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GSE130291:vernalization in Arabidopsis thaliana
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Results for AT4G01540
Z-value: 0.64
Transcription factors associated with AT4G01540
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
|
AT4G01540
|
AT4G01540 | NAC with transmembrane motif1 |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| NTM1 | arTal_v1_Chr4_-_672789_672789 | 0.68 | 7.0e-03 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| arTal_v1_Chr2_+_7845923_7845999 Show fit | 0.75 |
AT2G18050.2
AT2G18050.1 |
histone H1-3 |
|
| arTal_v1_Chr3_+_22216540_22216540 Show fit | 0.65 |
AT3G60140.2
AT3G60140.1 |
Glycosyl hydrolase superfamily protein |
|
| arTal_v1_Chr2_+_18347765_18347765 Show fit | 0.63 |
AT2G44460.2
|
beta glucosidase 28 |
|
| arTal_v1_Chr2_+_18346306_18346306 Show fit | 0.62 |
AT2G44460.1
|
beta glucosidase 28 |
|
| arTal_v1_Chr2_-_7919345_7919345 Show fit | 0.51 |
AT2G18193.1
|
P-loop containing nucleoside triphosphate hydrolases superfamily protein |
|
| arTal_v1_Chr3_-_3091766_3091766 Show fit | 0.50 |
AT3G10020.2
|
plant/protein |
|
| arTal_v1_Chr3_-_2699257_2699257 Show fit | 0.49 |
AT3G08860.2
|
PYRIMIDINE 4 |
|
| arTal_v1_Chr5_+_5237970_5238178 Show fit | 0.48 |
AT5G16030.1
AT5G16030.4 AT5G16030.2 AT5G16030.3 |
mental retardation GTPase activating protein |
|
| arTal_v1_Chr3_-_2699420_2699420 Show fit | 0.48 |
AT3G08860.1
|
PYRIMIDINE 4 |
|
| arTal_v1_Chr1_+_24472873_24472873 Show fit | 0.47 |
AT1G65800.1
AT1G65800.2 |
receptor kinase 2 |
Network of associatons between targets according to the STRING database.
First level regulatory network of AT4G01540
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 1.9 | GO:0019759 | S-glycoside catabolic process(GO:0016145) glycosinolate catabolic process(GO:0019759) glucosinolate catabolic process(GO:0019762) |
| 0.0 | 1.5 | GO:0009902 | chloroplast relocation(GO:0009902) establishment of plastid localization(GO:0051667) |
| 0.1 | 1.2 | GO:0010207 | photosystem II assembly(GO:0010207) |
| 0.0 | 1.2 | GO:0009694 | jasmonic acid metabolic process(GO:0009694) |
| 0.1 | 1.1 | GO:0031936 | nucleosome positioning(GO:0016584) negative regulation of chromatin silencing(GO:0031936) |
| 0.0 | 1.1 | GO:0043562 | cellular response to nitrogen levels(GO:0043562) |
| 0.1 | 0.9 | GO:0009061 | anaerobic respiration(GO:0009061) |
| 0.0 | 0.9 | GO:0048506 | regulation of timing of meristematic phase transition(GO:0048506) regulation of timing of transition from vegetative to reproductive phase(GO:0048510) |
| 0.0 | 0.9 | GO:0006338 | chromatin remodeling(GO:0006338) |
| 0.1 | 0.8 | GO:0048363 | mucilage pectin metabolic process(GO:0048363) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 4.3 | GO:0009534 | chloroplast thylakoid(GO:0009534) |
| 0.0 | 3.5 | GO:0042579 | peroxisome(GO:0005777) microbody(GO:0042579) |
| 0.1 | 1.2 | GO:0000786 | nucleosome(GO:0000786) |
| 0.0 | 1.2 | GO:0000790 | nuclear chromatin(GO:0000790) |
| 0.0 | 0.9 | GO:0031903 | peroxisomal membrane(GO:0005778) microbody membrane(GO:0031903) |
| 0.0 | 0.9 | GO:0009707 | chloroplast outer membrane(GO:0009707) |
| 0.0 | 0.8 | GO:0010598 | NAD(P)H dehydrogenase complex (plastoquinone)(GO:0010598) |
| 0.0 | 0.8 | GO:0009986 | cell surface(GO:0009986) |
| 0.0 | 0.7 | GO:0010319 | stromule(GO:0010319) |
| 0.0 | 0.6 | GO:0097346 | INO80-type complex(GO:0097346) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 3.4 | GO:0043531 | ADP binding(GO:0043531) |
| 0.1 | 2.3 | GO:0050135 | NAD(P)+ nucleosidase activity(GO:0050135) |
| 0.0 | 2.2 | GO:0051015 | actin filament binding(GO:0051015) |
| 0.0 | 2.1 | GO:0102483 | scopolin beta-glucosidase activity(GO:0102483) |
| 0.0 | 1.8 | GO:0003713 | transcription coactivator activity(GO:0003713) |
| 0.0 | 1.8 | GO:0003712 | transcription factor activity, transcription factor binding(GO:0000989) transcription cofactor activity(GO:0003712) |
| 0.1 | 1.2 | GO:0008453 | alanine-glyoxylate transaminase activity(GO:0008453) |
| 0.2 | 1.1 | GO:0031492 | nucleosomal DNA binding(GO:0031492) |
| 0.1 | 1.1 | GO:0016987 | core DNA-dependent RNA polymerase binding promoter specificity activity(GO:0000996) sigma factor activity(GO:0016987) |
| 0.0 | 0.9 | GO:0000156 | phosphorelay response regulator activity(GO:0000156) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 0.5 | NABA CORE MATRISOME | Ensemble of genes encoding core extracellular matrix including ECM glycoproteins, collagens and proteoglycans |
| 0.1 | 0.2 | PID DELTA NP63 PATHWAY | Validated transcriptional targets of deltaNp63 isoforms |
| 0.0 | 0.2 | PID REG GR PATHWAY | Glucocorticoid receptor regulatory network |
| 0.0 | 0.2 | PID SMAD2 3NUCLEAR PATHWAY | Regulation of nuclear SMAD2/3 signaling |
| 0.0 | 0.2 | PID AP1 PATHWAY | AP-1 transcription factor network |
| 0.0 | 0.2 | PID IL2 PI3K PATHWAY | IL2 signaling events mediated by PI3K |
| 0.0 | 0.2 | PID HIF1 TFPATHWAY | HIF-1-alpha transcription factor network |
| 0.0 | 0.1 | SIG CHEMOTAXIS | Genes related to chemotaxis |
| 0.0 | 0.1 | PID SHP2 PATHWAY | SHP2 signaling |
| 0.0 | 0.1 | PID ATF2 PATHWAY | ATF-2 transcription factor network |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 0.5 | REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION | Genes involved in GABA synthesis, release, reuptake and degradation |
| 0.1 | 0.4 | REACTOME RECYCLING OF BILE ACIDS AND SALTS | Genes involved in Recycling of bile acids and salts |
| 0.1 | 0.3 | REACTOME GASTRIN CREB SIGNALLING PATHWAY VIA PKC AND MAPK | Genes involved in Gastrin-CREB signalling pathway via PKC and MAPK |
| 0.0 | 0.2 | REACTOME SLC MEDIATED TRANSMEMBRANE TRANSPORT | Genes involved in SLC-mediated transmembrane transport |
| 0.0 | 0.2 | REACTOME FORMATION OF INCISION COMPLEX IN GG NER | Genes involved in Formation of incision complex in GG-NER |
| 0.0 | 0.2 | REACTOME RNA POL II PRE TRANSCRIPTION EVENTS | Genes involved in RNA Polymerase II Pre-transcription Events |
| 0.1 | 0.1 | REACTOME FRS2 MEDIATED CASCADE | Genes involved in FRS2-mediated cascade |
| 0.0 | 0.1 | REACTOME G2 M DNA DAMAGE CHECKPOINT | Genes involved in G2/M DNA damage checkpoint |
| 0.0 | 0.1 | REACTOME SIGNALING BY TGF BETA RECEPTOR COMPLEX | Genes involved in Signaling by TGF-beta Receptor Complex |
| 0.0 | 0.1 | REACTOME GLUCONEOGENESIS | Genes involved in Gluconeogenesis |