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GSE130291:vernalization in Arabidopsis thaliana
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Results for AT4G01500
Z-value: 2.90
Transcription factors associated with AT4G01500
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
|
AT4G01500
|
AT4G01500 | AP2/B3-like transcriptional factor family protein |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| NGA4 | arTal_v1_Chr4_+_639247_639247 | 0.66 | 1.1e-02 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| arTal_v1_Chr3_-_489467_489467 Show fit | 4.24 |
AT3G02380.1
|
CONSTANS-like 2 |
|
| arTal_v1_Chr4_-_18472048_18472048 Show fit | 3.71 |
AT4G39800.1
|
myo-inositol-1-phosphate synthase 1 |
|
| arTal_v1_Chr1_+_18546086_18546165 Show fit | 3.63 |
AT1G50050.2
AT1G50050.1 |
CAP (Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-related 1 protein) superfamily protein |
|
| arTal_v1_Chr2_+_16216752_16216752 Show fit | 3.59 |
AT2G38800.1
|
Plant calmodulin-binding protein-like protein |
|
| arTal_v1_Chr1_+_6763765_6763915 Show fit | 3.50 |
AT1G19530.1
AT1G19530.2 |
DNA polymerase epsilon catalytic subunit A |
|
| arTal_v1_Chr2_-_16603059_16603061 Show fit | 3.06 |
AT2G39800.2
AT2G39800.4 AT2G39800.3 |
delta1-pyrroline-5-carboxylate synthase 1 |
|
| arTal_v1_Chr5_-_22991530_22991530 Show fit | 3.00 |
AT5G56860.1
|
GATA type zinc finger transcription factor family protein |
|
| arTal_v1_Chr1_-_29459493_29459493 Show fit | 2.99 |
AT1G78290.2
AT1G78290.3 |
Protein kinase superfamily protein |
|
| arTal_v1_Chr1_-_450426_450426 Show fit | 2.90 |
AT1G02280.1
AT1G02280.2 |
translocon at the outer envelope membrane of chloroplasts 33 |
|
| arTal_v1_Chr3_-_20629295_20629295 Show fit | 2.84 |
AT3G55610.1
|
delta 1-pyrroline-5-carboxylate synthase 2 |
Network of associatons between targets according to the STRING database.
First level regulatory network of AT4G01500
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.8 | 11.1 | GO:0055129 | L-proline biosynthetic process(GO:0055129) |
| 0.1 | 6.8 | GO:0045036 | protein targeting to chloroplast(GO:0045036) establishment of protein localization to chloroplast(GO:0072596) |
| 0.0 | 5.6 | GO:0045892 | negative regulation of transcription, DNA-templated(GO:0045892) |
| 0.7 | 5.2 | GO:0090059 | protoxylem development(GO:0090059) |
| 0.4 | 5.0 | GO:0042753 | positive regulation of circadian rhythm(GO:0042753) |
| 0.5 | 4.8 | GO:0010031 | circumnutation(GO:0010031) multicellular organismal movement(GO:0050879) |
| 0.2 | 4.7 | GO:0006284 | base-excision repair(GO:0006284) |
| 1.5 | 4.6 | GO:0071461 | cellular response to redox state(GO:0071461) |
| 0.8 | 4.6 | GO:1902326 | positive regulation of chlorophyll biosynthetic process(GO:1902326) |
| 0.1 | 4.5 | GO:0048506 | regulation of timing of meristematic phase transition(GO:0048506) regulation of timing of transition from vegetative to reproductive phase(GO:0048510) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 61.5 | GO:0005829 | cytosol(GO:0005829) |
| 0.0 | 19.8 | GO:0009526 | plastid envelope(GO:0009526) |
| 0.1 | 11.5 | GO:0099503 | secretory vesicle(GO:0099503) |
| 0.0 | 6.2 | GO:0005730 | nucleolus(GO:0005730) |
| 0.0 | 5.6 | GO:0055044 | cell-cell junction(GO:0005911) plasmodesma(GO:0009506) cell junction(GO:0030054) symplast(GO:0055044) |
| 0.1 | 5.3 | GO:0000932 | cytoplasmic mRNA processing body(GO:0000932) |
| 0.1 | 5.1 | GO:0009707 | chloroplast outer membrane(GO:0009707) |
| 0.1 | 4.0 | GO:0016607 | nuclear speck(GO:0016607) |
| 0.1 | 3.7 | GO:0019005 | SCF ubiquitin ligase complex(GO:0019005) |
| 0.1 | 3.5 | GO:0000137 | Golgi cis cisterna(GO:0000137) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 14.5 | GO:0008270 | zinc ion binding(GO:0008270) |
| 2.8 | 11.1 | GO:0004350 | glutamate 5-kinase activity(GO:0004349) glutamate-5-semialdehyde dehydrogenase activity(GO:0004350) |
| 0.0 | 9.8 | GO:0003723 | RNA binding(GO:0003723) |
| 0.0 | 9.2 | GO:0005516 | calmodulin binding(GO:0005516) |
| 0.0 | 9.1 | GO:0004175 | endopeptidase activity(GO:0004175) |
| 0.0 | 6.7 | GO:0042803 | protein homodimerization activity(GO:0042803) |
| 1.3 | 5.2 | GO:0052593 | tryptamine:oxygen oxidoreductase (deaminating) activity(GO:0052593) aminoacetone:oxygen oxidoreductase(deaminating) activity(GO:0052594) aliphatic-amine oxidase activity(GO:0052595) phenethylamine:oxygen oxidoreductase (deaminating) activity(GO:0052596) |
| 0.7 | 5.2 | GO:0016781 | phosphotransferase activity, paired acceptors(GO:0016781) |
| 1.3 | 5.1 | GO:0004512 | inositol-3-phosphate synthase activity(GO:0004512) |
| 0.1 | 5.0 | GO:0003678 | DNA helicase activity(GO:0003678) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 1.7 | PID MTOR 4PATHWAY | mTOR signaling pathway |
| 0.2 | 1.2 | PID IL2 PI3K PATHWAY | IL2 signaling events mediated by PI3K |
| 0.2 | 1.1 | PID SHP2 PATHWAY | SHP2 signaling |
| 0.2 | 0.6 | PID IL8 CXCR1 PATHWAY | IL8- and CXCR1-mediated signaling events |
| 0.1 | 0.4 | SIG INSULIN RECEPTOR PATHWAY IN CARDIAC MYOCYTES | Genes related to the insulin receptor pathway |
| 0.1 | 0.4 | PID CMYB PATHWAY | C-MYB transcription factor network |
| 0.1 | 0.3 | PID ERA GENOMIC PATHWAY | Validated nuclear estrogen receptor alpha network |
| 0.0 | 0.2 | NABA ECM GLYCOPROTEINS | Genes encoding structural ECM glycoproteins |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 2.7 | REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S | Genes involved in Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S |
| 0.4 | 1.3 | REACTOME MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE | Genes involved in mRNA Decay by 5' to 3' Exoribonuclease |
| 0.4 | 1.1 | REACTOME DOWNSTREAM SIGNALING OF ACTIVATED FGFR | Genes involved in Downstream signaling of activated FGFR |
| 0.1 | 1.1 | REACTOME ABCA TRANSPORTERS IN LIPID HOMEOSTASIS | Genes involved in ABCA transporters in lipid homeostasis |
| 0.0 | 1.0 | REACTOME ABC FAMILY PROTEINS MEDIATED TRANSPORT | Genes involved in ABC-family proteins mediated transport |
| 0.1 | 0.9 | REACTOME UNWINDING OF DNA | Genes involved in Unwinding of DNA |
| 0.3 | 0.8 | REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM | Genes involved in Transport of Mature Transcript to Cytoplasm |
| 0.1 | 0.8 | REACTOME GLUCOSE METABOLISM | Genes involved in Glucose metabolism |
| 0.2 | 0.6 | REACTOME SIGNALING BY CONSTITUTIVELY ACTIVE EGFR | Genes involved in Signaling by constitutively active EGFR |
| 0.1 | 0.6 | REACTOME METABOLISM OF AMINO ACIDS AND DERIVATIVES | Genes involved in Metabolism of amino acids and derivatives |