GO terms cluster around biosynthesis of flavonoid pigments (kaempferol, cyanidin, anthocyanin) and related pathways, plus lignin metabolism and xenobiotic/glucuronidation detoxification, pointing to a plant secondary metabolism module involving pigment production and chemical modification. A single atypical term (paranode localization) may be noise. Confidence reflects a coherent plant metabolism theme, though some terms are outliers.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0002175","count":4},{"id":"GO:0030259","count":4},{"id":"GO:0009808","count":4},{"id":"GO:0033330","count":4},{"id":"GO:0052696","count":4}]},{"hash":"355509747634388183","title":"Unknown","description":"The top GO terms are highly heterogeneous, including histone methylation regulation, peroxisome targeting, forebrain and retina development, actin filament depolymerization, nuclear pore localization, SREBP signaling, fertilization, and DNA damage response. This mix covers chromatin modification, organelle targeting, development, cytoskeleton, and genome surveillance with no clear, shared functional axis. Without a dominant common function or process, a single intuitive label cannot be confidently assigned.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2001162","count":2},{"id":"GO:0006625","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0030042","count":2},{"id":"GO:0060041","count":2}]},{"hash":"1973027965539267084","title":"Ubiquitin-dependent proteolysis and histone turnover","description":"The cluster is dominated by GO terms related to ubiquitin-mediated protein catabolic processes (K48-linked and other ubiquitinations, autoubiquitination) and histone turnover (histone catabolic process, histone ubiquitination). Although there are immune-related terms (TNF signaling, V(D)J recombination), the core commonality across the proteins appears to be ubiquitin modification pathways driving proteolysis and histone remodeling, hence a label focused on ubiquitin-dependent degradation and histone turnover.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0070936","count":4},{"id":"GO:1903265","count":4},{"id":"GO:0036205","count":4},{"id":"GO:0085020","count":4}]},{"hash":"1627303327724022355","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0070979","count":3},{"id":"GO:1902104","count":3},{"id":"GO:0051759","count":3},{"id":"GO:0042787","count":3}]},{"hash":"1136647729705027122","title":"Developmental Signaling and Morphogenesis","description":"Top GO terms in this cluster point to signaling pathways (Wnt, TRK/neurotrophin, FGFR, PI3K-AKT) and morphogenic processes (optic nerve morphogenesis, angiogenesis), suggesting a coherent theme of development and tissue shaping. Some terms (alkaline pH response, symbiont-mediated host transformation) are less directly related but do not override the overall pattern toward developmental signaling and morphogenesis.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090263","count":5},{"id":"GO:0048011","count":4},{"id":"GO:0020021","count":4},{"id":"GO:0071469","count":4},{"id":"GO:0021631","count":4}]},{"hash":"2296731890981641024","title":"Wnt Signaling Regulation in Development","description":"The terms repeatedly highlight canonical Wnt signaling and its regulation (negative and positive regulation), suggesting the proteins influence Wnt activity during development. The accompanying developmental processes across multiple tissues (brain regions, skin structures, taste papillae, kidney) align with Wnt's broad role in organogenesis, while some terms point to general cellular mechanisms that commonly accompany signaling and morphogenesis.","confidence":"Medium","size":6,"edges":7,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071681","count":3},{"id":"GO:0061380","count":3},{"id":"GO:0000011","count":3},{"id":"GO:0044336","count":3},{"id":"GO:0090090","count":3}]},{"hash":"1712967202982247159","title":"Unknown","description":"The top GO terms are highly diverse, including polysaccharide biosynthesis (lipopolysaccharide, colanic acid), sugar and lipid biosynthesis (UDP-D-xylose, galactose via UDP-galactose, ether lipid), SAM biosynthesis, and even vertebrate development terms (hair follicle development, labyrinthine layer blood vessel development). There is no single coherent function tying these proteins together, so the cluster is best labeled Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0009103","count":1},{"id":"GO:0006556","count":1},{"id":"GO:0060716","count":1},{"id":"GO:0033499","count":1}]},{"hash":"865885579897201147","title":"Bacterial specialized metabolite and lipid biosynthesis","description":"These GO terms point to diverse biosynthetic pathways in bacteria, including menaquinone biosynthesis (a cofactor), siderophore production (iron chelation), lipoteichoic acid synthesis (cell envelope lipids), and fatty acid biosynthesis, plus nonribosomal peptide and phenylpropanoid metabolism. While the processes are varied, they share the theme of assembling specialized metabolites and lipid-related components critical for bacterial physiology. Therefore the label centers on bacterial biosynthesis of small-molecule cofactors, lipids, and secondary metabolites.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":5},{"id":"GO:0043041","count":4},{"id":"GO:0036112","count":4},{"id":"GO:0009698","count":4},{"id":"GO:0070395","count":4}]},{"hash":"1151046867496637116","title":"Translation and ribosome biogenesis","description":"This cluster is dominated by GO terms for translation (cytoplasmic and mitochondrial), ribosomal subunit biogenesis, translation, and tRNA modification, pointing to a cohesive role in the protein synthesis machinery and ribosome assembly. A few metabolic or cell-cycle related terms appear, but they are secondary to the central translation-focused theme.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":3},{"id":"GO:1990090","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0006007","count":1}]},{"hash":"930283574352966219","title":"Plant stress responses and hormone signaling","description":"These proteins collectively map to plant immune and developmental processes: responses to salicylic acid and chitin indicate defense signaling, while gibberellin and ACC (ethylene precursor) links point to hormone signaling and growth regulation. Additional terms cover boron deprivation and epidermal/tissue differentiation (atrichoblast, sclerenchyma), suggesting a broader theme of how plants integrate stress responses with development. Overall, the cluster seems to represent a module coordinating environmental responses with hormone-driven growth and tissue differentiation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009751","count":6},{"id":"GO:0010200","count":6},{"id":"GO:0009739","count":6},{"id":"GO:0009938","count":6},{"id":"GO:0080169","count":6}]},{"hash":"1616795419027154970","title":"Mitotic Chromosome Cohesion and Segregation","description":"This cluster is driven by GO terms for meiotic sister chromatid cohesion, mitotic sister chromatid separation, and spindle orientation checkpoint signaling, plus nuclear import. Together these point to a cohesive function in chromosome management during cell division and related nuclear transport, with slight noise from unrelated terms.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000060","count":2},{"id":"GO:0051754","count":2},{"id":"GO:0031578","count":2},{"id":"GO:0001938","count":1},{"id":"GO:0051306","count":1}]},{"hash":"1426539773484534345","title":"Regulated Exocytosis and Cell Migration","description":"Top GO terms are dominated by positive regulation of calcium ion-dependent exocytosis and cell migration, with additional signals for membrane trafficking (endosome-to-plasma membrane transport) and cytoskeletal remodeling (podosome assembly, dendritic spine development). The mix suggests a unifying theme of regulated membrane trafficking linked to motility and structural changes, rather than a single pathway, supporting the label.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045956","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0010227","count":1},{"id":"GO:0060999","count":1},{"id":"GO:1902307","count":1}]},{"hash":"1499321264455036000","title":"Unknown","description":"The top GO terms are highly diverse and there is no single cohesive biological theme linking them (ranging from microtubule nucleation and endocytosis regulation to astrocyte differentiation, metabolism, development, and signaling). With only singleton representations and just one edge, there isn\u2019t a clear, shared function to name this cluster beyond Unknown.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007020","count":1},{"id":"GO:0030100","count":1},{"id":"GO:0006468","count":1},{"id":"GO:0048708","count":1},{"id":"GO:0005980","count":1}]},{"hash":"1322983501524439024","title":"Plant abiotic stress response and metabolism","description":"The Top Terms are dominated by plant-related responses to abiotic stress, including abscisic acid signaling, cold acclimation, water deprivation, trehalose stimulus, and aerenchyma formation, suggesting a shared stress-response theme. Metabolic activity such as cellulose, diacylglycerol, and monoacylglycerol catabolism indicates remodeling of cellular components and energy usage under stress. An outlier term about retrograde endocannabinoid signaling in neurons is present but does not define the cluster. Overall, it seems to be a plant stress-response cluster with associated metabolic changes.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009737","count":1},{"id":"GO:0009631","count":1},{"id":"GO:0009414","count":1},{"id":"GO:0098921","count":1},{"id":"GO:0030245","count":1}]},{"hash":"31056614134880362","title":"Immune signaling regulators","description":"The terms point to modulation of signaling pathways (GTPase activity, Ras signaling, serine phosphorylation) and immune-related differentiation processes (lamellocyte differentiation, B cell receptor signaling, Th2 differentiation). While a few terms hint at non-immune development or metabolism, the strongest recurring theme across the cluster is regulation of signaling in immune contexts, suggesting these proteins act as immune signaling regulators.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0020021","count":2},{"id":"GO:2000753","count":2},{"id":"GO:0035171","count":2},{"id":"GO:0046579","count":2}]},{"hash":"1352026254102419931","title":"Organelle organization and protein turnover","description":"The top terms point to intracellular organization processes (Golgi, lipid droplets), autophagosome assembly, and ubiquitin-related protein quality control (ERAD, deubiquitination). These collectively suggest a cluster focused on maintaining cellular architecture and proteostasis, rather than a single, specific signaling pathway, hence a label around organelle organization and protein turnover.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030437","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0030154","count":2},{"id":"GO:0000045","count":1},{"id":"GO:1903094","count":1}]},{"hash":"2128103202467019141","title":"Ubiquitin-Dependent Protein Turnover","description":"Based on the top GO terms, the cluster is dominated by ubiquitin-related processes: monoubiquitination, deubiquitination, ubiquitin-dependent protein catabolic process, and histone ubiquitination, plus aggresome assembly. This suggests a shared theme in protein quality control and turnover via the ubiquitin-proteasome system. A few terms about RNA modification or chlorophyll biosynthesis appear, likely annotation noise or unrelated associations; overall the strongest signal is ubiquitin-mediated regulation and degradation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035520","count":1},{"id":"GO:0010216","count":1},{"id":"GO:0006511","count":1},{"id":"GO:0036353","count":1},{"id":"GO:0032088","count":1}]},{"hash":"1564264793386082749","title":"Unknown","description":"The top GO terms are very heterogeneous: translation initiation terms, peroxisome targeting, forebrain and retina development, actin depolymerization, fertilization, nuclear pore localization, and lipid signaling. There isn\u2019t a single cohesive function linking these proteins, so a clear, representative label with confidence cannot be assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:2001162","count":2},{"id":"GO:0006625","count":2},{"id":"GO:0030900","count":2}]},{"hash":"1863336035050885093","title":"Cellular Stress Response and Proteostasis","description":"The cluster is dominated by stress-related GO terms (cellular response to gamma radiation, stress-activated MAPK cascade, regulation of cellular response to heat) and protein homeostasis (protein stabilization), complemented by notes on transport regulation and lens morphogenesis. This pattern suggests a theme of maintaining protein function and cellular integrity under stress, rather than a single, narrow pathway. ","confidence":"Medium","size":6,"edges":12,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":3},{"id":"GO:0007568","count":2},{"id":"GO:0032387","count":2},{"id":"GO:0030308","count":2},{"id":"GO:0050821","count":2}]},{"hash":"459370797142921211","title":"Ciliary Hedgehog Signaling in Development","description":"The cluster\u2019s terms rally around non-motile cilium assembly and regulation of the Smoothened (Hedgehog) signaling pathway, both central to cilium-mediated developmental signaling. Hair follicle morphogenesis is a development process known to depend on SHH signaling and ciliary function, supporting this theme. There is an outlier plant immunity term that likely reflects annotation noise, but the dominant signals point to cilium-associated Hedgehog signaling in development.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0031069","count":1},{"id":"GO:0080185","count":1},{"id":"GO:1901622","count":1},{"id":"GO:1905515","count":1}]},{"hash":"488347130214215394","title":"Ubiquitin-like modification and autophagy regulation","description":"The top GO terms point to protein conjugation via ubiquitin-like modifiers (neddylation and ufmylation) and autophagy-related processes (macroautophagy and nucleophagy), suggesting a core theme of PTM signaling linked to autophagy regulation. However, several other terms (amygdala development, defense response to fungus, tRNA wobble thiolation, molybdopterin biosynthesis) are less coherent with this core, indicating a modest overall signal with notable noise. ","confidence":"Low","size":6,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":2},{"id":"GO:0050832","count":2},{"id":"GO:2000220","count":2},{"id":"GO:0045116","count":2},{"id":"GO:1990592","count":2}]},{"hash":"2105334580281619939","title":"Hormone biosynthesis and reproductive development","description":"The cluster is driven by biosynthetic processes for signaling molecules (prostaglandin, retinoic acid, calcitriol) and by development terms related to the uterus and female gonads, suggesting a cohesive theme around hormone/mediator production tied to female reproductive development, though some miscellaneous metabolic terms exist.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":6},{"id":"GO:0071615","count":5},{"id":"GO:0042904","count":5},{"id":"GO:0060065","count":5},{"id":"GO:0008585","count":5}]},{"hash":"445910211475411516","title":"Female reproductive development and retinoic acid metabolism","description":"The set shows strong signals for female genitalia/uterus development (GO:0008585, GO:0030540, GO:0060065) alongside retinoic acid biosynthesis and catabolism (GO:0042904, GO:0034653), suggesting a coordinated role in female reproductive development modulated by retinoic acid signaling. While there are additional terms related to xenobiotic metabolism and other pathways, the dominant theme is reproductive development tied to retinoic acid metabolism.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071615","count":3},{"id":"GO:0042904","count":3},{"id":"GO:0060065","count":3},{"id":"GO:0008585","count":3},{"id":"GO:0034653","count":3}]},{"hash":"855832086712890375","title":"Redox Homeostasis and Oxidative Stress Response","description":"The dominant GO terms cluster around managing oxidative stress and redox balance (cellular oxidant detoxification, cellular response to hydrogen peroxide, redox homeostasis, oxidative-reduction processes, cytochrome complex assembly), suggesting a theme of redox regulation and detoxification. Peripheral terms link metabolism and vascular/inflammatory signaling, which often accompany redox processes, but the core theme remains redox balance and oxidative defense.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:2000255","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006641","count":3},{"id":"GO:0070301","count":3}]},{"hash":"1163451582309875102","title":"Microtubule dynamics in mitosis and intracellular transport","description":"The top GO terms cluster around microtubule regulation and dynamics across mitotic events (centrosome/spindle separation, kinetochore attachment, cytokinesis) and microtubule-based transport and depolymerization (plus-end depolymerization, axonemal depolymerization, dendritic transport), with chloroplast movement reflecting microtubule-driven motility in plants.","confidence":"High","size":6,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007100","count":4},{"id":"GO:0009904","count":3},{"id":"GO:0032886","count":3},{"id":"GO:0098971","count":3},{"id":"GO:0070462","count":3}]},{"hash":"301786583954969045","title":"Golgi-ER Vesicle Trafficking & SNAREs","description":"This cluster centers on vesicle transport through the secretory pathway, including ER-to-Golgi and intra-Golgi transport, Golgi ribbon formation, and SNARE complex assembly, indicating SNARE-driven vesicle fusion as a core function. It also includes terms related to cargo delivery to the plasma membrane and receptor recycling, such as exocytic insertion of neurotransmitter receptors and positive regulation of receptor recycling, plus Golgi-to-endosome trafficking and trafficking events linked to synaptic potentiation. Collectively, these terms point to a coherent theme of Golgi- and SNARE-mediated vesicle trafficking in secretory and synaptic contexts, with receptor trafficking contributing to plasticity. ","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":5},{"id":"GO:0098967","count":5},{"id":"GO:0042147","count":5},{"id":"GO:0035493","count":5},{"id":"GO:0006888","count":5}]},{"hash":"351387113221957811","title":"Lignocellulose degradation and nitrogen/metal transport","description":"The top GO terms cluster around breakdown of plant cell wall components (cellulose, lignin) and nitrogen metabolism (denitrification, nitrate assimilation), plus transport of metals such as arsenate, copper, and iron. This points to a soil-associated microbe capable of degrading lignocellulose while managing nitrogen and metal homeostasis; occasional terms about antibiotic biosynthesis and sporulation reflect broader environmental adaptability but do not dominate the theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":5},{"id":"GO:0019333","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0046274","count":4},{"id":"GO:0030435","count":4}]},{"hash":"1171410532367071770","title":"Mucosal immunity and proteoglycan biosynthesis","description":"The cluster shows mucosal immune activity (immunoglobulin production in mucosal tissue, leukocyte tethering/rolling) together with glycosylation and proteoglycan synthesis (UDP-D-xylose metabolism, heparan proteoglycan biosynthesis), suggesting a mucosal immune\u2013glycosylation theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034116","count":2},{"id":"GO:0032868","count":2},{"id":"GO:0050901","count":2},{"id":"GO:0050892","count":2},{"id":"GO:0042403","count":2}]},{"hash":"2266020304944682996","title":"Sugar transport and osmotic stress response","description":"These proteins are enriched for transport of sugars and related metabolites (glucose, fructose, lactose, urate, dehydroascorbic acid) and for a cellular response to osmotic stress, suggesting a cohesive role in carbohydrate transport and osmotic adaptation under stress conditions.","confidence":"High","size":6,"edges":8,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":6},{"id":"GO:0070715","count":6},{"id":"GO:0044381","count":6},{"id":"GO:0071332","count":6},{"id":"GO:0015747","count":6}]},{"hash":"270110852393984569","title":"Embryonic Heart and Neural Crest Morphogenesis","description":"The top GO terms strongly cluster around embryonic development of heart and neural crest\u2013derived structures (heart development, angiogenesis, axonogenesis, Schwann cell development, embryonic cranial skeleton morphogenesis). This suggests a cohesive theme of coordinated morphogenesis for cardiovascular and craniofacial/nerve-lineages during early development, with some general cellular processes (cell cycle, apoptosis) that are broadly shared.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009636","count":5},{"id":"GO:0001525","count":5},{"id":"GO:0009738","count":5},{"id":"GO:0000086","count":5},{"id":"GO:0043065","count":5}]},{"hash":"122704586204094030","title":"ER Network Organization and Neural Development","description":"This cluster is enriched for terms tied to endoplasmic reticulum tubular network formation/maintenance and ER-dependent organization, plus nuclear pore complex assembly, suggesting a role in ER and nuclear envelope architecture. It also includes neural development terms such as negative regulation of axon extension, axonal fasciculation, and regulation of branching morphogenesis of a nerve, indicating involvement in neural morphogenesis. Some terms point to broader cellular remodeling processes (steroid biosynthetic process, epithelial-to-mesenchymal transition). Overall, the common thread appears to be proteins linked to ER morphology with ties to neural development, supporting this label.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030517","count":2},{"id":"GO:0071787","count":1},{"id":"GO:0007413","count":1},{"id":"GO:2000172","count":1},{"id":"GO:0060317","count":1}]},{"hash":"1838674225694467517","title":"Unknown","description":"The top GO terms span plants (pectin catabolic process, flower phyllotactic patterning, cell wall organization) and diverse non-plant processes (teichoic acid transport, ceramide/phospholipid translocation, cholesterol absorption, peroxisomal fatty acid import). There is no clear, single shared function or pathway linking these terms, and the network has no edges, so no cohesive cluster function can be inferred.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":2},{"id":"GO:0045490","count":2},{"id":"GO:0060773","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0015777","count":1}]},{"hash":"2099741159843013933","title":"Plasma membrane Ca2+ and amino acid exporters","description":"The cluster is best described by its two top GO terms, both indicating export across the plasma membrane for calcium ions and for amino acids, implying a shared transporter-related function focused on membrane export.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990034","count":2},{"id":"GO:0032973","count":2}]},{"hash":"2031360492837896718","title":"Plant development and hormone signaling","description":"The terms point to plant organ and flower development, meristem activity, axis and polarity specification, and hormone signaling (auxin, gibberellin), all tied to transcriptional control\u2014together suggesting a cluster of proteins involved in plant development with hormone regulation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009942","count":1},{"id":"GO:0010262","count":1},{"id":"GO:0010158","count":1},{"id":"GO:0048507","count":1},{"id":"GO:0009908","count":1}]},{"hash":"297652944167904418","title":"Regulation of cellular growth, differentiation, and migration","description":"The GO terms point to regulatory roles in proliferation/differentiation (neuroblast, osteoblast, macrophage), cell movement and cytoskeletal dynamics (fibroblast migration, pseudopodium assembly), and signaling/vesicle processes (Ras signaling, exosomal secretion). This pattern suggests a cohesive function centered on modulating cellular state transitions and motility rather than a single pathway.","confidence":"Medium","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032966","count":5},{"id":"GO:0046579","count":5},{"id":"GO:0010821","count":5},{"id":"GO:0010762","count":5},{"id":"GO:0031274","count":5}]},{"hash":"496497572364494098","title":"TLR4/MyD88 Innate Immune Signaling","description":"The GO terms indicate MyD88-dependent Toll-like receptor signaling, LPS detection, and robust cytokine production (including IL-6) with regulation of dendritic cell responses and activation of the JNK cascade, all pointing to an innate immune response to microbial components and viral defense.","confidence":"High","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002755","count":3},{"id":"GO:0034145","count":3},{"id":"GO:0032497","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0002374","count":3}]},{"hash":"600227619195661156","title":"Cerebral Cortical Development and Synaptic Assembly","description":"The cluster shows strong representation of neural development and synaptic organization terms: synapse assembly, vesicle fusion, and reelin-mediated signaling, plus radial glia\u2013guided cortical migration. Immune-related terms like phagocytosis regulation and B cell signaling may reflect microglial activity within the CNS or broader cell signaling contexts, but the dominant theme is cerebral cortex development and synaptic wiring.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007416","count":4},{"id":"GO:0050764","count":3},{"id":"GO:0006906","count":3},{"id":"GO:0050861","count":3},{"id":"GO:0021814","count":3}]},{"hash":"1637880660656489019","title":"Golgi trafficking and organelle dynamics","description":"The terms cluster around Golgi-associated transport (Golgi to vesicle/plasma membrane, protein localization to Golgi) and organelle turnover/dynamics (mitochondrial fission, phagophore assembly site related to autophagy), suggesting a core theme of intracellular trafficking and organelle remodeling. Some items, like development or apoptosis terms, appear peripheral to this main theme but may reflect broader cellular context.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055108","count":2},{"id":"GO:0000266","count":2},{"id":"GO:0034497","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0051301","count":2}]},{"hash":"829913939238844439","title":"Rho-driven neuronal spine plasticity","description":"Most terms point to Rho-mediated actin cytoskeleton regulation in neurons: Rho signal transduction, promotion of dendritic spine development and synaptic plasticity, and Arp2/3 actin nucleation control. The presence of neuron projection morphogenesis and podosome assembly further supports cytoskeletal remodeling underlying neurite growth and synapse formation. Growth factor responses (EGF, IGF) may modulate this signaling in neural contexts; a fungus defense signal appears unrelated, likely incidental.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007266","count":2},{"id":"GO:0060999","count":1},{"id":"GO:0031915","count":1},{"id":"GO:0034316","count":1},{"id":"GO:0071800","count":1}]},{"hash":"1484503345202047374","title":"Brain development and neuronal migration","description":"This cluster is mainly characterized by brain development (GO:0007420), reelin-mediated signaling (GO:0038026), and cortex radial glia guided migration (GO:0021814), suggesting a neurodevelopmental and neuronal-migration theme. Other terms appear as noise (e.g., B cell signaling, antibiotic response), but the core signals point to brain development and neuronal migration functions.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0050764","count":1},{"id":"GO:0006906","count":1},{"id":"GO:0050861","count":1},{"id":"GO:0021814","count":1}]},{"hash":"341094439761161831","title":"Microtubule-driven mitosis and intracellular transport","description":"The top GO terms point to microtubule dynamics in cell division (centrosome/spindle pole separation, kinetochore attachment, cytokinesis, plus-end depolymerization) and intracellular trafficking (dendritic transport, axonemal MTs). The chloroplast movement term also reflects MT involvement in plant cells, reinforcing a single theme: microtubule-based mitotic and transport processes.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007100","count":4},{"id":"GO:0009904","count":3},{"id":"GO:0032886","count":3},{"id":"GO:0098971","count":3},{"id":"GO:0070462","count":3}]},{"hash":"1254476728745327512","title":"RNA pseudouridylation","description":"Two GO terms point to tRNA and rRNA pseudouridine synthesis, suggesting the cluster centers on RNA modification via pseudouridine synthases. The other, more disparate terms may reflect multifunctionality or incidental annotations in a small protein set, but the RNA modification signal is clear and representative.","confidence":"High","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031119","count":2},{"id":"GO:0000455","count":2},{"id":"GO:0050764","count":1},{"id":"GO:0071364","count":1},{"id":"GO:0006906","count":1}]},{"hash":"2044720110350621299","title":"TLR-LPS Innate Immune Signaling","description":"This cluster centers on innate immune recognition and response, highlighted by GO terms for MyD88-dependent Toll-like receptor signaling, detection of lipopolysaccharide (LPS), defense response to virus, and cytokine production. While a few terms touch on dendritic cell regulation and neuronal development, the core theme is TLR-mediated sensing of pathogens and subsequent cytokine-driven immune activation.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:0002755","count":1},{"id":"GO:0032497","count":1},{"id":"GO:0051607","count":1},{"id":"GO:0033353","count":1}]},{"hash":"1146400842205337488","title":"TLR-MyD88 Innate Immune Signaling","description":"This cluster is dominated by GO terms related to Toll-like receptor signaling (MyD88-dependent), detection of LPS, and NF-kB activation (I-kappaB phosphorylation), along with downstream cytokine production and dendritic cell regulation. Although a couple of terms (like male gonad development and an obsolete oxidation-reduction process) are present, the immune signaling theme is strong and cohesive, suggesting a set of proteins involved in innate immune sensing and cytokine responses.","confidence":"High","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":2},{"id":"GO:0007252","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0002755","count":1},{"id":"GO:0034145","count":1}]},{"hash":"906231824106779039","title":"DNA replication and chromatin remodeling","description":"This cluster centers on core nuclear processes: DNA replication, DNA topological changes, and chromatin remodeling/nucleosome dynamics, with several related chromatin-modifying annotations. A few outlier terms touch on RNA processing and differentiation, but the dominant theme is genome replication coupled with chromatin state changes.","confidence":"Medium","size":5,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006265","count":2},{"id":"GO:0016584","count":2},{"id":"GO:1990417","count":2},{"id":"GO:0006306","count":2}]},{"hash":"893003768090462390","title":"Plant reproductive development","description":"The cluster includes pollen-pistil interaction and regulation of inflorescence meristem growth, both direct indicators of plant reproductive development. The presence of additional general metabolic and catabolic processes suggests some background annotations, but the reproductive terms give the strongest, coherent theme for this group. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009875","count":1},{"id":"GO:0018279","count":1},{"id":"GO:0009089","count":1},{"id":"GO:0006144","count":1},{"id":"GO:0006526","count":1}]},{"hash":"1474960134247693163","title":"Oxidative and nitrosative stress response and detoxification","description":"The GO terms are dominated by oxidative/nitrosative stress responses and detoxification processes (cellular oxidant detoxification, hydrogen peroxide catabolic process, response to nitrosative stress, response to toxic substance). This suggests the proteins in this cluster participate in defending against reactive oxygen/nitrogen species. A few terms (blood coagulation, mitotic sister chromatid cohesion, oxygen transport, collagen biosynthesis regulation) seem peripheral or incidental to the core theme.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007064","count":2},{"id":"GO:0032966","count":1},{"id":"GO:0051409","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0007596","count":1}]},{"hash":"52858253859903381","title":"Death receptor\u2013mediated apoptosis","description":"This cluster\u2019s top GO terms are dominated by extrinsic apoptotic signaling via death domain receptors (GO:0008625) and extrinsic apoptotic signaling in absence of ligand (GO:0097192), suggesting a primary association with death receptor\u2013mediated apoptosis. The other terms (e.g., ruffle assembly, negative regulation of ubiquitination, and other regulatory processes) are more diverse and likely reflect multifunctional proteins or annotation noise, but do not outweigh the apparent apoptotic theme. ","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0008625","count":2},{"id":"GO:0090367","count":1},{"id":"GO:0061084","count":1},{"id":"GO:0071364","count":1},{"id":"GO:0042993","count":1}]},{"hash":"45572224356796594","title":"Auxin-regulated meristem identity and leaf patterning","description":"The GO terms cluster around auxin signaling and plant development, including meristem development, leaf vascular tissue pattern formation, and transcriptional regulation, with responses to auxin and DNA-templated transcription highlighted. This suggests a set of proteins coordinating meristem identity and pattern formation under auxin control via transcriptional regulation.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009942","count":2},{"id":"GO:0048507","count":2},{"id":"GO:0010305","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0009734","count":2}]},{"hash":"377590612202311057","title":"Cajal body\u2013associated RNA localization and telomerase regulation","description":"The strongest GO terms point to localization of RNA to Cajal bodies and specifically telomerase RNA to Cajal bodies, plus general protein localization to Cajal bodies, which suggests a focus on nuclear RNA processing and telomere biology. Other terms in the cluster (cell division, protein stabilization, immune cytokine production, host-cell toxin transport, and sperm binding) are more peripheral or unrelated, making the core theme best described as Cajal body\u2013centered RNA localization and telomerase regulation.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1904871","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0044053","count":5},{"id":"GO:1901998","count":5},{"id":"GO:1904874","count":5}]},{"hash":"963172634047908787","title":"Microbial Energy Metabolism and Motility","description":"This cluster centers on energy-generating and redox-related processes across prokaryotes, including methanogenesis, formate and lactate-related oxidation, the TCA cycle, and photosystem I\u2013associated electron transport, with methanopterin biosynthesis as a key cofactor pathway. The presence of bacterial flagellum assembly points to motility, while tRNA queuosine biosynthesis and uracil catabolism reflect core microbial biosynthetic/catabolic activities. Altogether, the terms suggest a cohesive theme of prokaryotic energy metabolism and basic cellular functions rather than a single highly specific process.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0019385","count":2},{"id":"GO:0044780","count":2},{"id":"GO:0019516","count":2},{"id":"GO:1901285","count":2}]},{"hash":"563230803801514049","title":"Fe-S Cluster Biogenesis & Photosynthesis","description":"Top GO terms cluster around iron-sulfur cluster assembly, intracellular iron homeostasis, and maturation of Fe-S proteins, with photosynthesis (light reaction) and carbon utilization terms also present. This pattern suggests a function in assembling and delivering Fe-S cofactors to photosynthetic apparatus and related metabolic processes, aligning with chloroplast/cyanobacterial contexts. The presence of nitrogen fixation and transport terms further supports a broader role for Fe-S proteins in energy and nutrient metabolism in photosynthetic organisms. Overall, these proteins likely participate in Fe-S cofactor biogenesis linked to photosynthetic function.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071244","count":1},{"id":"GO:0015976","count":1},{"id":"GO:2000122","count":1},{"id":"GO:0009399","count":1},{"id":"GO:0016226","count":1}]},{"hash":"309705851499506394","title":"Auxin signaling and organ growth regulation","description":"The cluster is dominated by GO terms tied to auxin signaling (auxin-activated signaling pathway, auxin polar transport, response to auxin) and regulation of organ growth, indicating proteins likely involved in auxin-mediated growth control in plants; the other terms are minor contributors.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046620","count":2},{"id":"GO:0009734","count":2},{"id":"GO:0009926","count":2},{"id":"GO:0009733","count":2},{"id":"GO:0042853","count":1}]},{"hash":"650372660388656792","title":"Ferredoxin-Linked Energy Metabolism and Nitrogen Fixation","description":"Most terms cluster around core energy pathways: ATP synthesis coupled electron transport; ferredoxin metabolic process; nitrogen fixation; and catabolic processes (xanthine, phenylacetate) that feed into energy production. A few terms (vasculogenesis, lactation) appear unrelated and likely noise. The label captures the dominant theme of microbial energy metabolism and nitrogen fixation.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:2001213","count":2},{"id":"GO:0006124","count":2},{"id":"GO:0009115","count":2},{"id":"GO:0042773","count":2},{"id":"GO:0007595","count":2}]},{"hash":"2238068464652260444","title":"Mitochondrial lipid metabolism and CoQ biosynthesis","description":"Top terms point to mitochondrial-focused processes: ubiquinone (CoQ) biosynthesis, mitochondrial translation, and lipid homeostasis, plus apoptosis\u2014consistent with mitochondrial metabolism and quality control. Some neural development terms may reflect broader gene annotations, but the core signals cohere around mitochondria. Confidence in representative labeling is Medium.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010795","count":1},{"id":"GO:1901006","count":1},{"id":"GO:0021692","count":1},{"id":"GO:1902171","count":1},{"id":"GO:0055088","count":1}]},{"hash":"140411978258809035","title":"Redox balance and catecholamine metabolism with methylation","description":"This cluster centers on oxidative stress management (removal of superoxide radicals, redox homeostasis) and catecholamine pathways (dopamine/catecholamine metabolism), with adjacent methylation processes. While a few terms are unrelated (e.g., lignin biosynthesis, auditory development), the dominant themes connect redox regulation to catecholamine metabolism and methylation, suggesting a cohesive functional core.","confidence":"Medium","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019430","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0050668","count":2},{"id":"GO:0032259","count":2},{"id":"GO:0006479","count":2}]},{"hash":"441512465717235189","title":"Unknown","description":"Top terms are scattered across plant-specific processes and animal lipid metabolism and immune responses, with no single cohesive function tying them together; the absence of edges further suggests unrelated annotations. Therefore, Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":1},{"id":"GO:0010236","count":1},{"id":"GO:0006954","count":1},{"id":"GO:0055096","count":1},{"id":"GO:0080086","count":1}]},{"hash":"1553091941522495381","title":"DNA Replication and Repair","description":"The cluster is enriched for GO terms related to DNA topology changes, nucleotide-excision repair, DNA replication, and the SOS response, indicating a shared role in genome maintenance and DNA damage response. A couple of terms (hair cell differentiation, MDA-5 signaling) appear less central or incidental, but the dominant pattern points to DNA repair and replication functions.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006265","count":2},{"id":"GO:0006306","count":2},{"id":"GO:0035315","count":2},{"id":"GO:0000717","count":2},{"id":"GO:0009432","count":2}]},{"hash":"1430017932331158640","title":"Biosynthesis and Growth","description":"The Top Terms show multiple biosynthetic processes (biotin, antibiotic, menaquinone, chlorophyll) plus cell growth and cell cycle/division, with a few RNA modification terms. This suggests a cluster centered on basic biosynthetic metabolism that supports cell proliferation, so a name reflecting both biosynthesis and growth is appropriate.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0019878","count":2}]},{"hash":"1909246145920039916","title":"Ribosome maturation and translation regulation","description":"The top terms center on translation, with specific emphasis on maturation of LSU-rRNA and regulation of translation, indicating a cohesive cluster around ribosome biogenesis and control of protein synthesis. A single stress-response term is secondary and does not override the main theme. ","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000470","count":2},{"id":"GO:0006417","count":2},{"id":"GO:0006950","count":1}]},{"hash":"352307341786878375","title":"Gene Expression Regulation and Chromatin Remodeling","description":"The cluster\u2019s top terms include translation (protein synthesis), nucleosome assembly, and histone H3-K4 dimethylation, pointing to a shared theme of regulating gene expression at both transcriptional and translational levels. While there are also development and stimulus-response terms, the combination of chromatin-related processes with translation provides the strongest cohesive signal for a regulatory, gene-expression\u2013focused module.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0071314","count":1},{"id":"GO:0003290","count":1},{"id":"GO:0048316","count":1},{"id":"GO:0044648","count":1}]},{"hash":"42841663052654332","title":"Protein secretion and transmembrane transport","description":"The cluster contains GO terms centered on secretion and membrane transport: protein secretion (GO:0009306), protein transport by the Tat complex (GO:0043953), and intracellular protein transmembrane transport (GO:0065002). These repeatedly point to a shared role in exporting or moving proteins across membranes, which provides a coherent thematic label, despite the presence of several unrelated terms. Confidence reflects a moderate level of support given the small set and mixture of terms.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009306","count":1},{"id":"GO:0043953","count":1},{"id":"GO:0065002","count":1},{"id":"GO:1902458","count":1},{"id":"GO:0031427","count":1}]},{"hash":"387181000007619447","title":"Unknown","description":"The GO terms are highly diverse and span metabolism (ammonia assimilation, glucose response, glutamine biosynthesis, nitrogen starvation), cell signaling (glutamatergic synaptic transmission, epithelial proliferation, insulin secretion), and general protein interactions (homooligomerization) with a few obsolete terms. There isn't a clear, single biological theme binding these proteins, so a specific functional label can't be assigned.","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010756","count":1},{"id":"GO:0051260","count":1},{"id":"GO:0019676","count":1},{"id":"GO:0050679","count":1},{"id":"GO:0009749","count":1}]},{"hash":"248829611045674798","title":"Aminoacyl-tRNA Synthetases and Translation","description":"The cluster shows multiple aminoacyl-tRNA synthetases (isoleucyl-, leucyl-, methionyl-, valyl-) and the translation term, plus regulation of translational fidelity, which together indicate involvement in tRNA charging and protein synthesis. While there are a few unrelated terms (e.g., intron splicing, LPS biosynthesis, simple metabolic processes), the dominant theme across the top terms is translation machinery. This makes the label representative and specific to the cluster\u2019s core function.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000372","count":1},{"id":"GO:0006428","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0006429","count":1}]},{"hash":"2279238387717378782","title":"Sphingolipid and fatty acid biosynthesis","description":"The top terms cluster around lipid metabolism, including sphinganine and sphingosine biosynthesis, monounsaturated fatty acid biosynthesis, and responses to fatty acids, along with white fat cell differentiation. Although a few terms are unrelated, the dominant signal is lipid biosynthesis and adipogenesis, justifying a label focused on sphingolipid and fatty acid biosynthesis.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006667","count":1},{"id":"GO:0050872","count":1},{"id":"GO:0010205","count":1},{"id":"GO:1903966","count":1},{"id":"GO:0070542","count":1}]},{"hash":"341281175794532583","title":"Mycobacterial lipid and steroid metabolism","description":"This cluster prominently features lipid and fatty acid processes (fatty acid elongation; methyl-branched fatty acids; mycolic acid biosynthesis) and steroid turnover (androgen and steroid catabolic processes), which together point to lipid-rich envelope synthesis typical of mycobacteria. Additional cofactor/vitamin-related terms (tetrahydrobiopterin, phylloquinone, retinal metabolism) may reflect connected metabolic networks in these organisms. The clear signal of mycolic acid biosynthesis strongly supports a mycobacterial lipid/steroid metabolism theme.","confidence":"High","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0031427","count":5},{"id":"GO:0006710","count":5},{"id":"GO:0006729","count":5},{"id":"GO:0008207","count":5},{"id":"GO:1902321","count":5}]},{"hash":"1469642957325426223","title":"Actin cytoskeleton remodeling and morphogenesis","description":"Top GO terms center on actin dynamics (actin filament depolymerization; formin-nucleated actin cables) and morphogenetic processes (proboscis morphogenesis; establishment of bipolar cell polarity), with supporting signals from cytoskeleton involvement in karyogamy. While some terms are less direct or obsolete, the overarching theme is actin/ cytoskeleton\u2013driven remodeling during development and cell shape changes.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009652","count":1},{"id":"GO:1903033","count":1},{"id":"GO:0030042","count":1},{"id":"GO:0000742","count":1},{"id":"GO:1902405","count":1}]},{"hash":"919031558979962544","title":"Neural development and synaptic signaling","description":"Most top GO terms cluster around nervous system development and synaptic function (Schwann cell development, myoblast fusion, visual perception, excitatory postsynaptic potential, long-term potentiation). While terms like angiogenesis and ABA signaling are present, the dominant theme is neural development and synaptic signaling, with some general developmental/cell-cycle signals that are less central. Confidence: Medium","confidence":"","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0009738","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0060079","count":3}]},{"hash":"1494114780345578062","title":"Developmental Mitosis and Cell Division","description":"The cluster is defined by mitosis- and microtubule-related GO terms (mitotic cell cycle, microtubule nucleation, mitotic spindle pole body duplication, cell division) alongside developmental terms (angiogenesis, multicellular organism development, blastocyst development), suggesting proteins function in mitotic processes during development.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0007020","count":2},{"id":"GO:1903087","count":2},{"id":"GO:0051301","count":2}]},{"hash":"717255593488156701","title":"Unknown","description":"The listed terms include SMAD signaling, transcription initiation by RNA polymerase II and III, ascospore formation regulation, pheromone-related transcription regulation, actin-related cytoskeletal processes (mitotic contractile ring assembly, vesicle transport along actin), vacuole inheritance, and organ identity maintenance. The functions are diverse and only loosely connected through general cellular processes, so there is no clear, single theme to define a concise label.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060395","count":1},{"id":"GO:0060261","count":1},{"id":"GO:0075297","count":1},{"id":"GO:0007329","count":1},{"id":"GO:0070898","count":1}]},{"hash":"1213034510178395343","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by terms related to protein synthesis and ribosome assembly, including translation, ribosome biogenesis, ribosomal small subunit assembly, and translational fidelity/termination, indicating a core theme of the ribosome machinery and mRNA translation. A couple of outlier terms (viral genome replication, RNA decay) are less representative but do not override the main signal.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":2},{"id":"GO:0006407","count":2},{"id":"GO:0000028","count":2},{"id":"GO:0019079","count":1}]},{"hash":"1506088633015983242","title":"Innate Immune Activation and Antigen Presentation","description":"These proteins cluster around innate immune signaling and antigen processing/presentation: innate immune response-activating signaling, peptide antigen assembly with MHC class I, and positive regulation of phagocytosis, along with ER unfolded protein response and cellular senescence that often accompany immune and stress signaling. Some terms appear less related (developmental or reproductive), suggesting some annotation breadth, but the core theme is immune activation and antigen presentation.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"protein folding","top_go_terms":[{"id":"GO:0048916","count":4},{"id":"GO:0002502","count":4},{"id":"GO:0010204","count":4},{"id":"GO:0071157","count":4},{"id":"GO:0030968","count":4}]},{"hash":"1878027751380628435","title":"DNA Damage Response and Repair","description":"Top GO terms cluster around DNA repair and damage signaling (nucleotide-excision repair, SOS response, DNA integrity checkpoints) and responses to ionizing radiation, with supportive signals for telomere maintenance and cell-cycle regulation. The overall theme suggests a DNA damage response/repair functional cluster, despite a few terms that are less directly linked.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":3},{"id":"GO:0000722","count":2},{"id":"GO:0009432","count":2},{"id":"GO:0006363","count":2},{"id":"GO:0031573","count":1}]},{"hash":"1258648384500022817","title":"Ribosome biogenesis and cell cycle","description":"The cluster is dominated by GO terms for ribosome biogenesis and components of the cell cycle (cell division, mitotic cell cycle, cell cycle), with supporting terms for ribosomal subunit biogenesis and tRNA modification, suggesting a cohesive module governing growth-related protein synthesis and proliferation. A concise label focusing on ribosome assembly and cell cycle captures the core theme.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000747","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0000398","count":2}]},{"hash":"1160879963526641009","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":2},{"id":"GO:0006407","count":2},{"id":"GO:0001649","count":2},{"id":"GO:0000462","count":2}]},{"hash":"661734032640378030","title":"Unknown","description":"The GO terms across this cluster are highly heterogeneous (lymphangiogenesis, cell adhesion, glycogen regulation, transcription termination, cytokinesis localization, kinetochore-microtubule attachment, glucose signaling, apoptosis, DNA repeat maintenance, neuron differentiation), showing no single cohesive function or pathway. Therefore there is no clear, representative theme to name the cluster. ","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001946","count":3},{"id":"GO:0098609","count":2},{"id":"GO:0005979","count":2},{"id":"GO:0030846","count":2},{"id":"GO:1901901","count":2}]},{"hash":"379971082403113293","title":"RNA processing and translation initiation","description":"The terms cluster around mRNA maturation (polyadenylation, splicing, export) and translation machinery (reinitiation, preinitiation complex formation), indicating a cohesive set of proteins involved in RNA processing and initiation/resumption of translation.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0006406","count":2}]},{"hash":"503273316568590096","title":"Broad negative regulation of signaling and trafficking","description":"The cluster centers on negative regulation across diverse signaling and trafficking-related processes (TLR3 signaling, endocytosis, store-operated calcium channels, ER-stress\u2013induced apoptotic signaling, proteasomal degradation, and spontaneous neurotransmitter secretion). A few terms are positive regulators (erythrocyte differentiation, TNF-mediated signaling), but the dominant pattern is broad suppression/modulation of signaling and turnover pathways, suggesting a regulatory module that dampens multiple signaling routes.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0034140","count":3},{"id":"GO:1904049","count":3},{"id":"GO:0045648","count":3},{"id":"GO:1901799","count":3},{"id":"GO:1902236","count":3}]},{"hash":"921805838241857850","title":"Unknown","description":"GO terms across ribosome biogenesis, signaling, trafficking, development, immune processes, and cytoskeletal remodeling show no single cohesive function tying the proteins, making a concise, representative label impractical.","confidence":"","size":5,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0032147","count":2},{"id":"GO:0061059","count":2},{"id":"GO:0010227","count":1},{"id":"GO:0060999","count":1}]},{"hash":"1869347496858424770","title":"Viral replication and latency","description":"This cluster centers on viral infection processes. The top terms include establishment of proviral latency, viral life cycle, host-mediated activation of viral genome replication, RNA-templated DNA biosynthetic process (reverse transcription), and uncoating of virus, suggesting proteins involved in viral replication and latency control. A few terms like sepal formation or leukocyte migration may be incidental or reflect general host response, but the dominant theme is virus-host interaction and stages of viral replication and latency.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030466","count":2},{"id":"GO:0075713","count":1},{"id":"GO:0048453","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0006278","count":1}]},{"hash":"564215525789783794","title":"Prostaglandin and retinoid biosynthesis in development","description":"The top terms emphasize prostaglandin biosynthesis and retinoic acid biosynthesis, plus related retinoid metabolism and vitamin D biosynthesis, with accompanying terms for uterus and female gonad development. This pattern points to a cluster of proteins involved in lipid mediator and retinoid pathways that may influence developmental processes, including reproductive tissues, while some other terms appear incidental.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":5},{"id":"GO:0071615","count":3},{"id":"GO:0042904","count":3},{"id":"GO:0060065","count":3},{"id":"GO:0008585","count":3}]},{"hash":"972455994809325681","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":2},{"id":"GO:0000122","count":2},{"id":"GO:1990258","count":1},{"id":"GO:0008033","count":1},{"id":"GO:0048254","count":1}]},{"hash":"1915367433697671043","title":"Transmembrane Transporters for Sugars, Ions, and Neurotransmitters","description":"This cluster is dominated by GO terms describing transmembrane transport of diverse substrates (arabinose, galactose, sialic acid, 4-hydroxyphenylacetate, nitrate/nitrite) and ions (Na+, K+), plus a term for neurotransmitter loading into synaptic vesicles, indicating a common theme of membrane transport across substrates and cellular compartments.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0015757","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0042128","count":2}]},{"hash":"691252217278633489","title":"Bacterial polysaccharide and lipid biosynthesis","description":"This cluster is dominated by GO terms for the biosynthesis of surface components and related lipid pathways, including lipopolysaccharide biosynthesis, colanic acid biosynthesis, and various UDP-sugar and GDP-mannose pathways, plus ether lipid biosynthesis. These suggest a coherent theme around carbohydrate and lipid production used for bacterial cell surfaces and membranes. A few terms about hair follicle and labyrinthine layer development appear unrelated and likely noise. Overall, the core function appears to be bacterial glycan and lipid biosynthesis, with some noise from non-matching annotations.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902987","count":5},{"id":"GO:0009103","count":3},{"id":"GO:0060716","count":3},{"id":"GO:0033499","count":3},{"id":"GO:0019878","count":3}]},{"hash":"232430267295311261","title":"Transcription Regulation and Cell Cycle","description":"The top GO terms are dominated by DNA-templated transcription and its regulation, with several entries for cell division, indicating a core theme of transcriptional control during cell proliferation. The additional terms (aggresome assembly, amyloid formation, chaperone-related folding) likely reflect protein quality control processes that can accompany nuclear functions but do not define the cluster\u2019s primary function. Overall, the cluster appears to center on transcriptional control and cell cycle activity.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0070842","count":2},{"id":"GO:0060347","count":1}]},{"hash":"368721320169714530","title":"Tissue differentiation and transcription regulation","description":"The cluster\u2019s top GO terms mainly point to differentiation programs across diverse tissues (muscle, bone, neural, plant trichomes, and reproductive structures) along with DNA-templated transcription. This suggests a general role in coordinating gene expression during development rather than a single tissue-specific function, making \u201ctissue differentiation and transcription regulation\u201d an intuitive label.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0060766","count":2},{"id":"GO:0045668","count":2},{"id":"GO:2001016","count":2},{"id":"GO:0060415","count":1}]},{"hash":"783311250069938532","title":"Neural development signaling","description":"The cluster is enriched for neural and craniofacial development signals, including neurotrophin TRK receptor signaling, optic nerve morphogenesis, and face development, along with Wnt and FGFR-related pathways. This points to a coherent theme of developmentally orchestrated signaling in neural and craniofacial tissues, despite a few additional terms that may reflect general stress responses in developing cells.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":5},{"id":"GO:0048011","count":4},{"id":"GO:0090090","count":4},{"id":"GO:0020021","count":4},{"id":"GO:0071469","count":4}]},{"hash":"2299315674634396038","title":"Neural development and growth factor signaling","description":"This cluster is dominated by neural-development related GO terms: neurotrophin TRK receptor signaling, optic nerve morphogenesis, and face development, along with FGFR and PI3K/AKT signaling. Although there are a couple of broader or less specific terms, the strongest signals point to neural development and growth factor\u2013mediated pathways.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":5},{"id":"GO:0090090","count":5},{"id":"GO:0020021","count":5},{"id":"GO:0071469","count":5},{"id":"GO:0060324","count":5}]},{"hash":"1735678699936755918","title":"Unknown","description":"GO terms span development (muscle and brain), cell adhesion, metabolism, transcription termination, mitosis, apoptosis, and DNA repeat maintenance. No single predominant function ties these proteins together, so a coherent cluster label cannot be inferred.","confidence":"","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048741","count":4},{"id":"GO:0021762","count":4},{"id":"GO:0098609","count":3},{"id":"GO:0005979","count":3},{"id":"GO:0030846","count":3}]},{"hash":"995735650730267684","title":"TGF-\u03b2/BMP signaling regulation","description":"Most terms point to negative regulation of TGF-\u03b2/BMP signaling and related SMAD activity, including receptor signaling and SMAD complex assembly, plus a cellular response to TGF-\u03b2 stimulus. A few terms about peptidyl-threonine dephosphorylation and meristem identity suggest broader regulatory roles in developmental signaling.","confidence":"High","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0030514","count":2},{"id":"GO:0042347","count":2},{"id":"GO:0061191","count":2},{"id":"GO:0000173","count":2}]},{"hash":"941941556437846880","title":"Osmoregulation and solute transport","description":"The GO terms center on water and osmotic balance (intracellular water homeostasis, cellular response to water deprivation, hyperosmotic response) and solute/ion transport (potassium transport, acetate transport) with a note on endosomal acidification, suggesting roles in ion and pH homeostasis and related trafficking. Some terms like visual perception or pancreatic secretion may reflect multifunctional annotations, but the core theme points to osmoregulation and transport processes.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009992","count":1},{"id":"GO:0007601","count":1},{"id":"GO:0072232","count":1},{"id":"GO:0080029","count":1},{"id":"GO:0006846","count":1}]},{"hash":"930146791721096373","title":"mRNA Splicing and Translation Initiation","description":"The GO terms show involvement in mRNA processing and export (spliceosome-mediated splicing, alternative splicing, mRNA export) along with translation initiation steps (formation of preinitiation complex, translation reinitiation). This suggests a cluster of proteins coordinating RNA maturation with ribosome recruitment, despite some terms being labeled obsolete in the dataset.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0006378","count":1},{"id":"GO:0006406","count":1}]},{"hash":"31612631604667892","title":"Amino acid and cofactor biosynthesis","description":"This cluster\u2019s top GO terms span several biosynthetic processes, including multiple amino acids (alanine, phenylalanine, tyrosine, histidine, lysine), biotin, heme, and sphinganine (lipid) biosynthesis, plus fatty acid transport. The common theme is broad metabolic biosynthesis of amino acids, vitamins, and related cofactors rather than a single specific pathway, so the label reflects a general biosynthetic/metabolic function. ","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015908","count":1},{"id":"GO:0042853","count":1},{"id":"GO:0033585","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0019878","count":1}]},{"hash":"1069349584195318194","title":"Ribosome Biogenesis and rRNA Processing","description":"The dominant GO terms point to ribosome assembly and rRNA maturation (ribosome biogenesis, ribosomal large subunit biogenesis, maturation and processing of LSU and SSU rRNA, ITS1 cleavage), with supportive RNA modification steps (7-methylguanosine capping, guanine-N7 methylation). While there are some cell-cycle/ubiquitin-related terms, the core of the cluster is clearly ribosome biogenesis and rRNA processing.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0036265","count":2}]},{"hash":"2092106990689029760","title":"Sulfur assimilation and cysteine biosynthesis","description":"The cluster\u2019s top GO terms include sulfate assimilation, L-cysteine biosynthetic process, and hydrogen sulfide biosynthetic process, indicating a shared role in sulfur metabolism and cysteine production. Additional terms (phosphorylation, peroxisome targeting) are present but appear ancillary to the core theme. Thus, the proteins are best represented by a sulfur amino acid biosynthesis label.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":2},{"id":"GO:0000103","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0009086","count":2},{"id":"GO:0019344","count":2}]},{"hash":"1278086136729069822","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0009103","count":1}]},{"hash":"1485476086193105931","title":"Bacterial cell envelope biogenesis","description":"The top GO terms cluster around biosynthesis of cell envelope components: peptidoglycan, lipopolysaccharide, slime layer polysaccharides, and related lipid X metabolism. Also regulation of cell shape and morphogenesis hints at coordinated envelope assembly influencing cell morphology. Together these terms point to a cohesive theme of bacterial cell wall/envelope construction rather than a single metabolic pathway.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":1},{"id":"GO:0019877","count":1},{"id":"GO:0009089","count":1},{"id":"GO:0006535","count":1},{"id":"GO:0009103","count":1}]},{"hash":"2072383399837502748","title":"Unknown","description":"The terms span potassium transport, DNA replication, neural signaling and development (neurotrophin signaling, optic nerve morphogenesis, face development), Wnt pathway regulation, and stress/toxic responses, with no single unifying biological process. The mix suggests no coherent functional theme for this cluster, so a meaningful label cannot be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006813","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0048011","count":3},{"id":"GO:0090090","count":3},{"id":"GO:0020021","count":3}]},{"hash":"2015677756017215055","title":"Plant Hormone Biosynthesis and Catabolism","description":"The top GO terms are dominated by biosynthetic and catabolic processes for major plant hormones (ethylene, gibberellin, auxin, salicylic acid), with additional signals from secondary metabolism (proanthocyanidin) and stress-related responses (hydrogen peroxide\u2013mediated programmed cell death). An outlier term (penicillin biosynthetic process) suggests some annotation noise, but the core cluster clearly centers on hormone production/turnover and related metabolic responses.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009693","count":3},{"id":"GO:1902835","count":3},{"id":"GO:0042318","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0009686","count":3}]},{"hash":"611611886071011883","title":"Water stress response and metabolism","description":"The cluster's top GO terms include response to flooding and water deprivation, suggesting abiotic water-stress signaling. Glucose metabolic process and plant-type cell wall biogenesis point to metabolic remodeling and cell-wall changes during stress. Some terms (bacillithiol/mycothiol biosynthetic processes) are odd for plants and may reflect annotation noise, so the label is a best-fit with moderate confidence.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009413","count":1},{"id":"GO:0033577","count":1},{"id":"GO:0010555","count":1},{"id":"GO:0071793","count":1},{"id":"GO:0006006","count":1}]},{"hash":"1351548623503110199","title":"Bacterial Biosynthesis Pathways","description":"The GO terms point to various microbial biosynthetic processes (lipopolysaccharide, colanic acid, poly-hydroxybutyrate, methyl-branched fatty acids, phylloquinone) suggesting a cluster of bacterial metabolism and biosynthesis functions; a few outliers exist (drug response, androgen catabolism) but the dominant theme is microbial biosynthesis.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042619","count":3},{"id":"GO:0009103","count":2},{"id":"GO:0031427","count":2},{"id":"GO:0006710","count":2}]},{"hash":"1212215946474301750","title":"Small Molecule Metabolism and Stress Response","description":"The top GO terms point to metabolism of a variety of small organic molecules (furaldehyde, sorbitol, xylitol, pyruvate to ethanol, prostaglandin, retinoic acid) plus associated stress and inflammatory responses (nitrosative stress, LPS response) and blood pressure regulation. This pattern suggests proteins in a cluster that coordinates diverse carbohydrate/alcohol and lipid metabolizing pathways with linked stress signaling, rather than a single tightly focused pathway.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0033859","count":2},{"id":"GO:0006062","count":2},{"id":"GO:0043458","count":2},{"id":"GO:0051409","count":2},{"id":"GO:0045777","count":2}]},{"hash":"456896832341889863","title":"Stress-Responsive Transcription and DNA Repair","description":"Top terms are dominated by DNA-templated transcription and cellular stress responses to metals (cadmium, copper) and oxidative stimuli (singlet oxygen, nitroglycerin), plus a DNA repair regulation term. Together these suggest a cluster of proteins involved in transcriptional programs activated by stress and potential links to DNA damage response, despite limited interaction evidence between members. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:1900462","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0000304","count":3},{"id":"GO:2001033","count":3}]},{"hash":"119438117649278659","title":"Auxin signaling and growth regulation","description":"This cluster centers on auxin biology: multiple GO terms for auxin signaling, auxin transport, and response to auxin, plus regulation of organ growth, suggesting proteins participate in auxin-mediated growth control. The transcription and intron splicing terms may reflect downstream gene regulation or incidental connections but are less central to the core auxin theme.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046620","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0009926","count":1},{"id":"GO:0009733","count":1},{"id":"GO:0006351","count":1}]},{"hash":"228128999715207302","title":"Cell Morphogenesis and Migration","description":"These proteins collectively point to dynamic cellular remodeling and movement, including dendritic spine development, sprouting angiogenesis, fibroblast migration, vesicle regulation, and Ras signaling, with additional links to mitotic exit and mitochondrion organization. The common theme is cell shape changes, cytoskeletal dynamics, and trafficking governing morphogenesis and tissue remodeling rather than a single, narrow pathway.","confidence":"Medium","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060999","count":4},{"id":"GO:0000917","count":4},{"id":"GO:0097494","count":4},{"id":"GO:1904695","count":4},{"id":"GO:0032966","count":4}]},{"hash":"1309584636561702216","title":"Embryonic and placental development","description":"The top GO terms cluster around embryonic development and placental lineage processes (trophoblast differentiation, placenta development, left-right patterning, EMT in cardiac structures, cartilage morphogenesis), pointing to broad developmental differentiation. The inclusion of rDNA heterochromatin formation and rRNA methylation hints at nucleolar/epigenetic regulation supporting these programs, reinforcing a theme of development and lineage specification. Confidence is moderate, given the mix of tissues but a clear developmental signature.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":2},{"id":"GO:0060707","count":1},{"id":"GO:0060536","count":1},{"id":"GO:0060972","count":1},{"id":"GO:0060806","count":1}]},{"hash":"1628835154599841785","title":"Neural development signaling and morphogenesis","description":"Based on GO terms, the cluster is dominated by neural development and signaling processes (optic nerve morphogenesis, face development, neurotrophin TRK receptor signaling, FGFR apoptotic signaling, and PI3K/AKT signaling). Other terms like Wnt regulation and pH response appear secondary, and one term about symbiont-mediated host transformation may be an outlier, but the central theme is neural development signaling.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048011","count":1},{"id":"GO:0090090","count":1},{"id":"GO:0020021","count":1},{"id":"GO:0071469","count":1},{"id":"GO:0060324","count":1}]},{"hash":"383031088367597915","title":"Embryonic development and metabolism","description":"The terms point to developmental processes (gastrulation, multicellular organism development, pituitary gland development) coupled with diverse metabolic pathways (folate, glutathione, mercury detox, nitrate assimilation), suggesting a cluster tied to developmental biology with metabolic activity; a few terms are obsolete, but the overall theme is development plus metabolism.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007369","count":4},{"id":"GO:0007568","count":4},{"id":"GO:0021983","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0008283","count":3}]},{"hash":"654595345413546265","title":"Neural and craniofacial development signaling","description":"The top GO terms emphasize neural signaling and growth factor pathways (neurotrophin TRK signaling, FGFR apoptotic signaling, PI3K/AKT) together with craniofacial patterning (face development, optic nerve morphogenesis) and Wnt pathway regulation, suggesting a cohesive theme of neural and craniofacial development through key signaling cascades. Some terms are broader or peripheral, but the central theme remains development and signaling in the nervous system and face/eye structures.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048011","count":2},{"id":"GO:0090090","count":2},{"id":"GO:0020021","count":2},{"id":"GO:0071469","count":2},{"id":"GO:0060324","count":2}]},{"hash":"1417411242059801620","title":"RNA Pol II Transcription and mRNA Export","description":"These GO terms cluster around transcription by RNA polymerase II and subsequent RNA processing/export steps, including DNA-templated transcription, transcription elongation, and mRNA export. A few terms are obsolete or auxiliary, but the dominant signal is nuclear transcription and mRNA maturation/export.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043085","count":1},{"id":"GO:0071033","count":1},{"id":"GO:0061179","count":1},{"id":"GO:0006368","count":1},{"id":"GO:0051568","count":1}]},{"hash":"1825388308829765182","title":"Ubiquitin/SUMO-mediated Protein Quality Control","description":"Top GO terms cluster around sumoylation, ubiquitin-dependent ERAD, and regulation of proteasomal degradation and ER stress\u2013related apoptosis, pointing to a functional group focused on protein quality control via post-translational modification and degradation pathways. While additional terms touch on signaling, development, and differentiation, they appear peripheral to the central proteostasis theme.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0034140","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0035186","count":3}]},{"hash":"1686122921874034516","title":"ER Stress and Secretory Trafficking in Viral Infection","description":"Based on the GO terms, the proteins cluster around endoplasmic reticulum processes (unfolded protein response, ER localization, COPII vesicle budding, calcium homeostasis) indicating involvement in ER stress signaling and secretory trafficking, with a context of virus\u2013host interaction.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044791","count":1},{"id":"GO:0030968","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0006987","count":1},{"id":"GO:0090114","count":1}]},{"hash":"707012959702324729","title":"RNA and protein methylation","description":"This cluster is dominated by GO terms for various methylation processes, including tRNA methylation and wobble uridine modification, rRNA modification, and multiple protein methylations (peptidyl-lysine dimethylation, N-terminal trimethylation, arginine methylation, histone methylation). Together they point to a cohesive theme of RNA and protein methylation machinery, with a plant-specific hint from chlorophyll biosynthesis, which may reflect regulatory methylation in chloroplast-related processes. Confidence in this label is High.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":3},{"id":"GO:0036068","count":3},{"id":"GO:0000154","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0018027","count":3}]},{"hash":"987778345296270476","title":"SCF/Ubiquitin Proteasome Degradation and Metal Stress Response","description":"Top terms emphasize ubiquitin-dependent proteolysis via SCF and related cell-cycle regulation, suggesting a core role in targeted protein degradation; the presence of metal/stress response terms ties this degradation machinery to cellular responses to heavy metals and oxidative stress.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0071406","count":2},{"id":"GO:0021678","count":2}]},{"hash":"1592500579225248572","title":"Growth signaling and differentiation","description":"The GO terms cluster around signaling and growth control: Wnt and Hippo pathways; regulation of transcription; angiogenesis; keratinocyte differentiation; regulation of cell proliferation; apoptotic and stress responses; and metabolic cues (glucose stimulus). This pattern suggests proteins that coordinate tissue growth, development, and responses to stress, rather than a single narrowly defined function.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":3},{"id":"GO:0045766","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0014068","count":3},{"id":"GO:0071333","count":3}]},{"hash":"1720618384814591899","title":"Mitochondrial transport and energy metabolism","description":"The top GO terms cluster around mitochondrial metabolism, especially transport of metabolites across mitochondrial membranes (citrate, ornithine, CoA, phosphate), the malate-aspartate shuttle, and energy-related responses (adaptive thermogenesis, response to fatty acids). Together these terms point to a group of proteins involved in mitochondrial transport and energy metabolism.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990314","count":3},{"id":"GO:0070542","count":3},{"id":"GO:0048250","count":3},{"id":"GO:0034198","count":3},{"id":"GO:0035349","count":3}]},{"hash":"1225493871231097447","title":"Neurodevelopmental signaling and morphogenesis","description":"The top GO terms cluster around neural development and craniofacial morphogenesis: TRK receptor signaling, optic nerve morphogenesis, face development, and Wnt signaling regulation, with supporting roles for FGF-related apoptotic signaling. While other terms touch on cell division or stress responses, the dominant pattern points to developmental signaling guiding neural and facial structure formation. ","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007100","count":5},{"id":"GO:0048011","count":4},{"id":"GO:0090090","count":4},{"id":"GO:0020021","count":4},{"id":"GO:0071469","count":4}]},{"hash":"468428490356355278","title":"Ubiquitination and transcriptional regulation","description":"The strongest GO signals are ubiquitin-mediated processes (K63-linked ubiquitination and ERAD) alongside gene-expression activities (mRNA processing and DNA-templated transcription), suggesting a cluster centered on protein quality control linked to transcriptional regulation. Some developmental and stress-response terms appear but are less prominent.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006397","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1309366038569324397","title":"Ubiquitin-Dependent ERAD and ER Stress Signaling","description":"The cluster centers on ubiquitination and deubiquitination regulation, ER-associated degradation (ERAD), and ER stress\u2013triggered apoptotic signaling, with supporting terms about interferon response, TLR signaling, endocytosis, and microtubule organization\u2014together highlighting ubiquitin-driven quality control in the ER and related stress/immune pathways.","confidence":"High","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1903094","count":4},{"id":"GO:0030433","count":4},{"id":"GO:2000157","count":4},{"id":"GO:0006468","count":3},{"id":"GO:0034140","count":3}]},{"hash":"1565036805428689784","title":"Unknown","description":"The Top Terms are highly diverse, spanning DNA repair (base-excision repair), xenobiotic and stress responses, energy metabolism, and even bacterial-specific biosynthetic processes, with several terms labeled obsolete. There is no single cohesive function linking all five proteins, so a specific biological label isn\u2019t justified. ","confidence":"","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:0006284","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0009103","count":1},{"id":"GO:0009413","count":1}]},{"hash":"1217616768555816656","title":"Plant xylan/xyloglucan biosynthesis and cell wall modification","description":"This cluster is dominated by plant-specific cell wall terms: plant-type secondary cell wall biogenesis, plant-type cell wall modification, xylan biosynthetic process, and xyloglucan metabolic process, with an additional note on xylan acetylation. A freezing-response term suggests a possible link to cold-stress\u2013related cell wall remodeling. Overall, these proteins likely function in the biosynthesis and remodeling of the plant cell wall, potentially modulated under cold conditions.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":2},{"id":"GO:0050826","count":2},{"id":"GO:0009827","count":2},{"id":"GO:0045492","count":2},{"id":"GO:0010411","count":2}]},{"hash":"1559902902343176919","title":"DNA Damage Response and Apoptosis","description":"The proteins cluster around apoptotic processes, base-excision repair, and DNA catabolic activity, with supporting signals for xenobiotic and stress-related responses, pointing to a core DNA damage response pathway and regulation of cell fate. Some other GO terms appear peripheral and do not define the main theme.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:2000466","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0090502","count":3},{"id":"GO:0006284","count":3}]},{"hash":"1244462572323094487","title":"Ubiquitin-Dependent Proteasomal Degradation","description":"This cluster is dominated by GO terms related to ubiquitination (autoubiquitination, K48- and K63-linked ubiquitination) and ubiquitin-dependent protein catabolic processes (ERAD, SCF-dependent degradation). Together these indicate a core function in tagging proteins for proteasomal degradation, with some accompanying links to related signaling pathways like NF-\u03baB. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0070534","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0031146","count":3}]},{"hash":"910153453420842452","title":"Oocyte Meiosis I Spindle Assembly","description":"This cluster is dominated by terms related to oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization, pointing to a role in meiotic spindle formation during oocyte development. The presence of ubiquitin-proteasome\u2013mediated protein turnover terms supports a cell-cycle regulatory context. Some neural development terms are present but the core theme centers on meiosis/spindle dynamics in oocytes.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":4},{"id":"GO:0021678","count":4},{"id":"GO:0006516","count":4},{"id":"GO:0051436","count":4},{"id":"GO:0046785","count":4}]},{"hash":"965084591258677600","title":"Oocyte maturation and meiotic spindle assembly","description":"The top GO terms prominently center on oocyte maturation and spindle assembly in female meiosis I, with supporting terms tied to microtubule dynamics and cell-cycle\u2013related proteolysis, suggesting a core theme around meiotic progression in oocytes and associated spindle functions. Other development terms (neural tube, ventricle development) appear ancillary to this central meiotic theme.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":5},{"id":"GO:0021678","count":5},{"id":"GO:0006516","count":5},{"id":"GO:0051436","count":5},{"id":"GO:0046785","count":5}]},{"hash":"854281048086721256","title":"Plant hormone biosynthesis and fruit ripening","description":"These proteins show enrichment across multiple phytohormone biosynthesis/catabolic processes (ethylene, gibberellin, auxin, salicylic acid) and a clear link to fruit ripening, with additional related processes like proanthocyanidin biosynthesis and oxidative-stress\u2013linked programmed cell death. This combination points to a cohesive theme centered on plant hormone metabolism and maturation rather than a single specific pathway.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009693","count":2},{"id":"GO:0042318","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009686","count":2},{"id":"GO:0045487","count":2}]},{"hash":"2295890548151044821","title":"Nitrate transport and plant hormone signaling","description":"The cluster\u2019s top GO terms cluster around nitrate transport/assimilation (nitrate/nitrite transport, nitrate assimilation, response to nitrate) and plant hormone pathways (auxin-activated signaling, gibberellic acid homeostasis), with accompanying dipeptide/oligopeptide transport. This pattern suggests a cohesive module coordinating nutrient uptake with hormonal regulation in plants; the neurotransmitter-related term appears as noise rather than a core theme. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009734","count":4},{"id":"GO:0035672","count":4},{"id":"GO:0042128","count":4},{"id":"GO:0080055","count":4},{"id":"GO:0010167","count":4}]},{"hash":"824169835910049017","title":"RNA/tRNA Modification and Ribosome Methylation","description":"The top GO terms cluster around tRNA wobble uridine modification, tRNA methylation, and various forms of methylation of ribosomal/protein substrates (e.g., N-terminal alanine trimethylation and arginine dimethylation), suggesting a shared function in RNA modification and ribosome-associated methylation processes. Some terms like vitamin E/biotin biosynthesis or cell wall-related processes appear less coherent with this theme, but the dominant signal is methylation-driven modification connected to ribosome biology. Confidence: High","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0018012","count":2},{"id":"GO:0019919","count":2},{"id":"GO:0010189","count":2}]},{"hash":"181644553874841625","title":"Unknown","description":"The terms span diverse processes (cytoskeletal dynamics, peroxisome targeting, development, nuclear transport, lipid signaling, and epigenetic marks) with no clear unifying function; several terms are obsolete, so a single representative label cannot be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:2001162","count":2},{"id":"GO:0006625","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0030042","count":2}]},{"hash":"2209925240369279487","title":"Mitotic progression and transcriptional regulation","description":"These proteins show a strong enrichment for cell cycle and mitosis-related processes, including G1/S and G2/M transitions, spindle pole dynamics, and chromosome condensation (histone H3-S10 phosphorylation). They also relate to DNA-templated transcription and mRNA processing, indicating concurrent regulation of gene expression during cell division. A few terms (e.g., mammary gland proliferation, insulin signaling) appear tangential, but the dominant pattern supports mitotic progression and transcriptional control as the cluster\u2019s core function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000775","count":2},{"id":"GO:0033598","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000320","count":2},{"id":"GO:0010696","count":2}]},{"hash":"1134890510481493112","title":"Unknown","description":"No GO terms are provided in the Top Terms, so there is no shared function to define a label. The cluster has 5 proteins with 8 edges and 5 triangles and a max degree of 4, indicating some connectivity but without functional terms the cluster cannot be named meaningfully. Therefore the label Unknown is appropriate with no confidence.","confidence":"","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[]},{"hash":"2278002590690188190","title":"Neuronal vesicle trafficking and brain development","description":"This cluster shows strong signals for synaptic vesicle exocytosis regulation, vesicle fusion, and brain development (including cortical migration), pointing to a module of proteins involved in neuronal vesicle trafficking and neural development. Some unrelated terms appear (immune signaling, obsolete terms), but the core theme aligns with neuronal synaptic functions and brain formation.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000300","count":3},{"id":"GO:0031384","count":3},{"id":"GO:0010796","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0050764","count":2}]},{"hash":"1801386869297907507","title":"DNA Damage Response and Ubiquitin Signaling","description":"The terms cluster around DNA repair and genome maintenance (NER, V(D)J recombination, mitotic checkpoint signaling) and ubiquitin/neddylation pathways (K48-linked ubiquitination, protein degradation, MVB sorting). While the list spans other processes (viral processes, septin assembly), the common theme appears to be DNA damage response coupled with ubiquitin-mediated regulation of proteins. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006293","count":1},{"id":"GO:0070936","count":1},{"id":"GO:0044810","count":1},{"id":"GO:0042981","count":1},{"id":"GO:0033151","count":1}]},{"hash":"198250029532981834","title":"Unknown","description":"The GO terms are highly diverse, spanning phagocytosis regulation, vesicle fusion, immune signaling, neuronal migration, antibiotic response, aging, reelin signaling, transcription, and RNA export, with no clear cohesive function linking all four proteins. The sparse connections (low edges/triangles) support a lack of a unifying theme. ","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0050764","count":1},{"id":"GO:0006906","count":1},{"id":"GO:0050861","count":1},{"id":"GO:0021814","count":1},{"id":"GO:0071236","count":1}]},{"hash":"1683217189062688625","title":"TLR4-MyD88 Cytokine Signaling","description":"This cluster centers on MyD88-dependent toll-like receptor signaling, detection of lipopolysaccharide, and subsequent cytokine production, with regulation of dendritic cell cytokine output and JNK cascade\u2014reflecting innate immune activation via TLR4/LPS and related cytokine pathways (including IL-6 and interferon-related regulation).","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002755","count":2},{"id":"GO:0034145","count":2},{"id":"GO:0032497","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0002374","count":2}]},{"hash":"677577673728483793","title":"Metal ion and oxidative stress response","description":"GO terms point to cellular responses to cadmium, copper, singlet oxygen, and nitroglycerin, indicating a metal ion and oxidative stress-oriented cluster. The accompanying transcription-related terms (DNA-templated transcription, transcription regulation) suggest stress-driven gene regulation, though one developmental term and some obsolete terms imply annotation noise. Overall, the core theme is metal/oxidative stress response with linked transcriptional control.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035987","count":1},{"id":"GO:1900462","count":1},{"id":"GO:0071276","count":1},{"id":"GO:0000304","count":1},{"id":"GO:2001033","count":1}]},{"hash":"2272946122249793899","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"The terms cluster around actin dynamics\u2014positive regulation of actin filament polymerization, stress fiber and formin-nucleated cable assembly, pseudopodium formation, and regulation of fibroblast migration\u2014pointing to coordinated remodeling of the cytoskeleton to enable cell movement and related exocytosis processes. Ras signaling and mitochondrial organization appear as broader context, but the core theme is actin-driven remodeling and migration.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051496","count":4},{"id":"GO:2000300","count":4},{"id":"GO:0030838","count":4},{"id":"GO:0090338","count":4},{"id":"GO:0032966","count":3}]},{"hash":"662636745999292358","title":"Iron Homeostasis and Transport","description":"This cluster centers on iron metabolism: detoxification of iron, iron transport, and siderophore-mediated iron import, pointing to iron homeostasis as the shared function. Some unrelated or obsolete GO terms are present but do not undermine the core theme.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990461","count":1},{"id":"GO:1904234","count":1},{"id":"GO:0048147","count":1},{"id":"GO:0006950","count":1},{"id":"GO:0006880","count":1}]},{"hash":"1594113853270198780","title":"Oocyte meiosis and spindle assembly","description":"This cluster is dominated by GO terms related to oocyte maturation and spindle assembly in female meiosis I, along with supporting terms for microtubule polymerization and ubiquitin-protein ligase\u2013dependent proteasomal degradation, plus negative regulation of cell proliferation. Together, they point to proteins involved in meiotic progression and spindle dynamics in oocytes, with ubiquitin-mediated proteolysis possibly modulating meiotic transitions.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":4},{"id":"GO:0006516","count":4},{"id":"GO:0008285","count":4},{"id":"GO:0007057","count":4},{"id":"GO:0051436","count":4}]},{"hash":"1552846535338757395","title":"Oocyte maturation and meiosis spindle assembly","description":"These GO terms cluster around meiotic progression and spindle assembly in oocytes (e.g., oocyte maturation, spindle assembly in female meiosis I, microtubule polymerization), with additional hints from ubiquitin-proteasome\u2013mediated protein turnover and broader early development signals (neural tube/ventricle development). The core theme appears to be meiosis/oocyte development, supported by microtubule dynamics and proteolysis pathways.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":1},{"id":"GO:0021678","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0051436","count":1},{"id":"GO:0046785","count":1}]},{"hash":"1860414283831755468","title":"Microtubule-based transport and dynamics","description":"This cluster groups proteins linked to microtubule motor activity and remodeling: chloroplast movement, regulation of microtubule-based processes, plus-end directed transport, spindle and kinetochore dynamics, cytokinesis, and axonemal depolymerization. The convergence on plus-end dynamics, motor-driven vesicle transport, and spindle/mitotic events suggests a coherent theme of microtubule-dependent movement and remodeling.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009904","count":2},{"id":"GO:0032886","count":2},{"id":"GO:0098971","count":2},{"id":"GO:0070462","count":2},{"id":"GO:0000742","count":2}]},{"hash":"1698171630328693317","title":"Unknown","description":"The GO terms span several unrelated processes (lipopolysaccharide and carbohydrate biosynthesis, multiple metal ion transports, hormone response, P450 epoxygenase pathway, and dephosphorylation) with no single cohesive function evident for all four proteins. Because there isn\u2019t a clear shared theme, a generic Unknown label with no confidence is most appropriate.","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0009103","count":4},{"id":"GO:0070574","count":4},{"id":"GO:0046295","count":4},{"id":"GO:0046380","count":4},{"id":"GO:0006825","count":4}]},{"hash":"1703340681764301837","title":"Unknown","description":"The GO terms are spread across multiple, seemingly unrelated processes (protein folding/chaperone activity, amyloid fibril formation, cell division, heart and muscle development, TGF-beta signaling, and immune cell proliferation), with several obsolete annotations. There is no clear single function or pathway that ties these 4 proteins together, so a specific, confident label cannot be assigned. ","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0022417","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0051301","count":1},{"id":"GO:0060347","count":1},{"id":"GO:0061077","count":1}]},{"hash":"1409389559217209213","title":"Ribosome biogenesis and translation","description":"The strongest signals are translation and ribosome biogenesis, with supporting RNA modification terms (rRNA and tRNA wobble), pointing to a core function in ribosome assembly and protein synthesis. Peripheral terms like chlorophyll biosynthesis and methylation appear less central. Confidence: High","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0002098","count":1},{"id":"GO:0036068","count":1},{"id":"GO:0000154","count":1}]},{"hash":"464613263011297034","title":"Root cap vacuolar amino acid transport","description":"This cluster centers on amino acid transport across vacuolar membranes (lysine, histidine, asparagine) and their import/export in cells likely from root cap tissue, with additional GO terms pointing to oxidative stress and nutrient starvation responses common in plant cells. The strongest signal is vacuolar transport of amino acids in a root-related context, supporting a specific label around root cap vacuolar transport.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071447","count":1},{"id":"GO:1903204","count":1},{"id":"GO:1902083","count":1},{"id":"GO:2000487","count":1},{"id":"GO:0006867","count":1}]},{"hash":"1091325248961420475","title":"Cofactor biosynthesis and nucleotide metabolism","description":"This cluster\u2019s GO terms cluster around biosynthesis of essential cofactors (molybdopterin cofactor, lipoate, menaquinone, porphyrinogen IX, pyrroloquinoline quinone) and nucleotide-related metabolism (adenosine metabolism, purine catabolism), with phosphorylation/dephosphorylation also appearing as a general metabolic signal. The common theme appears to be metabolic pathways for cofactors and nucleotides, supporting a cohesive functional group.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046085","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0006195","count":1},{"id":"GO:0042426","count":1}]},{"hash":"2196822654545991537","title":"Transsulfuration and Cysteine Metabolism","description":"This cluster's GO terms cluster around sulfur amino acid pathways: transsulfuration, hydrogen sulfide production, and cysteine/homocysteine catabolism/biosynthesis, with supporting serine/threonine metabolism. The shared theme suggests proteins participate in the synthesis and degradation of cysteine and related sulfur-containing amino acids.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0018871","count":1},{"id":"GO:0046360","count":1},{"id":"GO:0043418","count":1},{"id":"GO:0006535","count":1},{"id":"GO:0009088","count":1}]},{"hash":"816053390061170856","title":"Mitochondrial lipid remodeling and biosynthesis","description":"This cluster's terms are dominated by lipid metabolism and remodeling. Key processes include phosphatidylcholine biosynthesis and acyl-chain remodeling, ether lipid biosynthesis, cardiolipin remodeling, and CDP-diacylglycerol biosynthesis, pointing to glycerophospholipid homeostasis. The link to mitochondrial ATP synthesis coupled electron transport reinforces a mitochondrial lipid context, likely tied to cardiolipin function. A couple of terms about glandular epithelial maturation and IL-2 production are less directly connected and may reflect broader cellular contexts or annotation overlaps.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2001246","count":3},{"id":"GO:0002071","count":3},{"id":"GO:0070970","count":3},{"id":"GO:0035965","count":3},{"id":"GO:0016024","count":3}]},{"hash":"2205893418035340614","title":"mRNA maturation and translation initiation","description":"The top GO terms point to multiple stages of mRNA processing\u2014splicing (spliceosome), polyadenylation, and nuclear export\u2014alongside processes related to translation initiation and reinitiation. This suggests the proteins function together in mRNA maturation and the formation or regulation of the translation initiation machinery, with some terms flagged as obsolete in the dataset. Confidence reflects coherent but modest evidence across several related processes.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":3},{"id":"GO:1900363","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0006378","count":2}]},{"hash":"914332482232778000","title":"Auxin-responsive gene expression and translation","description":"The terms point to auxin signaling and response (auxin-activated signaling, response to auxin, auxin polar transport) intertwined with general and mitochondrial translation and transcription elongation/regulation, suggesting a module where auxin cues influence gene expression at both transcriptional and translational levels, impacting organ growth.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046620","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0009926","count":1},{"id":"GO:0009733","count":1}]},{"hash":"1643814031443663955","title":"Organelle RNA Editing & Modification","description":"This cluster centers on RNA modification and editing, especially in mitochondria and chloroplasts (mitochondrial mRNA modification, chloroplast RNA modification, cytidine-to-uridine editing, and regulation of mitochondrial RNA catabolic processes). A couple terms relate to other processes (plant cell wall assembly, fatty acid transport), but the dominant signal is organelle RNA processing/modification.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071668","count":1},{"id":"GO:1902001","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0070453","count":1},{"id":"GO:0009451","count":1}]},{"hash":"141231182738996067","title":"Chloroplast Light-Harvesting and Stress-Response Proteins","description":"This cluster shows strong signals for photosynthesis and light harvesting (GO:0015979, GO:0009768) and for oxidative stress response (GO:0070301) as well as protein maintenance (GO:0030091, GO:0006464) and repair, pointing to chloroplast-associated proteins involved in energy capture and protection against reactive oxygen species. Some terms like monocyte differentiation and transcription regulation are broader or cross-species annotations, but the dominant theme is chloroplast-related photosynthetic function plus stress resilience.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:1990355","count":1},{"id":"GO:0006464","count":1},{"id":"GO:0030091","count":1},{"id":"GO:0070301","count":1}]},{"hash":"2367778796385946","title":"Central carbon metabolism and fatty acid biosynthesis","description":"The proteins in this cluster are linked primarily to core energy and carbon-flow pathways: glycolysis, gluconeogenesis, pyruvate decarboxylation to acetyl-CoA, the TCA cycle, and subsequent steps leading to fatty acid biosynthesis and malonyl-CoA production. Some catabolic routes for amino acids (leucine, lysine) feeding into acetyl-CoA are present, which reinforces the acetyl-CoA\u2013driven metabolism theme. A couple of outlier terms (fruit ripening and sodium transport) and an obsolete GO term are present, but the dominant signal is central carbon metabolism funneling into lipid biosynthesis. ","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":2},{"id":"GO:0033512","count":2},{"id":"GO:0009835","count":2},{"id":"GO:0006552","count":1},{"id":"GO:0006099","count":1}]},{"hash":"715331034866058709","title":"Mitotic spindle dynamics and microtubule regulation","description":"The top GO terms cluster strongly around microtubule-based processes involved in mitosis and spindle function\u2014centrosome/spindle pole separation, kinetochore attachment, and cytokinesis\u2014along with plus-end depolymerization and broader microtubule regulation. A few terms reference organelle/membrane movement still governed by microtubules, but the common thread is microtubule dynamics guiding cell division.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:0007100","count":3},{"id":"GO:0009904","count":2},{"id":"GO:0032886","count":2},{"id":"GO:0098971","count":2}]},{"hash":"230773814199037080","title":"ER Stress and Protein Quality Control","description":"The GO terms cluster around endoplasmic reticulum (ER) protein handling: ubiquitin-dependent ERAD, misfolded protein transport, ER stress\u2013driven translation initiation, and nuclear/ubiquitin-proteasome quality control. Together these point to a function in ER-associated protein quality control and maintenance of proteostasis. A few terms (DNA replication, sodium ion transport) seem peripheral or outdated, but the dominant theme remains ER quality control.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0006814","count":2},{"id":"GO:0036494","count":1}]},{"hash":"1093422011879893211","title":"Tetrapyrrole Biosynthesis (heme and chlorophyll)","description":"The cluster is dominated by GO terms for protoporphyrinogen IX biosynthetic, heme biosynthetic, and chlorophyll biosynthetic processes, pointing to tetrapyrrole production essential for heme and photosynthetic pigments. Supporting terms about proton-motive-force\u2013driven ATP synthesis and ion transport fit with energy metabolism in plastids/mitochondria, reinforcing a cohesive plant-energy/pigment biosynthesis theme; pollen development appears as a plant-specific context but does not override the main signal. ","confidence":"High","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006782","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0015995","count":1},{"id":"GO:0009555","count":1}]},{"hash":"1679333010696485962","title":"Synaptic vesicle cycling and GPCR trafficking","description":"Several GO terms point to neuronal synaptic processes: GABAergic synaptic transmission, positive regulation of synaptic vesicle recycling, and GPCR internalization, suggesting the proteins cluster around synaptic vesicle trafficking and receptor endocytosis. Other terms appear less related (muscle development, peroxisome organization), but the core theme is neuronal vesicle cycling.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901741","count":2},{"id":"GO:1900063","count":1},{"id":"GO:0060988","count":1},{"id":"GO:0051932","count":1},{"id":"GO:0003281","count":1}]},{"hash":"1899029683792916134","title":"Organelle translation and protein import","description":"The top GO terms cluster around translation-related processes (valyl-tRNA aminoacylation, translation initiation, RNA polymerase III transcription) and targeting/import into organelles (chloroplast stroma, mitochondrial matrix/inner membrane), plus chloroplast photosystem I activity. This suggests a theme of proteins involved in organelle-localized synthesis and trafficking, rather than a single cytosolic pathway, with a minor note of ER-stress\u2011related translation. Therefore, the label Organelle translation and protein import fits best.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006438","count":1},{"id":"GO:0009773","count":1},{"id":"GO:0045037","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0000002","count":1}]},{"hash":"2138585652263230000","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0007568","count":1},{"id":"GO:0071276","count":1},{"id":"GO:0045008","count":1},{"id":"GO:0043066","count":1}]},{"hash":"1137147946190831606","title":"Ribosome biogenesis and translation","description":"This cluster centers on ribosome assembly and protein synthesis, with GO terms spanning ribosome biogenesis, ribosomal subunit biogenesis, cytoplasmic translation, translational elongation and termination, and even mitochondrial translation, plus regulatory aspects of translation. The convergence on both ribosome construction and active translation suggests proteins linked to the ribosome machinery and translation control.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0042274","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0070125","count":1},{"id":"GO:0045901","count":1}]},{"hash":"1751357963867171133","title":"Neuronal endosomal trafficking and synaptic regulation","description":"These proteins show functions tied to endosomal/lysosomal transport and retrograde trafficking, combined with roles in synaptic maintenance and organization (dendritic spines, terminal boutons). The inclusion of dopamine receptor signaling and Wnt pathway regulation suggests modulation of neuronal signaling via endosomal trafficking. Overall, the cluster centers on neuronal endosomal pathways that support synaptic structure and signaling.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1905166","count":1},{"id":"GO:1902823","count":1},{"id":"GO:0090326","count":1},{"id":"GO:1902950","count":1},{"id":"GO:0031648","count":1}]},{"hash":"609015923812384588","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0070126","count":2},{"id":"GO:0042254","count":1},{"id":"GO:0006407","count":1},{"id":"GO:0000028","count":1}]},{"hash":"1860942833118204248","title":"Ribosome biogenesis and RNA processing","description":"The top terms are dominated by RNA-centric processes: mRNA processing and stability, spliceosome assembly, 90S preribosome assembly, rRNA processing, and box C/D snoRNP assembly, all pointing to ribosome biogenesis and RNA maturation. A couple developmental and DNA damage response terms are peripheral to the core function. ","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0000354","count":1},{"id":"GO:0007438","count":1},{"id":"GO:0006397","count":1}]},{"hash":"1682013467934246671","title":"Neurodevelopmental signaling and morphogenesis","description":"The top GO terms point to neural development and signaling pathways (neurotrophin TRK signaling, optic nerve morphogenesis, face development, Wnt and FGFR signaling) plus related development processes, suggesting a cluster involved in neural patterning and morphogenesis. Some terms about nuclear export and toxin response are peripheral but do not override the central developmental signaling theme.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0048011","count":3},{"id":"GO:0090090","count":3},{"id":"GO:0020021","count":3},{"id":"GO:0071469","count":3}]},{"hash":"309185296784379933","title":"RNA processing and translation","description":"These proteins appear linked to RNA metabolism and protein synthesis: spliceosome assembly, mRNA splicing, SSU-rRNA maturation, P-body assembly, and translation initiation. This points to a common theme of post-transcriptional gene expression control. Some chromatin-related terms and osteoblast differentiation appear less directly connected, possibly reflecting broader regulatory context or annotation noise.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":2},{"id":"GO:0001649","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006413","count":1}]},{"hash":"953906167737222228","title":"GABAergic synapse components","description":"The GO terms point to GABA secretion, receptor localization to synapse, and neurotransmitter-gated ion channel clustering, indicating a focus on GABAergic synaptic signaling and organization. Some other terms (adherens junctions, cardiac action potentials) appear tangential or incidental, but the dominant pattern supports a label centered on GABAergic synapses. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903760","count":3},{"id":"GO:0014051","count":3},{"id":"GO:0045186","count":3},{"id":"GO:1903753","count":3},{"id":"GO:0098912","count":3}]},{"hash":"1934803987945892114","title":"Malate and Pyruvate Metabolism Cluster","description":"The top GO terms are dominated by malate and pyruvate metabolic processes, with related NADP metabolism, suggesting a central carbon metabolism theme. A few terms (antibiotic/phosphinothricin biosynthesis, plasmodesmata transport) appear unrelated and may reflect annotation noise, but the core cluster centers on malate/pyruvate pathways. Confidence: Medium.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043464","count":1},{"id":"GO:0051262","count":1},{"id":"GO:0006108","count":1},{"id":"GO:1902031","count":1},{"id":"GO:0006090","count":1}]},{"hash":"1136509879895276558","title":"Epigenetic Regulation in Development","description":"GO terms cluster around gene expression control (negative regulation of transcription, histone methylation, DNA methylation) and various developmental/differentiation processes (neuron maturation, astrocyte differentiation, ventricular system development, pituitary gland development). Although some terms are plant-specific or obsolete, the common thread is epigenetic tuning of development and cell differentiation.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048712","count":2},{"id":"GO:2000820","count":2},{"id":"GO:2001038","count":2},{"id":"GO:0010228","count":2},{"id":"GO:0021591","count":1}]},{"hash":"128016083495750304","title":"Cardiac and Muscle Morphogenesis","description":"The cluster\u2019s GO terms mainly point to muscle and heart development, with strong signals for muscle tissue morphogenesis (GO:0060415), cardioblast migration (GO:0003259), and cardiac atrium formation (GO:0003210), plus integrin-mediated cell adhesion (GO:0033627) which supports tissue morphogenesis. While other terms touch neural differentiation and regulatory pathways (circadian regulation of gene expression, SREBP signaling), the prevailing theme is cardiac/muscle development and differentiation, with some ancillary signals from other lineages.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060415","count":4},{"id":"GO:0060163","count":4},{"id":"GO:0033627","count":4},{"id":"GO:0032922","count":4},{"id":"GO:0048712","count":4}]},{"hash":"165650506785826405","title":"Chromatin organization and heterochromatin maintenance","description":"The top GO terms are centered on chromatin structure and regulation: nucleosome positioning/density, DNA methylation-dependent heterochromatin formation, rDNA heterochromatin formation, and histone deacetylation, with additional signals for DNA-templated transcription and sister chromatid cohesion. These collectively point to a coherent theme of chromatin organization and maintenance of heterochromatin state, suggesting the proteins participate in chromatin remodeling and transcriptional silencing rather than cytosolic pathways.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016584","count":2},{"id":"GO:0006346","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070933","count":2},{"id":"GO:0000183","count":2}]},{"hash":"1866543397205779774","title":"Chromatin organization and transcription regulation","description":"These proteins show a cohesive theme around chromatin state maintenance and transcription control, with GO terms for heterochromatin formation/maintenance, DNA methylation-dependent chromatin regulation, nucleosome positioning, and transcriptional repression by RNA polymerase I. Some terms about signaling or development are present, but the strongest signal is chromatin organization and gene expression regulation.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010882","count":4},{"id":"GO:0016584","count":4},{"id":"GO:0031647","count":4},{"id":"GO:0007062","count":4},{"id":"GO:0006344","count":4}]},{"hash":"1236925674731386489","title":"Cardiac Muscle Development and Morphogenesis","description":"The cluster is dominated by terms tied to heart and muscle development, including muscle tissue morphogenesis, cardioblast migration, and atrium formation, plus integrin-mediated cell adhesion relevant to muscle/heart tissue morphogenesis. Some neural differentiation terms appear but do not override the core cardiac/muscle theme. Confidence: High","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060415","count":4},{"id":"GO:0060163","count":4},{"id":"GO:0033627","count":4},{"id":"GO:0032922","count":4},{"id":"GO:0048712","count":4}]},{"hash":"1392220917074013487","title":"Plant secondary metabolism and cell wall biosynthesis","description":"Top GO terms cluster around plant-specific pathways such as flavonoid, lignin, and cutin biosynthesis, indicating a coherent theme of plant secondary metabolism and protective barrier formation. A few vertebrate-related terms appear at low frequency, suggesting some noise or cross-annotation, so the label is reasonable but not perfect.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009963","count":2},{"id":"GO:0080088","count":2},{"id":"GO:0010252","count":2},{"id":"GO:0009809","count":2},{"id":"GO:0010143","count":2}]},{"hash":"1349849813832494558","title":"Neurodevelopmental Signaling and Morphogenesis","description":"This cluster centers on neural and craniofacial development cues, with terms for neurotrophin TRK signaling, optic nerve and face morphogenesis, and repression/activation of Wnt and PI3K/AKT pathways, plus cytoskeletal dynamics, suggesting coordinated signaling driving neural crest\u2013related morphogenesis and neural development.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":4},{"id":"GO:0090090","count":4},{"id":"GO:0020021","count":4},{"id":"GO:0071469","count":4},{"id":"GO:0060324","count":4}]},{"hash":"1747009750957510147","title":"Tissue Development and Differentiation","description":"Top terms point to broad developmental processes (multicellular development, angiogenesis, Schwann cell development, myoblast fusion) and tissue-specific functions (visual perception, excitatory signaling). The cluster appears to assemble proteins involved in morphogenesis and lineage differentiation across muscle, nerve, vasculature, and sensory tissues, with supporting cues from signaling and cell-cycle regulation. This common theme supports a label of tissue development and differentiation.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0009738","count":3},{"id":"GO:0007601","count":3}]},{"hash":"1739956384308307374","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0071787","count":3},{"id":"GO:1905869","count":3}]},{"hash":"1507593055640062234","title":"Glycolysis and Gluconeogenesis","description":"The top terms include canonical glycolysis (GO:0061621) and gluconeogenesis (GO:0006094), pointing to central carbohydrate metabolism and energy production. Other terms (urine volume regulation, renal development, cadmium response) are less cohesive with this theme and may reflect annotation noise or broad functions. Overall, the cluster appears driven by glycolytic and gluconeogenic activity, justifying a label focused on carbohydrate metabolism.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0061621","count":2},{"id":"GO:0035809","count":1},{"id":"GO:0018931","count":1}]},{"hash":"1169965148920176877","title":"ER stress response and protein folding","description":"The GO terms prominent in this cluster point to ER-associated protein handling and stress response, including cellular response to unfolded protein, SRP-dependent cotranslational targeting to the membrane and translocation to the ER, and negative regulation of ER-stress\u2013induced apoptotic signaling. While a few terms (DNA replication, karyogamy, iron-sulfur cluster assembly) are less clearly connected, the dominant theme is ER protein quality control and unfolded protein response.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0016226","count":1},{"id":"GO:1900035","count":1},{"id":"GO:0000902","count":1}]},{"hash":"1919268508208668538","title":"RNA Splicing and Translation Reinitiation","description":"The cluster\u2019s top GO terms are dominated by RNA processing and splicing via the spliceosome (alternative splicing, cis splicing, and splicing regulation) and mRNA export, with additional terms related to translation reinitiation (including viral contexts). A single nitrate assimilation term appears as an outlier, but the prevailing signal points to RNA maturation and translation control. Confidence: Medium","confidence":"","size":4,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:1900363","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0006378","count":1}]},{"hash":"183466416501111996","title":"DNA replication, repair, and transcription regulation cluster","description":"This cluster is dominated by GO terms related to DNA replication (including primer synthesis), regulation of DNA-templated transcription, and DNA repair (double-strand break repair via synthesis-dependent strand annealing). A few terms refer to obsolete or unrelated biosynthetic processes, likely annotation noise; overall, the proteins appear linked to DNA metabolism and its regulation.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006269","count":2},{"id":"GO:0045003","count":2},{"id":"GO:0006268","count":2}]},{"hash":"607735813146163536","title":"Wnt-regulated developmental signaling","description":"The top terms center on modulation of the canonical Wnt pathway, including negative regulation of Wnt signaling, along with several development-related terms spanning neural, sensory, and organ development (e.g., superior colliculus, fungiform papilla, hair follicle placode, renal outer medulla). This suggests the cluster reflects proteins involved in regulating Wnt signaling during development. A few terms (ERAD, vacuole inheritance, indole-3-methanol response) are less connected and may reflect annotation noise or broader roles, so the overall connection is moderate.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0071681","count":2},{"id":"GO:0061380","count":2},{"id":"GO:0000011","count":2},{"id":"GO:0044336","count":2}]},{"hash":"1385994967918538631","title":"Lipid metabolism and energy production","description":"This cluster centers on metabolic processes related to lipid biosynthesis and lipid-associated energy pathways (triglyceride and glycerophospholipid metabolism, glycerol-3-phosphate shuttle/catabolism, gluconeogenesis, NADPH regeneration, pantothenate/CoA biosynthesis), with a peroxisomal import angle. The GO terms collectively point to metabolism and energy production rather than a single specific enzymatic function, supporting a broad \u201clipid metabolism and energy production\u201d theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0046168","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0019432","count":1}]},{"hash":"66842215732306462","title":"Bacterial lipid and secondary metabolite biosynthesis","description":"The GO terms cluster around bacterial biosynthetic pathways, including fatty acid and lipoteichoic acid synthesis for membranes, menaquinone and long-chain fatty acid metabolism, nondribosomal peptide and siderophore biosynthesis, and related aromatic compound metabolism, which together point to lipid and secondary metabolite biosynthesis in bacteria.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043041","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0036112","count":2},{"id":"GO:0009698","count":2},{"id":"GO:0070395","count":2}]},{"hash":"849693142658104220","title":"Retinoic Acid Signaling in Embryogenesis","description":"The top GO terms cluster around retinoic acid biology (9-cis-retinoic acid biosynthesis and retinoic acid receptor signaling) together with numerous embryonic development processes across tissues (forebrain, pituitary, midgut, inner ear morphogenesis, pattern formation). This points to RA-mediated regulation of vertebrate embryonic development as the cohesive theme, with a secondary hypoxia response term present but not central. Confidence reflects a coherent link between RA signaling and developmental patterning in the cluster.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042904","count":4},{"id":"GO:0021983","count":4},{"id":"GO:0036293","count":4},{"id":"GO:0048384","count":4},{"id":"GO:0048566","count":4}]},{"hash":"1509407345882002571","title":"Bacterial polysaccharide and lipid biosynthesis","description":"Reasoning: The top GO terms cluster around biosynthetic processes for surface polysaccharides (lipopolysaccharide, colanic acid, UDP-xylose, galactose metabolism) and ether lipids, suggesting a shared role in producing envelope components in bacteria. Some terms are unrelated or obsolete noise, but the predominant theme is biosynthesis of polysaccharides and lipids.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0006556","count":3},{"id":"GO:0060716","count":3},{"id":"GO:0033499","count":3},{"id":"GO:0019878","count":3}]},{"hash":"632377307394362018","title":"DNA Repair and Redox Homeostasis","description":"The cluster prominently features GO terms for nucleotide-excision repair, cell redox homeostasis, and cellular oxidant detoxification, pointing to a function in maintaining genome integrity under oxidative stress. While other terms in the set (e.g., development and neuronal guidance) are present at low counts and may reflect broader or incidental annotations, the shared emphasis on DNA repair and redox balance best explains the cluster\u2019s core function.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070527","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0098869","count":2},{"id":"GO:2000691","count":1}]},{"hash":"716677244820980530","title":"DNA Replication and Chromosome Maintenance","description":"Based on the prominent GO terms dominated by DNA replication and chromosome maintenance (DNA replication; DNA-templated replication; primer synthesis; fork progression; rDNA maintenance; sister chromatid segregation; meiotic recombination intermediate resolution), the proteins in this cluster are best described as components of the DNA replication machinery and chromosome maintenance processes. The inclusion of related chromosomal dynamics terms supports a cohesive theme around replication and chromosome stability, despite the small cluster size and lack of reported interactions.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006261","count":1},{"id":"GO:0006265","count":1},{"id":"GO:0045870","count":1},{"id":"GO:0030263","count":1}]},{"hash":"406732795713670795","title":"Seed lipid metabolism and cold response","description":"The top GO terms point to seed-specific lipid storage and oilbody biogenesis, with an additional annotation for freezing response and related metabolic regulation. Although some transcriptional regulation terms (including obsolete ones) appear, the dominant theme centers on plant seed lipid metabolism and abiotic stress adaptation, suggesting these proteins cluster around seed oil production and cold response pathways.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019915","count":1},{"id":"GO:0009859","count":1},{"id":"GO:0010344","count":1},{"id":"GO:0050826","count":1},{"id":"GO:0043966","count":1}]},{"hash":"1077674509675843170","title":"Fungal Cell Wall Biosynthesis and Septum Assembly","description":"This cluster is defined by GO terms for fungal-type cell wall assembly and beta-D-glucan biosynthesis, along with division septum assembly, indicating proteins involved in fungal cell wall construction and septum formation during cytokinesis.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000917","count":1},{"id":"GO:0071970","count":1},{"id":"GO:0071940","count":1}]},{"hash":"1825174215869688837","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms related to ubiquitination and proteasomal degradation, including K48-linked ubiquitination, ubiquitin-dependent protein catabolic processes, ubiquitin-dependent ERAD, and protein autoubiquitination. Additional terms about receptor turnover (Wnt receptor catabolic process) and organ growth regulation fit with the theme of regulated protein degradation impacting signaling and growth, while peroxisomal import is a less central association. Overall, the clearest common function among the set is ubiquitin-mediated protein turnover.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046621","count":3},{"id":"GO:0070936","count":3},{"id":"GO:0060816","count":3},{"id":"GO:0038018","count":3},{"id":"GO:0051865","count":3}]},{"hash":"1959053815825000887","title":"Oocyte meiosis and spindle assembly","description":"These proteins are mainly linked to oocyte maturation, spindle assembly in female meiosis I, and microtubule dynamics, with supporting connections to ubiquitin-proteasome\u2013dependent protein turnover and cell-cycle regulation. While a few neural-development terms appear, the strongest common theme is coordination of meiosis/spindle formation during oocyte maturation.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":3},{"id":"GO:0021678","count":3},{"id":"GO:0006516","count":3},{"id":"GO:0051436","count":3},{"id":"GO:0046785","count":3}]},{"hash":"1755153671749046042","title":"Nucleotide Salvage and DNA Biosynthesis","description":"The top GO terms cluster around deoxyribonucleoside metabolism and nucleotide biosynthesis, including salvage pathways for deoxycytidine and deoxyguanosine, dGTP/pyrimidine nucleotide metabolism, and the DNA biosynthetic process. These together point to a function group focused on generating and recycling DNA building blocks, with a secondary note of chromosome organization and phosphorylation being less central in this cluster.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006193","count":1},{"id":"GO:0051276","count":1},{"id":"GO:0009213","count":1},{"id":"GO:0046092","count":1},{"id":"GO:0006180","count":1}]},{"hash":"498035116813111435","title":"Unknown","description":"The GO terms span diverse processes (ion transport, RNA processing, immune regulation, retina development, cytokine response, and metabolism) with little overlap, making it unlikely to assign a single coherent function to this small cluster.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006813","count":2},{"id":"GO:0044829","count":1},{"id":"GO:0000289","count":1},{"id":"GO:0045347","count":1},{"id":"GO:1904780","count":1}]},{"hash":"2130251477834390432","title":"Cardiac Action Potential Regulation","description":"The top GO terms cluster around cardiac electrophysiology, including membrane depolarization, ventricular and atrial repolarization, Purkinje fiber action potentials, and left ventricular tissue development. This points to proteins involved in regulating cardiac action potentials and myocardial membrane potential dynamics. Some terms (caffeine response, vasopressin secretion, thermoception) are less central and may reflect broader signaling roles or annotation noise, but the core theme is cardiac electrical activity.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071313","count":2},{"id":"GO:0060453","count":2},{"id":"GO:0060307","count":2},{"id":"GO:0048016","count":2},{"id":"GO:0086047","count":2}]},{"hash":"1987317159851611639","title":"Ubiquitin-Proteasome-Mediated Proteolysis","description":"Most top GO terms indicate ubiquitin-dependent protein catabolic processes and proteasomal degradation (e.g., GO:0031146, GO:0030433, GO:0042787, GO:0000209). These terms point to a common function in ubiquitin-proteasome system\u2013driven protein turnover, suggesting the proteins work together in targeted proteolysis. Some terms (development, defense) are less related and may reflect broader annotations, but the dominant signal supports UPS-mediated degradation.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0021678","count":2},{"id":"GO:0050830","count":2}]},{"hash":"948469969983413978","title":"Metabolic processes","description":"The top GO terms cover diverse metabolic pathways (glycolysis, gluconeogenesis, glycolate catabolism, photorespiration, nucleotide and amino acid biosynthesis, isoprenoid biosynthesis), suggesting a broad metabolic role rather than a single function; thus \"Metabolic processes\" is a suitable, representative label.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046296","count":2},{"id":"GO:0006144","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0060041","count":2}]},{"hash":"152563947723741593","title":"Protein complex assembly and vesicle transport","description":"This cluster appears enriched for processes involving assembly and organization of protein complexes (chaperone-mediated assembly, protein hexamerization) and vesicle trafficking/disassembly (inter-Golgi transport, SNARE complex disassembly, autophagosome maturation), suggesting a theme of protein quality control and vesicle-mediated transport. Some terms (mRNA export, UV-damage repair, blastocyst development) are less directly connected, so the overall interpretation has moderate confidence.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:1990171","count":3},{"id":"GO:0051131","count":3},{"id":"GO:0048219","count":3},{"id":"GO:0001824","count":3}]},{"hash":"1631707985298865014","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007626","count":3},{"id":"GO:0046038","count":3},{"id":"GO:0021895","count":3},{"id":"GO:0048813","count":3},{"id":"GO:0006207","count":3}]},{"hash":"388060722575636769","title":"ERAD and ER-Golgi Transport","description":"The top GO terms point to ubiquitin-dependent degradation in ER-associated degradation (ERAD) and SCF-mediated proteasomal proteolysis, plus ER-to-Golgi vesicle transport. This supports a theme of proteostasis and trafficking in the secretory pathway, even though some terms are obsolete or unrelated. Overall, the cluster seems tied to ER quality control and vesicular transport toward the Golgi.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0006888","count":3},{"id":"GO:2001162","count":2},{"id":"GO:0006625","count":2}]},{"hash":"485806259302532925","title":"Plant jasmonate/oxylipin biosynthesis and stress response","description":"The dominant terms point to jasmonic acid and oxylipin biosynthesis, fatty acid beta-oxidation, and responses to environmental stress (toxic substances, ozone), all characteristic of plant lipid signaling and defense pathways. Some unrelated terms appear, but the core signal is JA/oxylipin\u2013mediated stress response.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0033543","count":2},{"id":"GO:0010193","count":2},{"id":"GO:0048443","count":2},{"id":"GO:0009695","count":2}]},{"hash":"1905046417982800033","title":"Endoreduplication-driven placental differentiation","description":"The GO terms cluster around endoreduplication and mitosis-without-cytokinesis, including DNA endoreduplication and positive regulation of DNA endoreduplication, alongside trophoblast giant cell differentiation and sprouting angiogenesis. These collectively point to polyploid differentiation processes typical of placental/trophoblast development, even though some terms reflect broader developmental contexts. This supports a cohesive theme of endoreduplication-associated differentiation in placental-like tissue, with some cross-phenotype annotations.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":1},{"id":"GO:0045850","count":1},{"id":"GO:0033301","count":1},{"id":"GO:0002040","count":1},{"id":"GO:0070345","count":1}]},{"hash":"1642540947599881258","title":"Heavy Metal Transport and Homeostasis","description":"This cluster's GO terms predominantly describe transmembrane transport of multiple metal ions (cadmium, mercury, zinc, copper) and copper homeostasis, plus mercury detox and response, indicating a shared function in metal uptake/export and detoxification. The inclusion of regulation of iron transport and a superoxide metabolic process hints at broader metal-related homeostasis and oxidative stress handling.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":1},{"id":"GO:0050787","count":1},{"id":"GO:0015680","count":1},{"id":"GO:0015694","count":1},{"id":"GO:0060003","count":1}]},{"hash":"671766780628569572","title":"Mitochondrial Respiration and ATP Synthesis","description":"Dominant GO terms point to mitochondrial respiration and ATP production (complex IV assembly; electron transport; proton motive force). While there are ancillary terms about aging, ROS regulation, and transport, the core theme across the cluster centers on mitochondrial energy metabolism and associated stress responses.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0006123","count":1},{"id":"GO:0042776","count":1},{"id":"GO:0007568","count":1},{"id":"GO:0032387","count":1}]},{"hash":"1645015416139532265","title":"Redox homeostasis and anti-inflammatory regulation","description":"The top GO terms cluster around managing oxidative stress (cellular oxidant detoxification, redox homeostasis) and dampening inflammatory processes (negative regulation of acute inflammatory response, IL-1\u03b2 production, neutrophil aggregation). While other terms touch on signaling and development, the strongest shared theme is redox balance coupled with anti-inflammatory regulation, justifying this label. ","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0055119","count":1},{"id":"GO:0014003","count":1},{"id":"GO:2000429","count":1}]},{"hash":"881982046039618729","title":"Embryonic tissue morphogenesis and differentiation","description":"GO terms indicate development and morphogenesis across multiple tissues (uterus, atrial/ventricular septa, inner ear) and differentiation of various lineages (erythrocyte, basophil, pancreatic cells), with regulatory signals like estrogen response and Wnt involvement. This suggests the cluster reflects broad developmental programs rather than a single pathway. ","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":2},{"id":"GO:0003290","count":2},{"id":"GO:0003281","count":2},{"id":"GO:0043627","count":2},{"id":"GO:0042472","count":2}]},{"hash":"2203657157634062706","title":"Wnt signaling regulation","description":"Top terms suggest a module that tunes canonical Wnt signaling, with both positive and negative regulatory roles and connections to development; despite a few unrelated or obsolete terms, the Wnt regulation signals are the strongest theme for this cluster.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071681","count":1},{"id":"GO:0061380","count":1},{"id":"GO:0000011","count":1},{"id":"GO:0044334","count":1},{"id":"GO:0044336","count":1}]},{"hash":"1553730061504252021","title":"Developmental Transcription and Morphogenesis","description":"The terms cluster around transcriptional regulation (negative regulation of transcription by RNA polymerase II; DNA-templated transcription) together with diverse developmental and morphogenesis processes (heart morphogenesis, endocrine pancreas development, neural crest cell migration, embryonic digestive tract morphogenesis, ureteric bud morphogenesis, spermatid nucleus differentiation). This suggests the proteins may act as transcriptional regulators involved in multiple developmental programs across tissues, rather than a single pathway. The lack of direct protein-protein edges supports a broad, cohesive theme rather than a tightly connected complex, reinforcing a developmental-regulatory role.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0006351","count":2},{"id":"GO:0048557","count":2},{"id":"GO:0001755","count":2},{"id":"GO:0007289","count":2}]},{"hash":"1712841618769390752","title":"Unknown","description":"The GO terms span disparate regulatory processes (protein sumoylation, negative regulation of signaling pathways, vesicle trafficking, ER stress-related apoptosis, development of GnRH neurons, and differentiation signals). There is no clear, single functional theme uniting these terms across the four proteins, making a specific, cohesive label difficult. Consequently, Unknown with None confidence.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":4},{"id":"GO:0034140","count":3},{"id":"GO:1904049","count":3},{"id":"GO:0045648","count":3},{"id":"GO:1901799","count":3}]},{"hash":"1857774594494960396","title":"Unknown","description":"The listed GO terms span plant pollen tube growth, skin cell differentiation, apoptosis and DNA replication regulation, blood coagulation, and neural injury responses, showing no single cohesive function or pathway tying the proteins together. With zero edges and heterogeneous functions, a specific, representative label cannot be determined.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009860","count":1},{"id":"GO:0080092","count":1},{"id":"GO:0060548","count":1},{"id":"GO:0030195","count":1},{"id":"GO:0008284","count":1}]},{"hash":"1787622459861258048","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097171","count":1},{"id":"GO:0034628","count":1},{"id":"GO:0009611","count":1},{"id":"GO:0046444","count":1},{"id":"GO:1990966","count":1}]},{"hash":"1705351562450436083","title":"Retinoic acid metabolism and female reproductive development","description":"The set includes retinoic acid biosynthesis and catabolic processes (GO:0042904, GO:0034653) alongside GO terms for uterus and female genitalia development (GO:0060065, GO:0008585, GO:0030540), suggesting a theme of retinoid signaling influencing female reproductive development. Some other terms pertain to general xenobiotic or alkaloid metabolism, which are less connected but may reflect broader metabolic capabilities of the proteins. Overall, the core theme centers on RA metabolism tied to female reproductive development.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071615","count":3},{"id":"GO:0042904","count":3},{"id":"GO:0060065","count":3},{"id":"GO:0008585","count":3},{"id":"GO:0034653","count":3}]},{"hash":"1928104210911235726","title":"Auxin-regulated plant cell wall biosynthesis","description":"This cluster combines auxin signaling and transport with plant-specific cell wall biosynthetic and remodeling processes (xylan and xyloglucan metabolism, secondary cell wall biogenesis). The co-occurrence suggests a link where auxin controls growth by modulating cell wall components, potentially including responses to freezing that impact wall properties.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046620","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0009926","count":1},{"id":"GO:0009733","count":1},{"id":"GO:0009834","count":1}]},{"hash":"1386332681246223191","title":"Unknown","description":"These proteins carry a highly diverse set of GO terms, including glycerol catabolic processes, neuronal development and maturation, apoptosis, erythrocyte differentiation, immune response, and cell wall organization. There isn\u2019t a single coherent function or pathway tying these terms together, so there\u2019s no clear thematic label for the cluster beyond Unknown.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0019563","count":3},{"id":"GO:0021983","count":3},{"id":"GO:0046168","count":3},{"id":"GO:0050768","count":3},{"id":"GO:0006915","count":3}]},{"hash":"1283644493941132717","title":"Ubiquitin-mediated proteolysis in oocyte meiosis","description":"The cluster centers on ubiquitin-dependent protein degradation (positive regulation of protein polyubiquitination, SCF-dependent proteasomal catabolic process) and meiosis-related processes (oocyte maturation, spindle assembly in female meiosis I), indicating a module that links targeted protein turnover with meiotic progression in oocytes.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1902916","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0031571","count":3},{"id":"GO:0001556","count":2},{"id":"GO:0006516","count":2}]},{"hash":"1503060817192759804","title":"Cell Cycle, DNA Repair, and Proteostasis","description":"The GO terms point to mitosis and cell division controls (exit from mitosis; cell division) alongside DNA damage responses (double-strand break repair via NHEJ; apoptotic processes). There is also a strong emphasis on protein quality control and turnover (SCF-dependent ubiquitin-proteasomal degradation, K48-linked ubiquitination, ERAD, peroxisomal protein import). Taken together, these terms suggest a cohesive theme around maintaining genome integrity while managing the proteome, despite the absence of network connections in this cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0070987","count":2},{"id":"GO:0016558","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0016562","count":2}]},{"hash":"1054260463074918328","title":"Unknown","description":"The GO terms are broad and diverse (cell division and proliferation, TORC1 signaling, GTPase regulation, mRNA transport, actin depolymerization, peroxisome targeting, development, and histone modification) with no single cohesive function linking all proteins. The absence of edges and a clear shared theme suggests the cluster is heterogeneous, so a precise functional label cannot be confidently assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0070262","count":2}]},{"hash":"160429463410986523","title":"Embryogenesis and placental development","description":"This cluster\u2019s top GO terms are dominated by embryonic development and placental-related processes (trophoblast giant cell differentiation, placenta development, left/right patterning, endocardial cushion formation, etc.), with additional notes on endocrine development. While a couple terms cover general cellular processes (mRNA splicing, mitochondrial tRNA aminoacylation), the common thread across most terms points to embryogenesis and related organogenesis. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":1},{"id":"GO:0060536","count":1},{"id":"GO:0060972","count":1},{"id":"GO:0060806","count":1},{"id":"GO:0003323","count":1}]},{"hash":"823197272125383682","title":"Plant hormone signaling and pigment biosynthesis regulation","description":"This cluster\u2019s terms are centered on plant-specific processes: leaf senescence regulation, chlorophyll biosynthesis regulation, gibberellin response, osmotic stress response, and flavonol biosynthesis modulation, pointing to hormone-driven growth and pigment pathways affected by stress. While some terms (viral process, chromatin remodeling, snRNA transcription, telomeric D-loop disassembly) are less connected, the core theme of hormone signaling impacting chlorophyll and flavonoid biosynthesis is plausible for this cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900056","count":1},{"id":"GO:0010380","count":1},{"id":"GO:0009739","count":1},{"id":"GO:0006970","count":1},{"id":"GO:0016032","count":1}]},{"hash":"59320599810813119","title":"Plant ROS Defense and Lignin Remodeling","description":"The GO terms point to plant-specific redox and oxidative stress responses (response to oxidative stress, cellular oxidant detoxification, hydrogen peroxide catabolic process) alongside lignin-related cell wall processes (lignin catabolic process, plant-type cell wall organization). Together they suggest a theme of reactive oxygen species defense coupled with cell wall remodeling and lignin metabolism in plants, with some supporting redox-related terms like iron-sulfur cluster assembly and methylation. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016226","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0006979","count":1},{"id":"GO:0046274","count":1},{"id":"GO:0009664","count":1}]},{"hash":"2292220929506815979","title":"Neural development and neurotrophin signaling","description":"This cluster centers on neural development and associated signaling pathways, with strong representation of neurotrophin TRK receptor signaling (GO:0048011), optic nerve morphogenesis (GO:0021631), and face development (GO:0060324), as well as FGFR-related apoptotic signaling and PI3K/AKT signaling (GO:1902178, GO:0043491). While a few terms like Wnt regulation and responses to toxins appear, the dominant theme ties to neuronal growth factor signaling and neural tissue morphogenesis.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048011","count":4},{"id":"GO:0090090","count":4},{"id":"GO:0020021","count":4},{"id":"GO:0071469","count":4},{"id":"GO:0060324","count":4}]},{"hash":"467823369984712824","title":"Neurodevelopmental Signaling and Morphogenesis","description":"The cluster\u2019s prominent GO terms point to neural development and morphogenesis, including multicellular organism development, optic nerve morphogenesis, face development, and neurotrophin/FGFR signaling pathways, suggesting the proteins participate in neural patterning and craniofacial development. Some terms are less directly related (e.g., symbiont-mediated host transformation, alkaline pH response), but the core theme centers on neural development and morphogenesis.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0019233","count":2},{"id":"GO:0048011","count":1},{"id":"GO:0090090","count":1},{"id":"GO:0020021","count":1}]},{"hash":"650230008369028050","title":"Unknown","description":"The top terms are highly diverse, spanning lipopolysaccharide/colanic acid biosynthesis, various biosynthetic and metabolic pathways, and development processes (hair follicle and labyrinthine layer vascular development). With zero edges and no shared functional signal tying the proteins together, there is no coherent theme to label meaningfully.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":1},{"id":"GO:0060716","count":1},{"id":"GO:0033499","count":1},{"id":"GO:0008207","count":1},{"id":"GO:0019878","count":1}]},{"hash":"960436209469169687","title":"Glycosylation and mucosal tissue remodeling","description":"The top terms point to glycosylation and proteoglycan biosynthesis (UDP-D-xylose metabolic process, heparin proteoglycan biosynthetic process, glycosylation) together with mucosal immunity and adhesion-related processes (immunoglobulin production in mucosal tissue, leukocyte tethering/rolling, cell adhesion, tissue morphogenesis). This suggests a cohesive theme of extracellular matrix glycoprotein production supporting mucosal tissue structure and immune cell interactions.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034116","count":3},{"id":"GO:0032868","count":3},{"id":"GO:0050901","count":3},{"id":"GO:0050892","count":3},{"id":"GO:0042403","count":3}]},{"hash":"983574869760982763","title":"Plant light response and meristem signaling","description":"The top GO terms are largely plant-specific\u2014response to red/far-red light, gravitropism, and maintenance of meristem identity\u2014suggesting roles in light-driven growth and developmental signaling. While there are some terms associated with general signaling pathways (BMP, NF-kappaB, TGF-beta), the predominant themes point to plant development and signal regulation rather than a single enzymatic activity.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009639","count":1},{"id":"GO:0009959","count":1},{"id":"GO:0030514","count":1},{"id":"GO:0042347","count":1},{"id":"GO:0061191","count":1}]},{"hash":"1636679734713889582","title":"Cadmium and Zinc Ion Homeostasis and Transport","description":"This cluster centers on GO terms related to cadmium detoxification and transport, as well as zinc ion transport and homeostasis, suggesting a shared role in handling and regulating metal ions (cadmium and zinc) within the cell. Although a few terms are obsolete, the core theme of metal ion detoxification and transport ties the proteins together.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098849","count":1},{"id":"GO:0070574","count":1},{"id":"GO:0006876","count":1},{"id":"GO:0061090","count":1},{"id":"GO:0032119","count":1}]},{"hash":"1694120135982816284","title":"Acetylation and Polyamine Metabolism","description":"The top GO terms are dominated by acetylation-related processes (spermidine, putrescine, N-terminal, and histone H4 acetylation) and polyamine-related metabolism (biosynthesis and catabolism of spermidine, putrescine, and spermine), suggesting a core theme around acetylation chemistry linked to polyamine pathways. Some unrelated terms like centromeric cohesion appear less aligned, but do not overpower the acetylation signal. Thus, the cluster can be coherently named \"Acetylation and Polyamine Metabolism.\"","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032918","count":4},{"id":"GO:0043967","count":4},{"id":"GO:0006526","count":4},{"id":"GO:0032920","count":4},{"id":"GO:0006044","count":4}]},{"hash":"2060532988296837343","title":"Unknown","description":"No shared top GO terms or edges available to define a common function for this small cluster; with no functional signal, a meaningful label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1813918797561203682","title":"Pectin remodeling in GA-regulated pollen tube growth","description":"The cluster centers on pectin metabolism (pectin catabolic and mucilage pectin biosynthesis) and cell wall modification, together with pollen tube growth, suggesting a shared role in remodeling pectin-rich walls during pollen tube elongation. The presence of gibberellin-related terms (response to gibberellin, gibberellic acid signaling) points to hormonal regulation of this growth process; additional terms like negative regulation of catalytic activity and stress responses are supportive or incidental. Overall, these functions cohesively point to GA-controlled pectin remodeling in pollen tube development.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":2},{"id":"GO:0048358","count":2},{"id":"GO:0009860","count":2},{"id":"GO:0043086","count":2},{"id":"GO:0042545","count":2}]},{"hash":"1970893448823407156","title":"Cell Proliferation and Cytoskeleton Remodeling","description":"These proteins show signals for growth/proliferation control (Ras signaling; neuroblast, macrophage, and osteoblast proliferation) together with actin-driven motility and cytoskeletal remodeling (pseudopodium assembly, fibroblast migration). The common theme appears to be regulation of cell growth and movement via signaling and cytoskeletal dynamics, with ancillary roles in organelle and matrix-related processes. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0032966","count":3},{"id":"GO:0046579","count":3},{"id":"GO:0010821","count":3},{"id":"GO:0010762","count":3},{"id":"GO:0055108","count":3}]},{"hash":"2141032568605320865","title":"Developmental Gene Regulation and Chromatin Dynamics","description":"The terms converge on developmental processes (fertilization, brain development, male gonad development) and on gene expression control, including transcriptional regulation and chromatin-associated processes, suggesting a coherent theme of developmental gene regulation and chromatin dynamics rather than a single, narrow pathway.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0070481","count":1}]},{"hash":"282916571785336757","title":"Neural development and migration signaling","description":"The terms center on neural development and neuronal migration (reelin-mediated signaling, radial glia-guided migration) with supporting roles in growth-factor signaling and vesicle fusion, suggesting a neurodevelopmental/synaptic function theme. A few immune-related terms appear but are less prominent compared to the neural development signals.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0040019","count":2},{"id":"GO:0050764","count":2},{"id":"GO:0071364","count":2},{"id":"GO:0006906","count":2},{"id":"GO:0050861","count":2}]},{"hash":"1445394802357831202","title":"Energy metabolism and cell division regulation","description":"The cluster centers on energy production terms (positive regulation of oxidative phosphorylation; positive regulation of ATP biosynthetic process) and cell cycle-related processes (cell division; positive regulation of centriole elongation), with additional connections to transcription initiation and mRNA export, suggesting coordinated control of growth and gene expression. Some heat-stress related terms imply environmental responsiveness that can couple metabolism with proliferation, supporting a theme of growth/metabolism coupled with transcriptional regulation.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903724","count":2},{"id":"GO:0070370","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1903862","count":2}]},{"hash":"101975179811885034","title":"Membrane-targeted protein secretion (Sec/SRP)","description":"The top GO terms emphasize protein secretion and membrane targeting, including SRP-dependent cotranslational targeting and Sec complex\u2013driven transport, plus post-translational targeting to membranes. This points to a shared role in moving polypeptides to/through membranes and into secretory pathways, justifying the label.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009306","count":2},{"id":"GO:0006616","count":2},{"id":"GO:0006605","count":2},{"id":"GO:0043952","count":2},{"id":"GO:0031204","count":2}]},{"hash":"788123671248121771","title":"Regulation of cell growth and differentiation","description":"This cluster\u2019s GO terms point to broad regulatory roles across multiple processes and cell types, including signaling (Ras), differentiation (macrophages, osteoblasts, neuroblasts), migration and cytoskeletal changes (fibroblasts, pseudopodium), as well as mitochondrial organization and synaptic modification. The terms do not converge on a single pathway or process, but collectively emphasize regulatory functions governing cellular growth, differentiation, and morphology. Therefore, a concise label capturing this general regulatory theme is appropriate.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032966","count":3},{"id":"GO:0046579","count":3},{"id":"GO:0010821","count":3},{"id":"GO:0010762","count":3},{"id":"GO:0055108","count":3}]},{"hash":"2265504304083302346","title":"Plant photosynthesis and light-regulated defense","description":"The top GO terms strongly center on chloroplast-based photosynthesis (photosynthesis, carbon fixation, reductive pentose-phosphate cycle, photorespiration) and light-related regulation (absence of light, photoperiodism). There are also defense-related signals (salicylic acid response, insect defense) suggesting a plant-specific cluster where photosynthetic machinery is linked to light-responsive and defense pathways.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0009853","count":1},{"id":"GO:0015977","count":1},{"id":"GO:0019253","count":1},{"id":"GO:0009751","count":1}]},{"hash":"1751669847389478835","title":"Vascular development regulation","description":"The top GO terms point to negative regulation of vasculogenesis, endothelial cell differentiation, and VEGF signaling, indicating a shared function in modulating blood vessel formation and endothelial biology. While some terms (like sodium transport or various catabolic processes) are less related, the vascular-related terms provide a cohesive core theme for the cluster.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2001213","count":2},{"id":"GO:0006124","count":2},{"id":"GO:0009115","count":2},{"id":"GO:0042773","count":2},{"id":"GO:0007595","count":2}]},{"hash":"2103746267869867844","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009853","count":1},{"id":"GO:0015977","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0019253","count":1},{"id":"GO:0007049","count":1}]},{"hash":"2006663569649601869","title":"Chloroplast tRNA and protein methylation","description":"This cluster is dominated by GO terms for RNA methylation and various protein methylation events (tRNA wobble uridine modification; tRNA methylation; peptidyl-lysine dimethylation; N-terminal and arginine methylation), suggesting a group of methyltransferases. The presence of light-independent chlorophyll biosynthesis and vitamin E biosynthetic processes further points to chloroplast/plastid-associated functions. Taken together, these terms imply a cohesive theme of methylation enzymes operating in chloroplasts, affecting both RNA and proteins.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":1},{"id":"GO:0036068","count":1},{"id":"GO:0016049","count":1},{"id":"GO:0018027","count":1},{"id":"GO:0018012","count":1}]},{"hash":"332908479029360844","title":"Ribosome biogenesis and cell division","description":"The GO terms show a strong focus on ribosome assembly and translation-related processes (ribosomal small subunit biogenesis, ribosome biogenesis, tRNA modification) together with cell cycle and division functions (cell cycle, cell division, cell septum assembly). An outlier term for viral latency is present but does not define the core cluster function. Overall, the dominant theme is ribosome biogenesis coupled with cell division.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019042","count":1},{"id":"GO:1903833","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0051301","count":1}]},{"hash":"1268594786335852592","title":"Dendrite Morphogenesis and Neuronal Development","description":"The top GO terms are strongly centered on neuronal development, especially dendrite morphogenesis (GO:0048813) and nervous system development (GO:0007399), with supportive terms related to dendritic spine development. While other terms are more general (e.g., ribosome biogenesis, mitosis exit), the clear emphasis on dendritic architecture and neuron formation indicates a neuron-development theme. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048813","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0060999","count":1},{"id":"GO:0000917","count":1},{"id":"GO:0097494","count":1}]},{"hash":"1492938808999743793","title":"DNA replication and chromosome condensation cluster","description":"The top GO terms point to core genome maintenance: DNA replication, mitotic/cohesin-related chromosome condensation, and meiotic chromosome events, including cohesion maintenance and regulation of meiotic DSB formation. While a few terms like tRNA gene clustering and SOS response are less directly tied, the dominant theme is chromatin organization during DNA replication and chromosome condensation, suggesting a cohesive group of proteins involved in genome maintenance and structural chromosome dynamics.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":1},{"id":"GO:0061780","count":1},{"id":"GO:0070058","count":1},{"id":"GO:0009432","count":1},{"id":"GO:0010032","count":1}]},{"hash":"1714675721751236589","title":"Unknown","description":"The top GO terms are scattered across metabolism (glycerol/alkane catabolic), RNA modification, chromatin remodeling, and brain development, with several obsolete terms. There is no clear shared function tying the three proteins together, so a single cohesive label cannot be established. ","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019563","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0016575","count":2},{"id":"GO:0021983","count":2},{"id":"GO:0002098","count":2}]},{"hash":"1685755229975138565","title":"Unknown","description":"The GO terms are highly diverse, including redox and energy metabolism, multiple catabolic pathways, ion transport, vitamin A metabolism, and vascular development regulation, with no single coherent function tying the proteins together. ","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042572","count":2},{"id":"GO:2001213","count":1},{"id":"GO:0006124","count":1},{"id":"GO:0009115","count":1}]},{"hash":"1309335638518905022","title":"Photosystem I Electron Transport","description":"The GO terms point to core photosynthesis activities centered on Photosystem I, including NADP+ reduction and electron transport in PSI, plus stabilization of PSI, suggesting the proteins cluster are PSI components involved in the light reactions.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009780","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0009773","count":1},{"id":"GO:0042550","count":1}]},{"hash":"2038005531166071083","title":"Spliceosome-Driven mRNA Processing","description":"This cluster is dominated by GO terms related to regulation of mRNA splicing via the spliceosome, including alternative splicing and mRNA export, with additional signals from regulatory ncRNA-mediated gene silencing. While a few terms touch on translation reinitiation and viral mechanisms, the strongest pattern points to RNA processing and splicing control in the nucleus. Therefore, the label Spliceosome-Driven mRNA Processing best represents the core function of these proteins.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":2},{"id":"GO:0031047","count":2},{"id":"GO:1900363","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0075525","count":1}]},{"hash":"842890730333520894","title":"RNA processing and translation","description":"The proteins show a cohesive link to post-transcriptional RNA handling: spliceosome-mediated splicing, mRNA export, and splicing regulation, along with translation and translation reinitiation. This suggests a cluster focused on RNA maturation and subsequent protein synthesis, rather than solely on transcriptional regulation.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:1900363","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0006378","count":1}]},{"hash":"544956701596591674","title":"RNA and protein methylation enzymes","description":"The cluster centers on multiple methylation-related processes: tRNA wobble uridine modification, rRNA modification, mitochondrial tRNA methylation, peptidyl-lysine dimethylation, N-terminal methylation, and related methylation activities, plus nucleologenesis. This pattern suggests a group of methyltransferases involved in RNA processing, ribosome biogenesis, and associated protein modifications (with a note that chloroplast-related terms may reflect plastid RNA/protein methylation contexts). ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017126","count":1},{"id":"GO:0002098","count":1},{"id":"GO:0036068","count":1},{"id":"GO:0000154","count":1},{"id":"GO:0016049","count":1}]},{"hash":"715045830317427800","title":"Unknown","description":"The GO terms are diverse and show no single cohesive function: red blood cell homeostasis, NF-\u03baB signaling, cytochrome complex assembly, redox detoxification, reproduction, and various metabolic processes. While some terms relate to oxidative stress, others are unrelated, making a unified cluster function unclear.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034101","count":1},{"id":"GO:0007252","count":1},{"id":"GO:0017004","count":1},{"id":"GO:0098869","count":1},{"id":"GO:2000255","count":1}]},{"hash":"1383375767513406236","title":"Retroviral life cycle and translation factors","description":"The top GO terms are dominated by viral-related processes: viral life cycle, uncoating of virus, RNA-templated DNA biosynthetic process (reverse transcription), and establishment of integrated proviral latency, plus host-mediated activation of viral genome replication. Translation initiation terms also appear, suggesting virus\u2013host translation interactions. Some terms appear as noise (e.g., sepal formation), but the core signal points to retroviral replication and translation-associated factors.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0075713","count":1},{"id":"GO:0048453","count":1}]},{"hash":"2064413001885851927","title":"Redox-stress signaling and metal-ion responses","description":"This cluster centers on GO terms related to oxidative and chemical stress responses (glutathione metabolism; response to toxic substances), metal ion handling (zinc and manganese ion responses), and modulation of stress-related signaling (negative regulation of JNK activity) along with broader signaling inputs (EGF stimulus, light response) and cell-cycle regulation. Taken together, the proteins appear to participate in redox homeostasis and stress signaling with ancillary roles in metal ion response and growth-related signaling.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000429","count":2},{"id":"GO:0071364","count":2},{"id":"GO:2000030","count":2},{"id":"GO:0010043","count":2},{"id":"GO:1905804","count":2}]},{"hash":"2084105789511936051","title":"Glycan Biosynthesis and Cell Wall Formation","description":"The GO terms point to biosynthesis of polysaccharides and cell wall components (lipopolysaccharide, O antigen, peptidoglycan, extracellular polysaccharides), as well as sugar precursor pathways (dTDP-rhamnose) and storage polysaccharides (glycogen, starch). The inclusion of cell morphogenesis and regulation of cell shape suggests a broader role in structural assembly and maintenance. Overall, the cluster seems centered on glycan production and cell wall biogenesis across different organisms.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0019305","count":1},{"id":"GO:0000902","count":1},{"id":"GO:0045226","count":1}]},{"hash":"829392605390955489","title":"Virus-host entry and translation machinery","description":"The terms point to viral infection steps (virion attachment, membrane fusion, viral RNA genome replication) and to host translation/translation regulation (translation, cytoplasmic translation, tRNA aminoacylation, ribosomal RNA maturation, negative regulation of translational initiation). The coexistence of these viral and translation-related terms suggests a cluster tied to virus\u2013host interaction and the host protein synthesis apparatus, with some apoptosis/transcription terms reflecting cellular response to infection. Confidence: Medium.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006915","count":1},{"id":"GO:0006437","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0002181","count":1}]},{"hash":"2283768968012999852","title":"Adherens junctions and epithelial polarity","description":"The GO terms highlighted here include zonula adherens assembly and maintenance of epithelial cell apical/basal polarity, along with regulation of Rho protein signaling, which together point to a role in epithelial cell junctions and cytoskeletal dynamics. A number of other terms (renal phosphate absorption, bile acid secretion, Purkinje cell layer formation) appear unrelated or obsolete, suggesting some noise in the set, but the core signal supports adhesion and polarity processes.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903760","count":2},{"id":"GO:0097291","count":2},{"id":"GO:0045186","count":2},{"id":"GO:0032416","count":2},{"id":"GO:0051835","count":2}]},{"hash":"1316827925779554067","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034414","count":1},{"id":"GO:0090503","count":1},{"id":"GO:0046929","count":1},{"id":"GO:0006364","count":1},{"id":"GO:0034247","count":1}]},{"hash":"428989655114235894","title":"RNA processing and gene silencing","description":"This cluster shows several RNA-related GO terms, including pre-miRNA processing, mRNA processing, and RISC complex assembly, pointing to RNA maturation and RNA interference pathways. While there are also cell-cycle/division and virus-response terms present, the strongest recurring theme is RNA processing and silencing machinery, making this a plausible unified function. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0010020","count":1},{"id":"GO:0032955","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0035280","count":1}]},{"hash":"1287654324802578255","title":"Diverse carbohydrate metabolism and stress responses","description":"This cluster centers on multiple carbohydrate catabolic processes (sorbitol/xylitol catabolism, pyruvate fermentation to ethanol) alongside stress- and signaling-related terms (response to lipopolysaccharide, nitrosative stress; prostaglandin and retinoic acid metabolism). The GO terms point to two somewhat distinct threads\u2014carbohydrate metabolism and stress/immune signaling\u2014so a concise label that reflects both themes seems most representative. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":2},{"id":"GO:0033859","count":1},{"id":"GO:0006062","count":1},{"id":"GO:0043458","count":1},{"id":"GO:0051409","count":1}]},{"hash":"2270237537189174902","title":"Cell Growth and Metabolism Regulation","description":"This cluster\u2019s terms cluster around cell cycle processes (centriole elongation, cell division), energy production and metabolism (oxidative phosphorylation, ATP biosynthesis), and gene expression control (RNA Pol II transcription initiation, mRNA export). Some outliers (heat response, viral replication) are present but do not dominate the set, so a cohesive theme around growth and metabolic/gene regulatory control fits best.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903724","count":1},{"id":"GO:0070370","count":1},{"id":"GO:0019079","count":1},{"id":"GO:0051301","count":1},{"id":"GO:1903862","count":1}]},{"hash":"1893764481049237357","title":"Mitochondrial transcription and respiration","description":"The cluster\u2019s terms are strongly centered on mitochondrial gene expression\u2014transcription, its termination and regulation, and ribosome assembly\u2014as well as core energy metabolism processes like aerobic respiration and mitochondrial electron transport, with proton transmembrane transport. A couple of chloroplast/plastid terms appear, but the dominant signal ties to mitochondria-related transcription/translation and respiration, suggesting a mitochondrial-focused functional theme for this cluster.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009658","count":1},{"id":"GO:0042794","count":1},{"id":"GO:0061668","count":1},{"id":"GO:0006393","count":1},{"id":"GO:1903108","count":1}]},{"hash":"1056503036611881718","title":"Oocyte RNA processing and axis specification","description":"The proteins point to RNA processing and translation control (mRNA polyadenylation/splicing/export, translation reinitiation/elongation) with involvement in oocyte dorsal/ventral axis specification, suggesting a coordinated module for maternal mRNA regulation during oogenesis and axis patterning.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0008069","count":1},{"id":"GO:1900248","count":1}]},{"hash":"294247626813636842","title":"Plant development and cuticle biosynthesis","description":"The top terms point to plant developmental programs (bract and seed development, floral meristem growth, multicellular development) and epidermal barrier formation (cutin and wax biosynthesis), suggesting a cohesive theme around reproductive structure development and cuticle formation. A few terms (DNA repair, chitin response) are less central and may reflect broader cellular functions or context-specific responses.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0006284","count":1},{"id":"GO:0010200","count":1},{"id":"GO:0010432","count":1}]},{"hash":"2074574531668580579","title":"Unknown","description":"The GO terms are disparate (cobalamin biosynthetic process vs. protein-containing complex assembly) with only one occurrence each and no network connections, offering no clear single function to bind the cluster.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":1},{"id":"GO:0006461","count":1}]},{"hash":"2034897659332486776","title":"Mitochondrial respiration and ATP production","description":"The strongest signals are mitochondrial energy metabolism terms: mitochondrial respiratory chain complex III assembly, positive regulation of oxidative phosphorylation, and positive regulation of ATP biosynthetic process, indicating a core theme of respiration and ATP generation. Some unrelated terms (centriole elongation, heat acclimation, viral replication) appear but are likely incidental annotations; the dominant pattern supports mitochondrial energy production as the cluster's representative function.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034551","count":2},{"id":"GO:1903724","count":1},{"id":"GO:0070370","count":1},{"id":"GO:0019079","count":1},{"id":"GO:0051301","count":1}]},{"hash":"1435097970016552118","title":"Translation and ribosome assembly","description":"Most frequent GO terms in the cluster are ribosomal large subunit assembly and translation, each represented by two proteins, pointing to a core function in protein synthesis. The other terms appear only once and seem peripheral, suggesting noise or broader cellular responses. Therefore, a concise label reflecting the dominant translation/ribosome activity is appropriate, with moderate confidence due to the small cluster size and some extraneous terms.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0007568","count":1},{"id":"GO:0071276","count":1}]},{"hash":"2031076456711880060","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by GO terms related to ribosome assembly and function\u2014ribosomal subunit biogenesis (small and large), rRNA processing, and cytoplasmic translation\u2014pointing to a shared role in ribosome production and overall protein synthesis; ancillary terms like cell division may reflect growth coupling but do not redefine the main theme.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0002181","count":1},{"id":"GO:1903104","count":1},{"id":"GO:1903833","count":1}]},{"hash":"624553356527731863","title":"Heat-stress\u2013driven cell cycle and energy metabolism","description":"The top GO terms point to centriole elongation and cell division, suggesting cell cycle regulation, while oxidative phosphorylation and ATP biosynthetic process indicate energy metabolism changes. Cellular heat acclimation and transcription-related terms imply gene expression reprogramming under heat stress. Together, these hints suggest a cluster of proteins coordinating cell proliferation with energy supply and transcription during heat stress.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1903724","count":3},{"id":"GO:0070370","count":3},{"id":"GO:0019079","count":3},{"id":"GO:0051301","count":3},{"id":"GO:1903862","count":3}]},{"hash":"192222252333926601","title":"RNA processing and translation regulation","description":"GO terms in this cluster converge on RNA metabolism (splicing, rRNA maturation, RNA folding) and translational control (translation, translational fidelity), with a note of transcription-related terms and UV-responsive translation. This pattern supports a cohesive function in RNA processing and regulation of protein synthesis.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000372","count":1},{"id":"GO:0034337","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0046677","count":1}]},{"hash":"727090128900387389","title":"Steroid and lipid metabolism","description":"The GO terms are dominated by steroid and lipid-related processes (steroid androgen catabolic processes, C21-steroid hormone metabolism, retinol metabolism, methyl-branched fatty acid and mycolic acid biosynthesis, phylloquinone catabolism) with supporting redox/cofactor biosynthesis (BH4) and a drug response term. This pattern points to a cluster of proteins involved in lipid/steroid metabolic pathways and associated redox chemistry, rather than a single, narrowly defined reaction. High","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042572","count":3},{"id":"GO:0031427","count":2},{"id":"GO:0006710","count":2},{"id":"GO:0006729","count":2}]},{"hash":"1379437163864059158","title":"Oxidative stress response and redox homeostasis","description":"The majority of top GO terms point to handling of oxidative stress and maintenance of redox balance (oxidant detoxification, redox homeostasis, oxidative stress response, deglutathionylation). These processes reflect cellular defense against reactive species. A couple terms appear unrelated (neural crest migration, transcription regulation), likely noise, but do not outweigh the redox-centric signals.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0003147","count":1},{"id":"GO:1903026","count":1},{"id":"GO:2000651","count":1},{"id":"GO:0098869","count":1}]},{"hash":"408519014432551229","title":"RNA processing and RNAi machinery","description":"The cluster is dominated by RNA processing terms (tRNA processing, pre-miRNA processing, mRNA processing) and RISC complex assembly, pointing to RNA maturation and RNA interference pathways; a few virus-related terms may reflect antiviral RNA silencing roles. This makes RNA processing and RNAi machinery a cohesive, representative label.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":2},{"id":"GO:0035280","count":1},{"id":"GO:0031054","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0009615","count":1}]},{"hash":"2006345051715212238","title":"Ion and Metabolite Transport","description":"These terms cluster around transport across membranes for ions and small metabolites (sodium-dependent organic cation transport, glucose/fructose-related transport, nitrite/urate transport) and a vesicular neurotransmitter loading process, with some links to mitochondrial membrane regulation and osmotic stress response. The shared theme is membrane transport and metabolic handling of molecules, justifying this label, though the evidence is not exceptionally strong due to diverse functions represented. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010940","count":1},{"id":"GO:0035794","count":1},{"id":"GO:0010917","count":1},{"id":"GO:0006970","count":1},{"id":"GO:0070715","count":1}]},{"hash":"1294791268778630509","title":"Plant defense signaling and hormone responses","description":"The proteins in this cluster show plant-specific responses to defense-related cues (salicylic acid, chitin) and hormone-mediated regulation (gibberellin signaling, ACC/ethylene), along with antifungal innate immune modulation and development-related processes (atrichoblast/root epidermis differentiation, sclerenchyma formation). This combination points to a cohesive theme of plant immune signaling intertwined with growth and tissue differentiation, rather than a single non-plant process. ","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009751","count":1},{"id":"GO:0010200","count":1},{"id":"GO:0009739","count":1},{"id":"GO:0009938","count":1},{"id":"GO:0080169","count":1}]},{"hash":"1546676837019204423","title":"Viral life cycle and latency","description":"Most of the top GO terms cluster around steps of viral replication and latency: viral life cycle, uncoating, host-mediated activation of viral genome replication, RNA-templated DNA biosynthetic process, and establishment of integrated proviral latency. A stray plant-specific term (sepal formation) appears, but it likely represents noise. Overall the common theme is viruses exploiting host machinery for replication and latency, which justifies the label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":2},{"id":"GO:0075713","count":1},{"id":"GO:0048453","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0006278","count":1}]},{"hash":"777658346083449136","title":"RNA transcription and chromatin organization","description":"The cluster shows a focus on transcription by multiple RNA polymerases (I and III) and on chromatin organization, with related terms like ribosome biogenesis also appearing, suggesting a core theme around transcription machinery and chromatin dynamics. There are a couple of outlier/obsolete terms and one collagen catabolic term, but the dominant signal points to transcription-related processes.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034396","count":2},{"id":"GO:0035551","count":2},{"id":"GO:0034724","count":2},{"id":"GO:0030574","count":2},{"id":"GO:0006385","count":1}]},{"hash":"176621314511132687","title":"RNA Polymerase III Transcription Initiation","description":"The top GO terms cluster around RNA polymerase III\u2013driven transcription, including initiation at Pol III promoters, preinitiation complex assembly, and open complex formation, indicating the proteins are likely components or regulators of Pol III transcription initiation. Some unrelated terms appear (thrombocyte differentiation, LDL receptor regulation), suggesting noise in the annotations, but the Pol III initiation signal dominates.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002574","count":1},{"id":"GO:0006384","count":1},{"id":"GO:0070898","count":1},{"id":"GO:0070893","count":1},{"id":"GO:0001112","count":1}]},{"hash":"348370036349308868","title":"Unknown","description":"GO terms span plant reproductive development and meiotic DNA repair, but also include stress responses, metabolism, and several bacterial-specific pathways, plus an obsolete ER glycosylation term. The heterogeneous mix provides no clear shared function or pathway connecting the proteins, so a precise label is not identifiable.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009553","count":1},{"id":"GO:0009555","count":1},{"id":"GO:0007131","count":1},{"id":"GO:0006302","count":1},{"id":"GO:0009103","count":1}]},{"hash":"1841496270044039660","title":"Unknown","description":"This cluster shows two top GO terms with little overlap: mitotic spindle elongation (a mitosis process) and an obsolete GO term for Wnt signaling in osteoblast differentiation. With only 3 proteins and no edges, the set lacks a clear, cohesive biological theme, so a precise, representative label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000022","count":1},{"id":"GO:0044339","count":1}]},{"hash":"1765485205153847165","title":"Retinoic acid signaling in embryonic development","description":"The top GO terms center on 9-cis-retinoic acid biosynthesis and retinoic acid receptor signaling, with multiple embryonic development terms (forebrain, pituitary, midgut, inner ear morphogenesis, etc.), pointing to a cohesive RA-regulated developmental program.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042904","count":3},{"id":"GO:0021983","count":3},{"id":"GO:0036293","count":3},{"id":"GO:0048384","count":3},{"id":"GO:0048566","count":3}]},{"hash":"1972087990392483575","title":"Unknown","description":"The GO terms span glycerol metabolism, neuronal development, endocrine/pituitary processes, immune response, and detoxification, with no clear shared function across the cluster. The three proteins appear functionally diverse, so a single cohesive label is not supported.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019563","count":3},{"id":"GO:0021983","count":3},{"id":"GO:0046168","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0045648","count":3}]},{"hash":"312240114119099106","title":"Unknown","description":"The terms include methylation (general and protein-specific) and several dopamine/catecholamine metabolism terms, plus unrelated processes like lignin biosynthesis and auditory receptor development, giving no single cohesive function for the cluster.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050668","count":3},{"id":"GO:0032259","count":3},{"id":"GO:0006479","count":3},{"id":"GO:0045963","count":3},{"id":"GO:0009809","count":3}]},{"hash":"1688179265298978206","title":"Mitochondrial apoptosis and ROS signaling","description":"The cluster centers on mitochondrial pathways: apoptotic process, cytochrome c\u2013related activity, mitochondrial electron transport, cytochrome c-heme linkage, and hydrogen peroxide metabolism, indicating a mitochondrial stress response and ROS-regulated apoptosis. An outlier GO term for photosynthesis appears, but the dominant pattern supports a mitochondrial apoptosis/oxidative stress theme.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0008635","count":3},{"id":"GO:0015979","count":3},{"id":"GO:0006470","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0006123","count":3}]},{"hash":"278301445757641810","title":"Angiogenesis inhibition","description":"Based on the top GO terms, there is a consistent signal for negative regulation of vascular processes (vasculogenesis, endothelial differentiation, VEGF signaling), suggesting the proteins may function to restrain blood vessel formation. The other terms (ferrodoxin metabolism, xanthine catabolic process, ATP-linked electron transport, sodium ion transport, nitrogen fixation, lactation) appear incidental and do not define a cohesive vascular theme. Therefore, this label captures the strongest shared function in the cluster.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2001213","count":1},{"id":"GO:0006124","count":1},{"id":"GO:0009115","count":1},{"id":"GO:0042773","count":1},{"id":"GO:0007595","count":1}]},{"hash":"798854936452558277","title":"Redox Detoxification and ROS Scavenging","description":"The term set centers on oxidation-reduction processes and detoxification of reactive oxygen species (e.g., hydrogen peroxide catabolic process, removal of superoxide radicals, cellular oxidant detoxification) and mitochondrial redox components (cytochrome complex assembly). While a signaling term like I-kappaB phosphorylation is present, the dominant pattern is redox balance and oxidative stress response, justifying this label as representative of the cluster.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0034101","count":1},{"id":"GO:0007252","count":1},{"id":"GO:0017004","count":1},{"id":"GO:2000255","count":1}]},{"hash":"2212376882390892150","title":"Mitosis: spindle-kinetochore attachment","description":"The top GO terms include explicit mitosis-related processes such as attachment of spindle microtubules to the kinetochore and regulation of protein localization to the cell division site, which point to a core function in chromosome segregation during mitosis. While several other terms are present (e.g., neuron differentiation, DNA repeats, metal ion response), the strongest signal centers on spindle-kinetochore interactions and cytokinesis-related localization. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0098609","count":3},{"id":"GO:0005979","count":3},{"id":"GO:0030846","count":3},{"id":"GO:1901901","count":3},{"id":"GO:0051315","count":3}]},{"hash":"476945177781695865","title":"Zinc and Cadmium Ion Homeostasis and Detoxification","description":"The top GO terms cluster around cadmium ion transmembrane transport, intracellular zinc ion homeostasis, and detoxification of zinc ions, with a few zinc-related response and transport regulation terms. This points to a cohesive theme of maintaining intracellular zinc levels and detoxifying cadmium, rather than other metal processes, so the label captures the primary function of these proteins.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":2},{"id":"GO:0006882","count":2},{"id":"GO:0010312","count":2},{"id":"GO:0098849","count":1},{"id":"GO:0006876","count":1}]},{"hash":"2195882003861946523","title":"Neuronal mitochondrial function and synaptic signaling","description":"The GO terms point to neuron-specific processes (behavioral fear response, learning, neuron-neuron synaptic transmission) together with mitochondrial-related functions (calcium import into the mitochondrion, protein import into the mitochondrial matrix, and regulation of mitochondrial autophagy) and oxidative stress/ion transport. This pattern suggests a cluster centered on mitochondrial roles in neuronal activity and synaptic communication, rather than generic metabolism. Confidence: High","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001662","count":1},{"id":"GO:2000378","count":1},{"id":"GO:1903959","count":1},{"id":"GO:0006820","count":1},{"id":"GO:1903146","count":1}]},{"hash":"252669570329208468","title":"Unknown","description":"The Top Terms are highly heterogeneous (lipopolysaccharide biosynthesis; metal ion transport; autophosphorylation; T-tubule organization; hormone and pheromone responses; membrane repolarization), and there are no interactions among the proteins (Edges 0, Triangles 0). This lacks a single, cohesive function or pathway tying the cluster together, so there is no reliable common theme to assign a specific label. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0070574","count":2},{"id":"GO:1990938","count":2},{"id":"GO:0033292","count":2},{"id":"GO:0006825","count":2}]},{"hash":"644083641213233130","title":"RNA-guided chromatin remodeling and splicing regulation","description":"The GO terms cluster around RNA-mediated regulation of gene expression (regulatory ncRNA-mediated gene silencing; snoRNA processing) and chromatin dynamics (chromatin remodeling, nucleosome positioning, DNA topology changes), plus spliceosome-dependent mRNA splicing control. Together, these suggest proteins function in nuclear RNA-guided chromatin state regulation and RNA processing.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0006265","count":2},{"id":"GO:0016584","count":2},{"id":"GO:1990417","count":2}]},{"hash":"400740301991518506","title":"Chromatin Remodeling and DNA Topology","description":"The cluster\u2019s top GO terms cluster around chromatin dynamics: DNA topological change and chromatin remodeling, with supporting hints toward nucleosome positioning. Although several terms are marked obsolete, the recurring theme centers on changing chromatin structure and DNA accessibility, suggesting the proteins function in chromatin organization rather than a distinct enzymatic pathway. The small size and some noise reduce confidence, but the core linkage to chromatin remodeling remains solid.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006265","count":1},{"id":"GO:0016584","count":1},{"id":"GO:1990417","count":1},{"id":"GO:0006306","count":1},{"id":"GO:0006605","count":1}]},{"hash":"2224043599615999599","title":"Unknown","description":"The top GO terms span chaperone-assisted protein folding, LPS biosynthesis, multiple ion transport processes (cadmium, copper, sodium, monoatomic cations), signaling, T-tubule organization, pheromone response, and more. They do not cohere around a single clear biological function, so a unified label is not justifiable.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070389","count":2},{"id":"GO:0009103","count":1},{"id":"GO:0070574","count":1},{"id":"GO:1990938","count":1},{"id":"GO:0099132","count":1}]},{"hash":"2279182247237936363","title":"mRNA processing and translation initiation","description":"Proteins here show strong ties to post-transcriptional gene expression: multiple GO terms point to splicing and mRNA maturation (spliceosome-mediated splicing, polyadenylation-related regulation, and mRNA export), alongside initiation stage of translation (preinitiation complex formation and reinitiation events). This pattern suggests the cluster centers on coordinating RNA processing with translation readiness.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0006406","count":2}]},{"hash":"1653563250344175709","title":"Chromatin remodeling and DNA topology","description":"The top GO terms are dominated by chromatin-related processes: chromatin remodeling (GO:0043044) and DNA topological change (GO:0006265), with additional references to nucleosome positioning and related chromatin dynamics. Although a few terms are historical/obsolete and there is a minor nod to RNA processing, the central theme ties to regulation of chromatin structure and DNA topology in the nucleus. Confidence: High","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":2},{"id":"GO:0072711","count":1},{"id":"GO:0006265","count":1},{"id":"GO:0016584","count":1},{"id":"GO:1990417","count":1}]},{"hash":"1107328049914361299","title":"Amino acid and cofactor biosynthesis","description":"GO terms in the cluster span several amino acid biosynthesis (tyrosine, histidine, lysine), along with heme, biotin, and sphinganine biosynthesis, plus a fatty acid transport term. This suggests a broad metabolic biosynthesis theme rather than a single, tightly defined function. Thus the label captures a cohesive theme of amino acid and cofactor biosynthesis across the proteins.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0015908","count":3},{"id":"GO:0042853","count":3},{"id":"GO:0033585","count":3},{"id":"GO:0006783","count":3},{"id":"GO:0019878","count":3}]},{"hash":"1892340144195645738","title":"Flower development and ABA-related stress responses","description":"The top GO terms mix flower development (petal development; organ boundary specification) with abiotic stress responses (desiccation, high light) and ABA biosynthesis regulation. This suggests proteins involved in floral development that are also linked to ABA signaling and stress adaptation. Although the evidence is modest (few annotations), the shared themes support a label that captures both developmental and ABA-associated stress roles.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010199","count":1},{"id":"GO:0048441","count":1},{"id":"GO:0009269","count":1},{"id":"GO:0010116","count":1},{"id":"GO:0009644","count":1}]},{"hash":"2176580592762697181","title":"Unknown","description":"The top GO terms are broad and disperse across transcription, mRNA export, vesicle transport, stress response, development, and mitochondrial autophagy, with only three proteins and no strong shared functional signal. There isn\u2019t a cohesive theme to tie these proteins to a single biological function, so the cluster remains Unknown.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0071899","count":3},{"id":"GO:1990171","count":3},{"id":"GO:0051131","count":3}]},{"hash":"1323185542166891248","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031440","count":1},{"id":"GO:0001193","count":1},{"id":"GO:0031564","count":1},{"id":"GO:0045899","count":1},{"id":"GO:0051123","count":1}]},{"hash":"1851856730313113093","title":"Amino acid biosynthesis and related metabolism","description":"The GO terms are dominated by amino acid pathways (valine, alanine, methionine cycle) and related metabolism such as dicarboxylic acid and methylamine metabolism, plus pyridoxine (vitamin B6) biosynthesis. A few peripheral terms (hypoxia response, fat cell differentiation) are less central, but do not override the main theme. Overall, the cluster appears to group proteins involved in amino acid metabolism and vitamin-related biosynthesis.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009099","count":2},{"id":"GO:0009097","count":2},{"id":"GO:0050872","count":1},{"id":"GO:0042853","count":1},{"id":"GO:0033353","count":1}]},{"hash":"368033874110930751","title":"Unknown","description":"The GO terms are highly heterogeneous (lipid/metabolic enzymes, various ion transports, vacuole and membrane organization, structural membrane features, bacterial LPS synthesis, and pheromone-induced processes), with only a single edge and no clear shared function. There isn\u2019t a cohesive theme to tie the proteins to a single biological role, so a specific label isn\u2019t supported.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019373","count":2},{"id":"GO:0009103","count":1},{"id":"GO:0070574","count":1},{"id":"GO:1990938","count":1},{"id":"GO:0099132","count":1}]},{"hash":"1631648015846175381","title":"Sugar alcohol and carbohydrate metabolism","description":"Several GO terms converge on metabolism of sugar alcohols and related carbohydrate pathways (D-sorbitol and xylitol catabolism, furaldehyde metabolism, pyruvate fermentation to ethanol, and ethanol oxidation). Additional terms touch on broader lipid-related metabolism (retinoic acid, prostaglandin) and stress/immune responses (response to lipopolysaccharide, nitrosative stress), suggesting a primary focus on carbohydrate processing with ancillary metabolic and defensive roles. Confidence: Medium","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0033859","count":3},{"id":"GO:0006062","count":3},{"id":"GO:0043458","count":3},{"id":"GO:0051409","count":3},{"id":"GO:0045777","count":3}]},{"hash":"2108473553314642559","title":"Diverse Biosynthetic Metabolism","description":"The terms are dominated by various biosynthetic processes (biotin, beta-alanine, protoporphyrinogen IX) and related metabolic activities, with a few auxiliary oxidation-reduction terms and some obscure/obsolete annotations. This suggests the cluster centers on broad metabolic biosynthesis and cofactor production rather than a single specific function, hence a general metabolic biosynthesis label.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0048148","count":1},{"id":"GO:0009413","count":1},{"id":"GO:0009447","count":1},{"id":"GO:0017000","count":1}]},{"hash":"967828333639218863","title":"Lipid and Steroid Metabolism","description":"The proteins\u2019 GO annotations are dominated by lipid- and steroid-related metabolic processes, such as androgen catabolic process, C21-steroid hormone metabolic process, steroid catabolic process, and fatty acid elongation/mycolic acid biosynthesis. While several other terms appear (retinal metabolism, methyl-branched fatty acid biosynthesis, cofactor and vitamin metabolism), the strongest cohesive signal is metabolism of lipids and steroids.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031427","count":1},{"id":"GO:0006710","count":1},{"id":"GO:0006729","count":1},{"id":"GO:0008207","count":1},{"id":"GO:1902321","count":1}]},{"hash":"2208172124409681352","title":"Plant metabolism and cell wall assembly","description":"These proteins point to plant-specific processes, with GO terms for plant-type cell wall assembly, fatty acid transmembrane transport, and heme biosynthesis/regulation. While the terms span distinct pathways (cell wall biogenesis, lipid transport, and heme synthesis), they collectively indicate a plant-focused metabolic cluster involving membrane-associated lipid/heme processes and cell wall formation.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071668","count":1},{"id":"GO:1902001","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0070453","count":1}]},{"hash":"509728988783516203","title":"Nucleotide metabolism and salvage","description":"The cluster is dominated by GO terms related to nucleotide metabolism and salvage (purine ribonucleotide interconversion, ADP/CDP biosynthesis, ITP metabolism, nucleoside monophosphate phosphorylation, and AMP salvage). A couple of terms on development (liver/brain) and photosystem II assembly appear as outliers, suggesting the core signal is nucleotide biosynthesis/salvage with some noise. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001889","count":2},{"id":"GO:0015951","count":2},{"id":"GO:0006172","count":2},{"id":"GO:0046041","count":2},{"id":"GO:0007420","count":2}]},{"hash":"1517190429984953663","title":"Unknown","description":"The terms indicate several distinct, poorly connected processes (centriole elongation and cell division; heat acclimation; oxidative phosphorylation and ATP biosynthesis; transcription preinitiation and mRNA export; even viral genome replication). There is no clear shared function or pathway linking all proteins, and the zero edges offer little context, so a concise, cohesive label isn\u2019t supported.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903724","count":2},{"id":"GO:0070370","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1903862","count":2}]},{"hash":"455451292875408847","title":"Unknown","description":"The three proteins show GO terms across a wide range of processes (plant phototransduction, ethylene signaling, animal cytokine signaling, DNA repair, metabolism, and kinase regulation) with no clear shared function or common pathway, so a specific, representative label cannot be confidently assigned.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030511","count":1},{"id":"GO:0006265","count":1},{"id":"GO:0006298","count":1},{"id":"GO:0071353","count":1},{"id":"GO:1901856","count":1}]},{"hash":"1930655201511992496","title":"Oxidative stress and inflammatory response","description":"The cluster\u2019s top GO terms converge on redox biology and inflammation, including hydrogen peroxide catabolic process, cellular oxidant detoxification, and positive/negative regulation related to SOD activity and inflammatory response. There are additional hints of stress-related transcriptional control (nuclear localization) and ubiquitin-proteasome signaling, suggesting a module where redox stress intersects inflammatory signaling. Overall, a redox/inflammation-focused label fits best, with some peripheral terms introducing noise.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1903094","count":3},{"id":"GO:0006954","count":3},{"id":"GO:1900182","count":3},{"id":"GO:1901671","count":3},{"id":"GO:2000825","count":3}]},{"hash":"784654872951244043","title":"Innate Immunity and Antigen Presentation","description":"Based on the top GO terms, the proteins cluster around innate immune activation (GO:0010204), MHC class I\u2013associated antigen assembly (GO:0002502), and phagocytosis regulation (GO:0050766), pointing to a module involved in innate immune signaling and antigen processing/presentation. Some additional terms reflect cellular stress responses (ER unfolded protein response, cellular senescence) that can intersect immunity, while a few terms (developmental processes, sperm\u2013zona pellucida binding) may be less connected noise. Overall, the central theme appears to be innate immune function and antigen presentation.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"protein folding","top_go_terms":[{"id":"GO:0048916","count":3},{"id":"GO:0002502","count":3},{"id":"GO:0010204","count":3},{"id":"GO:0071157","count":3},{"id":"GO:0030968","count":3}]},{"hash":"1480942670266754716","title":"Neural, retinal, and cardiac development","description":"The GO terms point to nervous system and visual processes (axonogenesis, Schwann cell development, visual perception) and heart/vascular development (angiogenesis, heart development). Together, they suggest a cluster of proteins involved in tissue differentiation and organogenesis across neural and cardiac lineages.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0043065","count":2},{"id":"GO:0014850","count":2}]},{"hash":"2144822708683794101","title":"Plant floral and seed development with hormone signaling","description":"The cluster centers on plant reproductive development (bract development, seed development, floral meristem growth) and multiple hormone pathways (ethylene, ABA, auxin signaling), with additional terms for epidermal lipid biosynthesis (cutin, wax regulation) and general transcriptional control. A defense-related term (response to chitin) is present but does not negate the developmental theme and may reflect signaling cross-talk. Overall, these terms point to coordinated developmental programs governed by hormonal signals and epidermal maturation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010200","count":1},{"id":"GO:0010432","count":1},{"id":"GO:0048316","count":1},{"id":"GO:0060774","count":1},{"id":"GO:0010451","count":1}]},{"hash":"1005322502671436975","title":"Floral development and hormone-regulated cuticle biosynthesis","description":"Based on GO terms including floral meristem growth, seed and bract development, and multiple hormone signaling pathways (ethylene, ABA, auxin), alongside cutin and wax biosynthesis, the cluster seems centered on plant reproductive development with regulation of the epidermal cuticle by hormonal signals; the single stress-related term (response to chitin) may be an outlier but does not dominate the theme.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010200","count":2},{"id":"GO:0010432","count":2},{"id":"GO:0048316","count":2},{"id":"GO:0060774","count":2},{"id":"GO:0010451","count":2}]},{"hash":"2178239566696283150","title":"Catabolic metabolism","description":"The cluster\u2019s GO terms are largely focused on various catabolic processes (camphor, L-alanine, alkane catabolism) and a cofactor-related metabolic process (dihydrolipoamide metabolic process), suggesting enzymes involved in energy-releasing oxidation pathways. A few terms related to development and neuron maturation appear only once and seem incidental rather than defining; overall the dominant signal is catabolic metabolism, so the label is appropriate though not perfectly cohesive. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019383","count":2},{"id":"GO:0007568","count":1},{"id":"GO:0016575","count":1},{"id":"GO:0021983","count":1},{"id":"GO:0042853","count":1}]},{"hash":"1606789623530181427","title":"Steroid-regulated development and differentiation","description":"Top GO terms show keratinocyte development and differentiation (epidermal differentiation), and several terms point to glucocorticoid signaling and metabolism, indicating steroid hormone regulation. Additional terms touch on neural development and general signaling control, suggesting a broader developmental context where steroid pathways modulate differentiation. Overall, the cluster seems to reflect steroid-influenced developmental and differentiation processes.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0003334","count":2},{"id":"GO:0000079","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0006605","count":2},{"id":"GO:0030216","count":2}]},{"hash":"1723133394656706590","title":"Unknown","description":"No shared GO terms or functional signals are presented (empty Top Terms; single edge). With such sparse data, there is no clear theme to unite these proteins, so the appropriate label is Unknown and confidence is None.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"633366974411805327","title":"Unknown","description":"The top GO terms are highly diverse, spanning RNA decay, chromatin remodeling, heterochromatin formation, Rho signaling, innate mucosal immunity, cell migration, fertilization, and vitellogenesis. There is no clear shared function or pathway linking these proteins, and the cluster has no edges, so a specific, representative name cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070481","count":1},{"id":"GO:0033128","count":1},{"id":"GO:0034184","count":1},{"id":"GO:0031508","count":1},{"id":"GO:0031509","count":1}]},{"hash":"1639131788252468011","title":"Ubiquitin-Driven Signaling and Apoptosis Regulation","description":"The top GO terms heavily emphasize ubiquitination (K48- and K63-linked), regulation of apoptosis, and immune signaling pathways (NF-\u03baB activation, TNF signaling). While a few terms are more peripheral (V(D)J recombination, peroxisome import), the common thread is ubiquitin-mediated control of signaling processes that govern cell survival and immune responses, suggesting a cluster centered on ubiquitin-regulated signaling and apoptosis.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070936","count":2},{"id":"GO:0042981","count":2},{"id":"GO:0033151","count":2},{"id":"GO:0070535","count":2},{"id":"GO:1901253","count":2}]},{"hash":"389886817836004147","title":"RNA and protein methylation enzymes","description":"GO terms strongly bias toward RNA modification (rRNA, tRNA wobble) and various protein methylation events (peptidyl-lysine, arginine dimethylation), implying a cluster of RNA-modifying and methyltransferase proteins; nucleologenesis aligns with ribosome biogenesis, while a chlorophyll term appears peripheral noise.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032775","count":1},{"id":"GO:0017126","count":1},{"id":"GO:0002098","count":1},{"id":"GO:0036068","count":1},{"id":"GO:0000154","count":1}]},{"hash":"1201793183947616273","title":"Plant leaf development and transcriptional regulation","description":"This cluster centers on plant developmental processes, especially leaf morphogenesis and shoot formation, with accompanying transcriptional regulation (DNA-templated transcription) and hormone/biochemical regulation (response to gibberellin, regulation of chlorophyll biosynthesis). The terms together point to a cohesive theme of plant leaf development and gene expression control. The viral process term seems incidental. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045962","count":1},{"id":"GO:0009965","count":1},{"id":"GO:0006351","count":1},{"id":"GO:2000032","count":1},{"id":"GO:0006355","count":1}]},{"hash":"1048697814764891724","title":"Signaling and Carbohydrate Catabolism","description":"The top GO terms show both diverse signaling pathway involvement (MAPKKK cascade, cytokinin, insulin receptor signaling) and several carbohydrate catabolic processes (glucosinolates, cellulose, lactose). This indicates a cluster of proteins linked to general signaling and metabolic breakdown rather than a single specific function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090080","count":1},{"id":"GO:0019762","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0008286","count":1},{"id":"GO:0030245","count":1}]},{"hash":"1598319899127046380","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"The dominant GO terms point to oocyte maturation and spindle assembly in female meiosis I, supported by microtubule polymerization and ubiquitin-proteasome\u2013mediated protein turnover\u2014hallmarks of meiotic progression and cell-cycle regulation during oogenesis. Neural development terms appear less central to the cluster\u2019s core theme, so the label emphasizes meiosis/oocyte-related processes. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":2},{"id":"GO:0021678","count":2},{"id":"GO:0006516","count":2},{"id":"GO:0051436","count":2},{"id":"GO:0046785","count":2}]},{"hash":"1840923293975021613","title":"Wnt-Hippo Signaling in Development","description":"This cluster centers on canonical Wnt signaling (both activation and inhibition) and Hippo pathway terms, with related developmental processes like face development and keratinocyte differentiation, and apoptosis. Together, these suggest a regulatory module where Wnt/Hippo signaling governs development and cell fate decisions. Some terms may reflect broader signaling contexts or annotation noise.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0060044","count":3},{"id":"GO:0030216","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0035329","count":3}]},{"hash":"1539487629092921563","title":"Neural development and ion transport","description":"This cluster is characterized by neural development and sensory signaling (multicellular organism development, face development, optic nerve morphogenesis, pain perception) plus neuronal ion transport processes (sodium import, potassium export) and neurotrophin signaling, suggesting a theme of nervous system formation and function, including neuronal signaling. Some terms are more general, but the core appears to center on neural development and excitability.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0019233","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0048011","count":1}]},{"hash":"1000065447927822698","title":"Retinoic acid metabolism and female reproductive development","description":"These proteins show enrichment in retinoic acid\u2013related processes (9-cis-retinoic acid biosynthetic and retinoic acid catabolic processes) and female reproductive development terms (uterus development, female gonad/genitalia development), suggesting a theme around retinoic acid signaling in reproductive tissue development. Some other terms (carbazole and isoquinoline alkaloid metabolism) are broader metabolic annotations and less central to this theme, but do not override the core RA-development signal.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071615","count":2},{"id":"GO:0042904","count":2},{"id":"GO:0060065","count":2},{"id":"GO:0008585","count":2},{"id":"GO:0034653","count":2}]},{"hash":"1620865977140838347","title":"Plant cell wall biosynthesis and modification","description":"The strongest signals are plant-type secondary cell wall biogenesis, cell wall modification, xylan biosynthetic process, and xyloglucan metabolic process, with related terms like xylan acetylation; these together indicate a cluster focused on plant cell wall polysaccharide synthesis and remodeling, rather than core metabolism. A few sugar metabolism terms appear ancillary. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":2},{"id":"GO:0050826","count":2},{"id":"GO:0009827","count":2},{"id":"GO:0045492","count":2},{"id":"GO:0010411","count":2}]},{"hash":"2191040466725205812","title":"Protein acetylation","description":"The top terms are dominated by diverse acetylation events (spermidine, putrescine, histone H4, peptidyl-lysine, N-terminal methionine, and N-acetylglucosamine/mycothiol processes), suggesting the cluster centers on acetyltransferase activity or substrates undergoing acetylation. While a couple of terms touch broader metabolism (arginine and mycothiol biosynthesis), the unifying theme is acetyl group transfer to various targets.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032918","count":3},{"id":"GO:0043967","count":3},{"id":"GO:0006526","count":3},{"id":"GO:0032920","count":3},{"id":"GO:0006044","count":3}]},{"hash":"302242226086972048","title":"BMP/TGF-\u03b2 Signaling Regulation","description":"This cluster is dominated by GO terms indicating negative regulation of BMP signaling and negative regulation of TGF-\u03b2 receptor signaling, with supporting terms on SMAD regulation and related downstream responses. Additional terms point to broader signaling regulation and development (e.g., meristem identity, cellular response to TGF-\u03b2). The strongest cohesive theme is modulation of BMP/TGF-\u03b2 pathways, though there are peripheral connections to other signaling processes. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030514","count":3},{"id":"GO:0042347","count":3},{"id":"GO:0061191","count":3},{"id":"GO:0000173","count":3},{"id":"GO:0046827","count":3}]},{"hash":"2228204136730037175","title":"Immune signaling and stress responses","description":"The terms point to immune and signaling pathways (Fc-epsilon receptor signaling, inflammatory response regulation, viral process, Wnt-related signaling) alongside stress response elements (zinc/cadmium ion responses, proteasome assembly). Taken together, they suggest a cluster centered on immune signaling and cellular stress responses rather than a single, cohesive function. Confidence: Medium","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0038095","count":2},{"id":"GO:0090090","count":2},{"id":"GO:0061418","count":2},{"id":"GO:0010043","count":2},{"id":"GO:0080129","count":2}]},{"hash":"1537069734119107894","title":"Mitotic spindle and microtubule dynamics","description":"The top GO terms are dominated by mitosis- and microtubule-related processes (mitotic centrosome separation, mitotic spindle assembly, plus-end directed microtubule sliding, and regulation of microtubule-based processes), indicating a cohesive role in spindle formation and cytoskeletal dynamics. Some terms touch on cell junctions and neural structure, but the central theme remains mitotic/cytoskeletal regulation, justifying this label.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007100","count":3},{"id":"GO:0000742","count":2},{"id":"GO:0031535","count":2},{"id":"GO:0045218","count":2},{"id":"GO:0048364","count":2}]},{"hash":"401388443334040692","title":"Plant Cell Wall Synthesis and Plasmodesmata","description":"This cluster is dominated by GO terms tied to plant cell wall biology, including regulation of plant-type cellulose biosynthesis, plasmodesma organization, and plant-type cell wall modification during growth. While a few other terms appear, the strongest, recurring signal points to cell wall synthesis and intercellular connectivity in plants.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001009","count":1},{"id":"GO:0009663","count":1},{"id":"GO:0009831","count":1},{"id":"GO:0070329","count":1},{"id":"GO:0006071","count":1}]},{"hash":"1503129231903410040","title":"Plant Cell Wall Formation and Root Hair Development","description":"Top GO terms indicate plant cell-wall biosynthesis and remodeling (cell wall organization, cellulose and secondary cell wall biogenesis, cell plate assembly, rhamnogalacturonan II biosynthesis) together with root hair development, suggesting a cohesive role in cell-wall construction and root hair differentiation; a few terms like chitin biosynthesis and infection-structure formation may reflect related extracellular matrix processes.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0010306","count":2},{"id":"GO:0080147","count":2},{"id":"GO:0075015","count":1},{"id":"GO:0009834","count":1}]},{"hash":"101954845805363786","title":"Plant ABA signaling and chloroplast movement","description":"The top GO terms point to abscisic acid homeostasis and chloroplast avoidance movement, both characteristic plant-specific responses to environmental cues. The additional terms reference general cellular processes like nuclear migration and cell division, suggesting the cluster broadly relates to plant development and movement/organization at the cellular level, rather than a single narrowly defined function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902265","count":1},{"id":"GO:0045035","count":1},{"id":"GO:0031022","count":1},{"id":"GO:0009903","count":1}]},{"hash":"198012852163299657","title":"Plant hormone signaling in defense and nodulation","description":"The GO terms point to plant-specific hormone signaling (cytokinin-activated, gibberellin-mediated), along with defense responses and nodulation, suggesting a module around hormone-regulated biotic interactions in plants. Transport terms for ions and amino acids support membrane signaling activity found in these pathways. Given the small cluster size and broad terms, the label is plausible but not highly specific, so Confidence: Medium.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990034","count":1},{"id":"GO:0032973","count":1},{"id":"GO:0009607","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0006952","count":1}]},{"hash":"225773649528419020","title":"Retroviral latency and replication","description":"Most top GO terms point to retroviral lifecycle steps: establishment of proviral latency, host activation of viral genome replication, RNA-templated DNA biosynthetic process, and general viral lifecycle/uncoating. A few terms (sepal formation, leukocyte migration) are off-target noise, but overall the cluster centers on retroviral infection processes.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0075713","count":1},{"id":"GO:0048453","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0006278","count":1},{"id":"GO:0019061","count":1}]},{"hash":"530835120946179420","title":"Plant ER-targeted protein transport","description":"The GO terms mainly point to SRP-dependent and post-translational targeting of proteins to membranes, especially the ER, along with ER-to-cytosol retrograde transport and GTPase-regulated processes that can affect the cytoskeleton. The presence of plant-specific terms like xylem/phloem pattern formation and plant-type cell wall biogenesis suggests a plant-centered theme around ER-targeted transport related to plant development. Despite zero edges, the functional theme is coherent, giving a representative, moderate- to high-confidence label; I assign Medium.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006616","count":1},{"id":"GO:0000060","count":1},{"id":"GO:0030970","count":1},{"id":"GO:0031204","count":1},{"id":"GO:0043547","count":1}]},{"hash":"1957529192522755915","title":"Unknown","description":"There are no Top Terms listed for this cluster, and with three proteins but only a single edge and no triangles, there is no clear shared function to base a label on. Without functional terms to tie the proteins together, the appropriate designation is Unknown, with no confidence.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]}]