TissueCFM000937's detailed annotation
|
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 |
| This network produced by cytoscapeweb |
Module annotation (GSEA enrichment result)
| Function Annotation | FDR | Gene Ontolog |
|---|---|---|
| cytoplasmic ubiquitin ligase complex | 0.005397871 | GO:0000153 |
| trans, trans-farnesyl diphosphate biosynthesis | 0.007547646 | plantCyc |
| geranylgeranyl diphosphate biosynthesis | 0.007547646 | plantCyc |
| polyisoprenoid biosynthesis | 0.007547646 | plantCyc |
| superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) | 0.007547646 | plantCyc |
| superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) | 0.007547646 | plantCyc |
| Atg8 ligase activity | 0.007852993 | GO:0019776 |
| Z-farnesyl diphosphate synthase activity | 0.007852993 | GO:0033850 |
| actin filament-based process | 0.008990488 | GO:0030029 |
| mitophagy | 0.008990488 | GO:0000422 |
| farnesyl diphosphate biosynthetic process | 0.008990488 | GO:0045337 |
| nucleophagy | 0.008990488 | GO:0044804 |
| autophagosome assembly | 0.009245446 | GO:0000045 |
| geranyltranstransferase activity | 0.01308426 | GO:0004337 |
| non-hydrolytic cleavage of glycosidic bonds, Polysaccharide Lyases: PL4 | 0.014920056 | cazy family |
| Transcription_related, Transcription factor: C2C2-GATA | 0.014920056 | TF family |
| dimethylallyltranstransferase activity | 0.019616243 | GO:0004161 |
| pectate lyase activity | 0.023520022 | GO:0030570 |
| structural constituent of cytoskeleton | 0.023520022 | GO:0005200 |
| Autophagy - animal | 0.025955975 | KEGG pathway |
| Terpenoid backbone biosynthesis | 0.033631312 | KEGG pathway |
| pectin catabolic process | 0.037986535 | GO:0045490 |
| protein transport | 0.037986535 | GO:0015031 |
| Pentose and glucuronate interconversions | 0.041204612 | KEGG pathway |
Module member annotation
| Gene ID | Ortholog in Arabidopsis (Blast E-value) | Annotation in Arabidopsis |
|---|---|---|
| CRO_T002095 | AT1G04680 (1.00E-140) | Pectin lyase-like superfamily protein |
| CRO_T008314 | AT1G63640 (0) | P-loop nucleoside triphosphate hydrolases superfamily protein with CH (Calponin Homology) domain |
| CRO_T008558 | - | - |
| CRO_T013147 | AT5G66320 (7.00E-55) | GATA5|GATA transcription factor 5 |
| CRO_T015546 | AT5G47770 (3.00E-144) | FPS1|farnesyl diphosphate synthase 1 |
| CRO_T018429 | AT5G61500 (8.00E-166) | ATATG3; ATG3|autophagy 3 (APG3) |
| CRO_T025049 | AT2G37620 (2.00E-22) | AAc1|ARABIDOPSIS ACTIN 1; ACT1|actin 1 |
| CRO_T030288 | AT4G25310 (6.00E-57) | 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein |
Direct connection functional modules
| Module ID | Function Annotation | Overlap condition |
|---|---|---|
| TissueCFM000241 | homogentisate 1,2-dioxygenase activity homogentisate catabolic process tyrosine catabolic process non-hydrolytic cleavage of glycosidic bonds, Polysaccharide Lyases: PL4 L-phenylalanine catabolic process pectate lyase activity Tyrosine metabolism pectin catabolic process Pentose and glucuronate interconversions integral component of membrane Purine metabolism | details |
| TissueCFM000444 | actin filament-based process ubiquinone biosynthetic process non-hydrolytic cleavage of glycosidic bonds, Polysaccharide Lyases: PL4 Ubiquitin_Proteasome_system, DUB: OTU pectate lyase activity structural constituent of cytoskeleton Thiamine metabolism Lysosome pectin catabolic process single-organism metabolic process lipid binding Pentose and glucuronate interconversions | 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 |
| TissueCFM000733 | Transcription_related, Transcription factor: BBR-BPC L-valine degradation I non-hydrolytic cleavage of glycosidic bonds, Polysaccharide Lyases: PL4 D-gluconate catabolic process Carbon metabolism gluconokinase activity receptor activity aldehyde dehydrogenase (NAD) activity malonate-semialdehyde dehydrogenase (acetylating) activity protein phosphatase inhibitor activity pectate lyase activity abscisic acid binding methylmalonate-semialdehyde dehydrogenase (acylating) activity regulation of protein serine/threonine phosphatase activity | 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 |
| TissueCFM001241 | uracil degradation I (reductive) non-hydrolytic cleavage of glycosidic bonds, Polysaccharide Lyases: PL4 protein targeting to membrane uracil catabolic process beta-ureidopropionase activity MAPK signaling pathway - yeast Pyrimidine metabolism SNARE interactions in vesicular transport vesicle docking microtubule-based movement vesicle fusion response to stimulus pectin catabolic process pectate lyase activity protein domain specific binding Pentose and glucuronate interconversions SNARE binding SNAP receptor activity microtubule motor activity | details |
| TissueCFM001499 | leucopelargonidin and leucocyanidin biosynthesis phosphoprotein binding Transcription_related, Transcription factor: HB lipid binding dioxygenase activity | 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 |
| TissueCFM001579 | Transcription_related, Transcription factor: BBR-BPC Transcription_related, Transcription factor: NF-YC L-valine degradation I RIG-I-like receptor signaling pathway phosphoprotein binding malonate-semialdehyde dehydrogenase (acetylating) activity methylmalonate-semialdehyde dehydrogenase (acylating) activity receptor activity abscisic acid binding protein phosphatase inhibitor activity aldehyde dehydrogenase (NAD) activity glutathione metabolic process abscisic acid-activated signaling pathway RNA secondary structure unwinding regulation of protein serine/threonine phosphatase activity negative regulation of catalytic activity Glutathione metabolism | 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 |
| TissueCFM001639 | L-cysteine biosynthesis I formation of glycosidic bonds, GlycosylTransferases: GTnc hydrolysis and/or rearrangement of glycosidic bonds, Glycoside Hydrolases: GHnc plant-type cell wall organization cellular amino acid biosynthetic process cysteine biosynthetic process from serine cell wall cysteine synthase activity beta-galactosidase activity | details |
| TissueCFM001640 | Antigen processing and presentation cell wall hydrolysis and/or rearrangement of glycosidic bonds, Glycoside Hydrolases: GHnc cytoplasmic, membrane-bounded vesicle plant-type cell wall organization protein catabolic process beta-galactosidase activity aspartic-type endopeptidase activity dioxygenase activity carbohydrate binding | details |
| TissueCFM001657 | leucopelargonidin and leucocyanidin biosynthesis phosphoprotein binding Protein_kinases_phosphatases, PPC:4.2.6: IRE/NPH/PI dependent/S6 Kinase Transcription_related, Transcription factor: HB water transport glycerol transport cellular water homeostasis glycerol channel activity water channel activity ion transmembrane transport lipid binding | details |
| TissueCFM001759 | regulation of nucleobase-containing compound metabolic process positive regulation of chromatin organization xylogalacturonan biosynthesis regulation of macromolecule metabolic process hydrolysis and/or rearrangement of glycosidic bonds, Glycoside Hydrolases: GHnc non-hydrolytic cleavage of glycosidic bonds, Polysaccharide Lyases: PL4 xyloglucan metabolic process cell wall biogenesis pectin catabolic process single-organism cellular process pectate lyase activity xyloglucan:xyloglucosyl transferase activity Pentose and glucuronate interconversions Purine metabolism | 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 |
| TissueCFM001824 | Transcription_related, Transcription regulator: SWI/SNF-SWI3 cytoplasmic ubiquitin ligase complex uracil phosphoribosyltransferase activity beta-ketoacyl-acyl-carrier-protein synthase III activity Atg8 ligase activity 3-oxoacyl-[acyl-carrier-protein] synthase activity histone H3-K4 methylation nucleophagy pyrimidine nucleoside salvage UMP biosynthetic process uracil salvage mitophagy pyrimidine nucleobases salvage I superpathway of pyrimidine nucleobases salvage superpathway of pyrimidine ribonucleosides salvage autophagosome assembly fatty acid biosynthesis initiation I spermine and spermidine degradation III pyrimidine salvage pathway uridine kinase activity potassium ion binding pyruvate kinase activity chloroplast cytosol Rubisco shunt glycolysis IV (plant cytosol) Autophagy - animal Pyrimidine metabolism glycolysis I (from glucose 6-phosphate) glycolytic process Fatty acid metabolism protein transport fatty acid biosynthetic process | details |
Expression profiles
 Show details about module gene expression profiling |