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GSE130291:vernalization in Arabidopsis thaliana
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Results for AT2G46680
Z-value: 2.81
Transcription factors associated with AT2G46680
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
|
AT2G46680
|
AT2G46680 | homeobox 7 |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| HB-7 | arTal_v1_Chr2_-_19166949_19166967 | 0.76 | 1.7e-03 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| arTal_v1_Chr5_-_22712441_22712441 Show fit | 3.74 |
AT5G56080.1
|
nicotianamine synthase 2 |
|
| arTal_v1_Chr3_+_20612693_20612693 Show fit | 3.67 |
AT3G55580.1
|
Regulator of chromosome condensation (RCC1) family protein |
|
| arTal_v1_Chr4_-_7401951_7401951 Show fit | 3.39 |
AT4G12470.1
|
azelaic acid induced 1 |
|
| arTal_v1_Chr2_-_6493512_6493512 Show fit | 3.36 |
AT2G15020.1
|
hypothetical protein |
|
| arTal_v1_Chr3_+_4729399_4729438 Show fit | 3.29 |
AT3G14210.1
AT3G14210.2 |
GDSL-like lipase/acylhydrolase superfamily protein |
|
| arTal_v1_Chr3_+_6023844_6023929 Show fit | 3.27 |
AT3G17609.2
AT3G17609.3 AT3G17609.4 AT3G17609.1 |
HY5-homolog |
|
| arTal_v1_Chr4_+_10707344_10707378 Show fit | 3.09 |
AT4G19690.2
AT4G19690.1 |
iron-regulated transporter 1 |
|
| arTal_v1_Chr3_-_2699257_2699257 Show fit | 2.97 |
AT3G08860.2
|
PYRIMIDINE 4 |
|
| arTal_v1_Chr3_-_2699420_2699420 Show fit | 2.88 |
AT3G08860.1
|
PYRIMIDINE 4 |
|
| arTal_v1_Chr1_-_5765798_5765798 Show fit | 2.87 |
AT1G16850.1
|
transmembrane protein |
Network of associatons between targets according to the STRING database.
First level regulatory network of AT2G46680
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 15.1 | GO:0019759 | S-glycoside catabolic process(GO:0016145) glycosinolate catabolic process(GO:0019759) glucosinolate catabolic process(GO:0019762) |
| 0.0 | 11.1 | GO:0006468 | protein phosphorylation(GO:0006468) |
| 0.2 | 10.7 | GO:0048510 | regulation of timing of meristematic phase transition(GO:0048506) regulation of timing of transition from vegetative to reproductive phase(GO:0048510) |
| 0.0 | 9.9 | GO:0043043 | peptide biosynthetic process(GO:0043043) |
| 0.1 | 9.1 | GO:0016036 | cellular response to phosphate starvation(GO:0016036) |
| 1.4 | 8.7 | GO:0055129 | L-proline biosynthetic process(GO:0055129) |
| 0.2 | 8.3 | GO:0072665 | protein targeting to vacuole(GO:0006623) protein localization to vacuole(GO:0072665) establishment of protein localization to vacuole(GO:0072666) |
| 0.2 | 8.1 | GO:0072596 | protein targeting to chloroplast(GO:0045036) establishment of protein localization to chloroplast(GO:0072596) |
| 0.1 | 7.5 | GO:0006457 | protein folding(GO:0006457) |
| 0.5 | 7.2 | GO:0010100 | negative regulation of photomorphogenesis(GO:0010100) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 113.5 | GO:0005829 | cytosol(GO:0005829) |
| 0.0 | 90.0 | GO:0009536 | plastid(GO:0009536) |
| 0.1 | 31.7 | GO:0009532 | plastid stroma(GO:0009532) |
| 0.0 | 26.4 | GO:0005886 | plasma membrane(GO:0005886) |
| 0.1 | 25.4 | GO:0022626 | cytosolic ribosome(GO:0022626) |
| 0.1 | 17.7 | GO:0000790 | nuclear chromatin(GO:0000790) |
| 0.1 | 15.8 | GO:0009579 | thylakoid(GO:0009579) |
| 0.3 | 15.3 | GO:0009707 | chloroplast outer membrane(GO:0009707) |
| 0.1 | 13.7 | GO:0005730 | nucleolus(GO:0005730) |
| 0.1 | 13.3 | GO:0022627 | cytosolic small ribosomal subunit(GO:0022627) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 35.8 | GO:0003729 | mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822) |
| 0.0 | 32.9 | GO:0003700 | nucleic acid binding transcription factor activity(GO:0001071) transcription factor activity, sequence-specific DNA binding(GO:0003700) |
| 0.0 | 20.6 | GO:0008270 | zinc ion binding(GO:0008270) |
| 0.1 | 19.5 | GO:0003735 | structural constituent of ribosome(GO:0003735) |
| 0.2 | 18.1 | GO:0051082 | unfolded protein binding(GO:0051082) |
| 0.0 | 17.0 | GO:0004674 | protein serine/threonine kinase activity(GO:0004674) |
| 0.1 | 15.2 | GO:0005509 | calcium ion binding(GO:0005509) |
| 0.1 | 13.9 | GO:0043531 | ADP binding(GO:0043531) |
| 0.3 | 12.0 | GO:0050135 | NAD(P)+ nucleosidase activity(GO:0050135) |
| 0.1 | 11.6 | GO:0000978 | RNA polymerase II core promoter proximal region sequence-specific DNA binding(GO:0000978) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 3.3 | NABA CORE MATRISOME | Ensemble of genes encoding core extracellular matrix including ECM glycoproteins, collagens and proteoglycans |
| 0.7 | 2.1 | SIG CHEMOTAXIS | Genes related to chemotaxis |
| 0.4 | 1.9 | PID S1P META PATHWAY | Sphingosine 1-phosphate (S1P) pathway |
| 0.6 | 1.8 | PID HNF3B PATHWAY | FOXA2 and FOXA3 transcription factor networks |
| 0.3 | 1.6 | ST B CELL ANTIGEN RECEPTOR | B Cell Antigen Receptor |
| 0.2 | 1.5 | PID HIF1 TFPATHWAY | HIF-1-alpha transcription factor network |
| 0.2 | 1.2 | PID AP1 PATHWAY | AP-1 transcription factor network |
| 0.1 | 1.0 | PID NOTCH PATHWAY | Notch signaling pathway |
| 0.3 | 0.9 | PID NFAT TFPATHWAY | Calcineurin-regulated NFAT-dependent transcription in lymphocytes |
| 0.4 | 0.8 | PID INTEGRIN3 PATHWAY | Beta3 integrin cell surface interactions |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 2.2 | 6.7 | REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION | Genes involved in GABA synthesis, release, reuptake and degradation |
| 0.8 | 3.4 | REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES | Genes involved in Recruitment of mitotic centrosome proteins and complexes |
| 0.1 | 3.2 | REACTOME NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX | Genes involved in Nonsense Mediated Decay Enhanced by the Exon Junction Complex |
| 0.3 | 2.7 | REACTOME SIGNALING BY RHO GTPASES | Genes involved in Signaling by Rho GTPases |
| 0.7 | 2.0 | REACTOME APOPTOTIC EXECUTION PHASE | Genes involved in Apoptotic execution phase |
| 0.1 | 1.9 | REACTOME ABC FAMILY PROTEINS MEDIATED TRANSPORT | Genes involved in ABC-family proteins mediated transport |
| 0.6 | 1.8 | REACTOME POTASSIUM CHANNELS | Genes involved in Potassium Channels |
| 0.2 | 1.7 | REACTOME RNA POL II TRANSCRIPTION PRE INITIATION AND PROMOTER OPENING | Genes involved in RNA Polymerase II Transcription Pre-Initiation And Promoter Opening |
| 0.2 | 1.6 | REACTOME UNWINDING OF DNA | Genes involved in Unwinding of DNA |
| 0.5 | 1.4 | REACTOME ABACAVIR TRANSPORT AND METABOLISM | Genes involved in Abacavir transport and metabolism |