TissueCFM001824's detailed annotation
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Protein: Yellow color--query protein Green color--interaction proteins. Interaction line: Pink--proteins own interaction and positive co-expression relationship with target protein Blue--proteins own interaction and negative co-expression relationship with target protein Orange--proteins own interaction and protein-protein relationship with target protein |
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Module annotation (GSEA enrichment result)
| Function Annotation | FDR | Gene Ontolog |
|---|---|---|
| Transcription_related, Transcription regulator: SWI/SNF-SWI3 | 0.000886394 | TF family |
| cytoplasmic ubiquitin ligase complex | 0.004048762 | GO:0000153 |
| uracil phosphoribosyltransferase activity | 0.004887091 | GO:0004845 |
| beta-ketoacyl-acyl-carrier-protein synthase III activity | 0.004887091 | GO:0033818 |
| Atg8 ligase activity | 0.004887091 | GO:0019776 |
| 3-oxoacyl-[acyl-carrier-protein] synthase activity | 0.005497572 | GO:0004315 |
| histone H3-K4 methylation | 0.00686944 | GO:0051568 |
| nucleophagy | 0.00686944 | GO:0044804 |
| pyrimidine nucleoside salvage | 0.00686944 | GO:0043097 |
| UMP biosynthetic process | 0.00686944 | GO:0006222 |
| uracil salvage | 0.00686944 | GO:0006223 |
| mitophagy | 0.00686944 | GO:0000422 |
| pyrimidine nucleobases salvage I | 0.00752274 | plantCyc |
| superpathway of pyrimidine nucleobases salvage | 0.00752274 | plantCyc |
| superpathway of pyrimidine ribonucleosides salvage | 0.00752274 | plantCyc |
| autophagosome assembly | 0.007569284 | GO:0000045 |
| fatty acid biosynthesis initiation I | 0.011728539 | plantCyc |
| spermine and spermidine degradation III | 0.011728539 | plantCyc |
| pyrimidine salvage pathway | 0.012026605 | plantCyc |
| uridine kinase activity | 0.013188323 | GO:0004849 |
| potassium ion binding | 0.013602979 | GO:0030955 |
| pyruvate kinase activity | 0.013602979 | GO:0004743 |
| chloroplast | 0.01654079 | GO:0009507 |
| cytosol | 0.01654079 | GO:0005829 |
| Rubisco shunt | 0.021876488 | plantCyc |
| glycolysis IV (plant cytosol) | 0.024753611 | plantCyc |
| Autophagy - animal | 0.02579591 | KEGG pathway |
| Pyrimidine metabolism | 0.02579591 | KEGG pathway |
| glycolysis I (from glucose 6-phosphate) | 0.02648625 | plantCyc |
| glycolytic process | 0.027172125 | GO:0006096 |
| Fatty acid metabolism | 0.029426642 | KEGG pathway |
| protein transport | 0.032607858 | GO:0015031 |
| fatty acid biosynthetic process | 0.039275722 | GO:0006633 |
Module member annotation
| Gene ID | Ortholog in Arabidopsis (Blast E-value) | Annotation in Arabidopsis |
|---|---|---|
| CRO_T000921 | AT1G32440 (9.00E-70) | PKp3|plastidial pyruvate kinase 3 |
| CRO_T009684 | AT1G62830 (0) | ATLSD1|ARABIDOPSIS LYSINE-SPECIFIC HISTONE DEMETHYLASE; LDL1|LSD1-like 1; LSD1|LYSINE-SPECIFIC HISTONE DEMETHYLASE |
| CRO_T018429 | AT5G61500 (8.00E-166) | ATATG3; ATG3|autophagy 3 (APG3) |
| CRO_T021123 | AT3G27440 (1.00E-18) | UKL5|uridine kinase-like 5 |
| CRO_T023472 | - | - |
| CRO_T030368 | AT4G22740 (1.00E-59) | glycine-rich protein |
Direct connection functional modules
| Module ID | Function Annotation | Overlap condition |
|---|---|---|
| TissueCFM000420 | peptidyl-arginine methylation FAD metabolic process response to high light intensity Riboflavin metabolism diaminohydroxyphosphoribosylaminopyrimidine deaminase activity 5-amino-6-(5-phosphoribosylamino)uracil reductase activity riboflavin biosynthetic process pyruvate kinase activity histone-arginine N-methyltransferase activity potassium ion binding protein-arginine omega-N asymmetric methyltransferase activity RNA modification flavin biosynthesis I (bacteria and plants) glycolysis I (from glucose 6-phosphate) glycolysis IV (plant cytosol) Rubisco shunt chloroplast chloroplast organization glycolytic process NADP binding | details |
| TissueCFM000537 | non-hydrolytic cleavage of glycosidic bonds, Polysaccharide Lyases: PL4 pectate lyase activity regulation of nucleobase-containing compound metabolic process homogentisate catabolic process tyrosine catabolic process pectin catabolic process positive regulation of chromatin organization trans, trans-farnesyl diphosphate biosynthesis geranylgeranyl diphosphate biosynthesis L-cysteine biosynthesis I polyisoprenoid biosynthesis superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) homogentisate 1,2-dioxygenase activity Z-farnesyl diphosphate synthase activity Atg8 ligase activity D-myo-inositol (1,4,5)-trisphosphate degradation farnesyl diphosphate biosynthetic process regulation of macromolecule metabolic process L-phenylalanine catabolic process mitotic chromosome condensation mitophagy nucleophagy Pentose and glucuronate interconversions Cell cycle - yeast RIG-I-like receptor signaling pathway Tyrosine metabolism autophagosome assembly condensed chromosome cytoplasmic ubiquitin ligase complex | details |
| TissueCFM000589 | Cytochrome_P450, Cytochrome P450: CYP94D extended VTC2 cycle pyrimidine nucleobases salvage I superpathway of pyrimidine nucleobases salvage superpathway of pyrimidine ribonucleosides salvage VTC2 cycle endoplasmic reticulum tubular network organization intracellular protein transport barrier septum site selection uracil salvage UMP biosynthetic process uracil phosphoribosyltransferase activity calcium-dependent ATPase activity GDP-D-glucose phosphorylase activity pyrimidine nucleoside salvage pyrimidine salvage pathway chloroplast fission L-ascorbate biosynthesis I (L-galactose pathway) Ascorbate and aldarate metabolism Autophagy - yeast Pyrimidine metabolism aromatase activity uridine kinase activity glucose metabolic process endoplasmic reticulum tubular network vesicle docking Transcription_related, Transcription factor: M-type vesicle fusion | details |
| TissueCFM000729 | pyrimidine nucleobases salvage I superpathway of pyrimidine nucleobases salvage superpathway of pyrimidine ribonucleosides salvage regulation of phosphorylation regulation of nitrogen utilization uracil salvage regulation of fatty acid biosynthetic process uracil phosphoribosyltransferase activity acetylglutamate kinase regulator activity UMP biosynthetic process anthocyanin-containing compound biosynthetic process pyrimidine nucleoside salvage pyrimidine salvage pathway formation of glycosidic bonds, GlycosylTransferases: GTnc uridine kinase activity Pyrimidine metabolism vindoline and vinblastine biosynthesis cell wall organization or biogenesis regulation of catalytic activity response to cytokinin | details |
| TissueCFM000937 | cytoplasmic ubiquitin ligase complex trans, trans-farnesyl diphosphate biosynthesis geranylgeranyl diphosphate biosynthesis polyisoprenoid biosynthesis superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) Atg8 ligase activity Z-farnesyl diphosphate synthase activity actin filament-based process mitophagy farnesyl diphosphate biosynthetic process nucleophagy autophagosome assembly geranyltranstransferase activity non-hydrolytic cleavage of glycosidic bonds, Polysaccharide Lyases: PL4 Transcription_related, Transcription factor: C2C2-GATA dimethylallyltranstransferase activity pectate lyase activity structural constituent of cytoskeleton Autophagy - animal Terpenoid backbone biosynthesis pectin catabolic process protein transport Pentose and glucuronate interconversions | details |
| TissueCFM001036 | pyrimidine nucleobases salvage I superpathway of pyrimidine nucleobases salvage superpathway of pyrimidine ribonucleosides salvage Cytochrome_P450, Cytochrome P450: CYP94D barrier septum site selection formate catabolic process uracil salvage serine family amino acid biosynthetic process pyrimidine salvage pathway formate dehydrogenase (NAD+) activity uracil phosphoribosyltransferase activity calcium-dependent ATPase activity UMP biosynthetic process Transcription_related, Transcription factor: OFP pyrimidine nucleoside salvage phosphoglycerate dehydrogenase activity chloroplast fission Wnt signaling pathway uridine kinase activity aromatase activity ubiquitin binding regulation of cell shape Pyrimidine metabolism Ras signaling pathway Endocytosis Transcription_related, Transcription factor: M-type | details |
| TissueCFM001170 | spermine and spermidine degradation III Transcription_related, Transcription regulator: SWI/SNF-SWI3 formation of glycosidic bonds, GlycosylTransferases: GTnc U2AF histone H3-K4 methylation Spliceosome mRNA splicing, via spliceosome | details |
| TissueCFM001183 | Autophagy - animal Atg8 ligase activity Protein_kinases_phosphatases, PPC:1.13.3: Leucine Rich Repeat Kinase III Transcription_related, Transcription factor: C2C2-GATA cytoplasmic ubiquitin ligase complex fruit ripening nucleophagy mitophagy autophagosome assembly nucleosome assembly | details |
| TissueCFM001397 | Transcription_related, Transcription regulator: SWI/SNF-SWI3 formation of glycosidic bonds, GlycosylTransferases: GTnc spermine and spermidine degradation III plant sterol biosynthesis Ubiquitin_Proteasome_system, DUB: USP steroid biosynthetic process histone H3-K4 methylation protein deubiquitination Steroid biosynthesis 3-beta-hydroxy-delta5-steroid dehydrogenase activity thiol-dependent ubiquitinyl hydrolase activity Spliceosome Golgi membrane integral component of membrane oxidation-reduction process cell wall organization | details |
| TissueCFM001470 | Phagosome microtubule-based process structural constituent of cytoskeleton microtubule GTPase activity GTP binding glycolysis I (from glucose 6-phosphate) glycolysis IV (plant cytosol) Rubisco shunt Ubiquitin_Proteasome_system, E3: U-box potassium ion binding pyruvate kinase activity cytoplasm glycolytic process | details |
| TissueCFM001576 | pyruvate decarboxylation to acetyl CoA tyrosine catabolic process homogentisate catabolic process actin filament-based process homogentisate 1,2-dioxygenase activity Atg8 ligase activity nucleophagy L-phenylalanine catabolic process mitophagy cytoplasmic ubiquitin ligase complex autophagosome assembly Autophagy - animal Tyrosine metabolism Transcription_related, Transcription factor: C2C2-GATA cytosolic ribosome structural constituent of cytoskeleton | details |
| TissueCFM001613 | cytoplasmic ubiquitin ligase complex hydroxymethylglutaryl-CoA synthase activity Atg8 ligase activity Z-farnesyl diphosphate synthase activity geranyltranstransferase activity autophagosome assembly farnesyl diphosphate biosynthetic process nucleophagy mitophagy trans, trans-farnesyl diphosphate biosynthesis geranylgeranyl diphosphate biosynthesis mevalonate pathway I polyisoprenoid biosynthesis superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) dimethylallyltranstransferase activity Autophagy - animal Butanoate metabolism isoprenoid biosynthetic process Terpenoid backbone biosynthesis protein transport Ubiquitin_Proteasome_system, E3 adaptor: DWD | details |
| TissueCFM001620 | Transcription_related, Transcription regulator: SWI/SNF-SWI3 spermine and spermidine degradation III leucyl-tRNA aminoacylation histone H3-K4 methylation regulation of translational fidelity leucine-tRNA ligase activity oxidoreductase activity aminoacyl-tRNA editing activity Aminoacyl-tRNA biosynthesis oxidation-reduction process Spliceosome | details |
| TissueCFM001645 | Phagosome microtubule-based process structural constituent of cytoskeleton microtubule cytoplasm GTP binding 1-acyl-2-lysophosphatidylserine acylhydrolase activity GTPase activity 5-amino-6-(5-phosphoribosylamino)uracil reductase activity phosphatidylserine 1-acylhydrolase activity phosphatidylcholine 1-acylhydrolase activity diaminohydroxyphosphoribosylaminopyrimidine deaminase activity FAD metabolic process response to high light intensity Riboflavin metabolism potassium ion binding pyruvate kinase activity riboflavin biosynthetic process RNA modification chloroplast chloroplast organization glycolytic process flavin biosynthesis I (bacteria and plants) glycolysis I (from glucose 6-phosphate) glycolysis IV (plant cytosol) phosphatidylcholine acyl editing phospholipases Rubisco shunt triacylglycerol degradation NADP binding | details |
| TissueCFM001806 | spermine and spermidine degradation III Transcription_related, Transcription regulator: SWI/SNF-SWI3 histone H3-K4 methylation Transcription_related, Transcription factor: WRKY | details |
| TissueCFM001820 | pyruvate decarboxylation to acetyl CoA Carbon metabolism transferase activity, transferring acyl groups formate dehydrogenase (NAD+) activity Atg8 ligase activity homogentisate 1,2-dioxygenase activity phosphoglycerate dehydrogenase activity tyrosine catabolic process homogentisate catabolic process serine family amino acid biosynthetic process formate catabolic process Tyrosine metabolism L-phenylalanine catabolic process nucleophagy mitophagy cytoplasmic ubiquitin ligase complex Autophagy - animal autophagosome assembly cytosolic ribosome cytosol chloroplast part protein transport NAD binding dioxygenase activity | details |
Expression profiles
 Show details about module gene expression profiling |