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GSE130291:vernalization in Arabidopsis thaliana
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Results for AT4G25480
Z-value: 2.35
Transcription factors associated with AT4G25480
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
|
AT4G25480
|
AT4G25480 | dehydration response element B1A |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| DREB1A | arTal_v1_Chr4_-_13019400_13019400 | 0.40 | 1.6e-01 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| arTal_v1_Chr2_-_17712290_17712330 Show fit | 10.95 |
AT2G42540.2
AT2G42540.4 AT2G42540.1 AT2G42540.3 |
cold-regulated 15a |
|
| arTal_v1_Chr5_+_5209717_5209717 Show fit | 9.36 |
AT5G15960.1
|
stress-responsive protein (KIN1) / stress-induced protein (KIN1) |
|
| arTal_v1_Chr2_-_17710433_17710433 Show fit | 8.51 |
AT2G42530.1
|
cold regulated 15b |
|
| arTal_v1_Chr5_+_21240717_21240717 Show fit | 7.47 |
AT5G52310.1
|
low-temperature-responsive protein 78 (LTI78) / desiccation-responsive protein 29A (RD29A) |
|
| arTal_v1_Chr1_+_3019639_3019639 Show fit | 6.88 |
AT1G09350.1
|
galactinol synthase 3 |
|
| arTal_v1_Chr1_-_10289666_10289666 Show fit | 6.72 |
AT1G29395.1
|
COLD REGULATED 314 INNER MEMBRANE 1 |
|
| arTal_v1_Chr1_+_3020221_3020221 Show fit | 6.45 |
AT1G09350.2
|
galactinol synthase 3 |
|
| arTal_v1_Chr4_-_7401951_7401951 Show fit | 6.30 |
AT4G12470.1
|
azelaic acid induced 1 |
|
| arTal_v1_Chr5_+_5211719_5211719 Show fit | 5.77 |
AT5G15970.1
|
stress-responsive protein (KIN2) / stress-induced protein (KIN2) / cold-responsive protein (COR6.6) / cold-regulated protein (COR6.6) |
|
| arTal_v1_Chr5_-_22712441_22712441 Show fit | 5.61 |
AT5G56080.1
|
nicotianamine synthase 2 |
Network of associatons between targets according to the STRING database.
First level regulatory network of AT4G25480
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.8 | 49.7 | GO:0009631 | cold acclimation(GO:0009631) |
| 0.6 | 17.4 | GO:0006012 | galactose metabolic process(GO:0006012) |
| 1.5 | 13.6 | GO:0009819 | drought recovery(GO:0009819) |
| 2.3 | 11.3 | GO:0072708 | response to sorbitol(GO:0072708) |
| 0.2 | 11.2 | GO:0006972 | hyperosmotic response(GO:0006972) |
| 0.3 | 9.8 | GO:0055072 | iron ion homeostasis(GO:0055072) |
| 0.7 | 7.4 | GO:0009608 | response to symbiont(GO:0009608) |
| 1.7 | 6.8 | GO:0030417 | nicotianamine metabolic process(GO:0030417) nicotianamine biosynthetic process(GO:0030418) tricarboxylic acid biosynthetic process(GO:0072351) |
| 0.2 | 6.4 | GO:0000413 | protein peptidyl-prolyl isomerization(GO:0000413) |
| 0.3 | 5.7 | GO:0045338 | farnesyl diphosphate metabolic process(GO:0045338) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 78.4 | GO:0005829 | cytosol(GO:0005829) |
| 0.1 | 36.3 | GO:0009570 | chloroplast stroma(GO:0009570) |
| 0.0 | 34.5 | GO:0009506 | cell-cell junction(GO:0005911) plasmodesma(GO:0009506) cell junction(GO:0030054) symplast(GO:0055044) |
| 0.0 | 24.4 | GO:0005886 | plasma membrane(GO:0005886) |
| 0.0 | 24.3 | GO:0005794 | Golgi apparatus(GO:0005794) |
| 0.0 | 13.8 | GO:0005783 | endoplasmic reticulum(GO:0005783) |
| 0.2 | 12.1 | GO:0009707 | chloroplast outer membrane(GO:0009707) |
| 0.1 | 11.8 | GO:0080008 | Cul4-RING E3 ubiquitin ligase complex(GO:0080008) |
| 0.0 | 11.4 | GO:0005730 | nucleolus(GO:0005730) |
| 0.1 | 11.2 | GO:0005802 | trans-Golgi network(GO:0005802) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 28.4 | GO:0044822 | mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822) |
| 0.6 | 19.0 | GO:0048029 | monosaccharide binding(GO:0048029) |
| 1.9 | 17.2 | GO:0047216 | inositol 3-alpha-galactosyltransferase activity(GO:0047216) |
| 0.8 | 11.3 | GO:0016157 | sucrose synthase activity(GO:0016157) |
| 1.0 | 8.7 | GO:0004869 | cysteine-type endopeptidase inhibitor activity(GO:0004869) |
| 0.8 | 8.3 | GO:0000293 | ferric-chelate reductase activity(GO:0000293) oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor(GO:0016723) |
| 0.1 | 7.3 | GO:0102483 | scopolin beta-glucosidase activity(GO:0102483) |
| 0.1 | 7.2 | GO:0043621 | protein self-association(GO:0043621) |
| 0.3 | 7.0 | GO:0005381 | iron ion transmembrane transporter activity(GO:0005381) |
| 1.7 | 6.8 | GO:0030410 | nicotianamine synthase activity(GO:0030410) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 1.6 | PID CIRCADIAN PATHWAY | Circadian rhythm pathway |
| 0.2 | 1.2 | PID CXCR4 PATHWAY | CXCR4-mediated signaling events |
| 0.1 | 1.2 | PID ATR PATHWAY | ATR signaling pathway |
| 0.3 | 1.0 | PID HNF3B PATHWAY | FOXA2 and FOXA3 transcription factor networks |
| 0.3 | 0.8 | PID RAS PATHWAY | Regulation of Ras family activation |
| 0.2 | 0.8 | PID ECADHERIN NASCENT AJ PATHWAY | E-cadherin signaling in the nascent adherens junction |
| 0.1 | 0.8 | PID HIF1 TFPATHWAY | HIF-1-alpha transcription factor network |
| 0.1 | 0.6 | PID S1P S1P1 PATHWAY | S1P1 pathway |
| 0.1 | 0.4 | PID AP1 PATHWAY | AP-1 transcription factor network |
| 0.1 | 0.4 | SIG INSULIN RECEPTOR PATHWAY IN CARDIAC MYOCYTES | Genes related to the insulin receptor pathway |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.7 | 6.8 | REACTOME LOSS OF NLP FROM MITOTIC CENTROSOMES | Genes involved in Loss of Nlp from mitotic centrosomes |
| 2.1 | 6.2 | REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION | Genes involved in GABA synthesis, release, reuptake and degradation |
| 0.3 | 2.1 | REACTOME LIPID DIGESTION MOBILIZATION AND TRANSPORT | Genes involved in Lipid digestion, mobilization, and transport |
| 0.1 | 1.9 | REACTOME FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION | Genes involved in Factors involved in megakaryocyte development and platelet production |
| 0.6 | 1.8 | REACTOME ABACAVIR TRANSPORT AND METABOLISM | Genes involved in Abacavir transport and metabolism |
| 0.4 | 1.6 | REACTOME BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION | Genes involved in BMAL1:CLOCK/NPAS2 Activates Circadian Expression |
| 0.2 | 1.0 | REACTOME PI METABOLISM | Genes involved in PI Metabolism |
| 0.1 | 1.0 | REACTOME POL SWITCHING | Genes involved in Polymerase switching |
| 0.1 | 1.0 | REACTOME METABOLISM OF CARBOHYDRATES | Genes involved in Metabolism of carbohydrates |
| 0.3 | 0.9 | REACTOME AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION | Genes involved in Amino acid synthesis and interconversion (transamination) |