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GSE130291:vernalization in Arabidopsis thaliana
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Results for AT3G56850
Z-value: 1.95
Transcription factors associated with AT3G56850
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
|
AT3G56850
|
AT3G56850 | ABA-responsive element binding protein 3 |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| AREB3 | arTal_v1_Chr3_-_21048614_21048614 | 0.44 | 1.1e-01 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| arTal_v1_Chr2_-_17712290_17712330 Show fit | 7.62 |
AT2G42540.2
AT2G42540.4 AT2G42540.1 AT2G42540.3 |
cold-regulated 15a |
|
| arTal_v1_Chr1_+_28975255_28975255 Show fit | 3.93 |
AT1G77120.1
|
alcohol dehydrogenase 1 |
|
| arTal_v1_Chr2_-_6493512_6493512 Show fit | 3.88 |
AT2G15020.1
|
hypothetical protein |
|
| arTal_v1_Chr1_+_3019639_3019639 Show fit | 3.79 |
AT1G09350.1
|
galactinol synthase 3 |
|
| arTal_v1_Chr5_-_17199793_17199910 Show fit | 3.75 |
AT5G42900.1
AT5G42900.3 AT5G42900.2 |
cold regulated protein 27 |
|
| arTal_v1_Chr1_+_3020221_3020221 Show fit | 3.53 |
AT1G09350.2
|
galactinol synthase 3 |
|
| arTal_v1_Chr2_+_19245591_19245684 Show fit | 3.50 |
AT2G46830.1
AT2G46830.2 |
circadian clock associated 1 |
|
| arTal_v1_Chr2_-_19370478_19370478 Show fit | 3.32 |
AT2G47180.1
|
galactinol synthase 1 |
|
| arTal_v1_Chr2_+_19246681_19246681 Show fit | 3.27 |
AT2G46830.3
|
circadian clock associated 1 |
|
| arTal_v1_Chr5_+_5206156_5206156 Show fit | 3.03 |
AT5G15950.2
|
Adenosylmethionine decarboxylase family protein |
Network of associatons between targets according to the STRING database.
First level regulatory network of AT3G56850
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 26.1 | GO:0048511 | circadian rhythm(GO:0007623) rhythmic process(GO:0048511) |
| 0.4 | 11.2 | GO:0006012 | galactose metabolic process(GO:0006012) |
| 1.6 | 9.7 | GO:0042754 | negative regulation of circadian rhythm(GO:0042754) |
| 1.6 | 9.5 | GO:0009413 | response to flooding(GO:0009413) |
| 1.0 | 9.2 | GO:0009819 | drought recovery(GO:0009819) |
| 0.1 | 9.0 | GO:0031146 | SCF-dependent proteasomal ubiquitin-dependent protein catabolic process(GO:0031146) |
| 0.1 | 8.9 | GO:0015995 | chlorophyll biosynthetic process(GO:0015995) |
| 0.2 | 7.0 | GO:0055072 | iron ion homeostasis(GO:0055072) |
| 0.9 | 5.6 | GO:0055129 | L-proline biosynthetic process(GO:0055129) |
| 0.6 | 5.1 | GO:1902882 | regulation of response to oxidative stress(GO:1902882) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 30.0 | GO:0009941 | chloroplast envelope(GO:0009941) |
| 0.1 | 15.6 | GO:0009579 | thylakoid(GO:0009579) |
| 0.0 | 14.6 | GO:0005794 | Golgi apparatus(GO:0005794) |
| 0.1 | 11.0 | GO:0031969 | chloroplast membrane(GO:0031969) |
| 0.1 | 10.4 | GO:0019005 | SCF ubiquitin ligase complex(GO:0019005) |
| 0.0 | 10.0 | GO:0009570 | chloroplast stroma(GO:0009570) |
| 0.1 | 6.8 | GO:0031978 | chloroplast thylakoid lumen(GO:0009543) plastid thylakoid lumen(GO:0031978) |
| 0.1 | 6.6 | GO:0005770 | late endosome(GO:0005770) |
| 0.1 | 6.5 | GO:0080008 | Cul4-RING E3 ubiquitin ligase complex(GO:0080008) |
| 0.2 | 4.9 | GO:0009898 | cytoplasmic side of plasma membrane(GO:0009898) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 42.5 | GO:0003700 | nucleic acid binding transcription factor activity(GO:0001071) transcription factor activity, sequence-specific DNA binding(GO:0003700) |
| 1.2 | 10.5 | GO:0047216 | inositol 3-alpha-galactosyltransferase activity(GO:0047216) |
| 0.0 | 8.6 | GO:0005524 | ATP binding(GO:0005524) |
| 0.1 | 8.1 | GO:0000978 | RNA polymerase II core promoter proximal region sequence-specific DNA binding(GO:0000978) |
| 1.1 | 6.8 | GO:0019904 | protein domain specific binding(GO:0019904) |
| 0.2 | 6.7 | GO:0000156 | phosphorelay response regulator activity(GO:0000156) |
| 0.2 | 6.2 | GO:0048029 | monosaccharide binding(GO:0048029) |
| 1.4 | 5.6 | GO:0004349 | glutamate 5-kinase activity(GO:0004349) glutamate-5-semialdehyde dehydrogenase activity(GO:0004350) |
| 0.8 | 4.9 | GO:0019144 | ADP-sugar diphosphatase activity(GO:0019144) ADP-ribose pyrophosphohydrolase activity(GO:0080041) |
| 0.3 | 4.8 | GO:0016157 | sucrose synthase activity(GO:0016157) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 1.1 | PID MTOR 4PATHWAY | mTOR signaling pathway |
| 0.3 | 0.8 | PID HNF3B PATHWAY | FOXA2 and FOXA3 transcription factor networks |
| 0.1 | 0.4 | PID S1P S1P1 PATHWAY | S1P1 pathway |
| 0.0 | 0.4 | PID RAC1 PATHWAY | RAC1 signaling pathway |
| 0.1 | 0.3 | PID HES HEY PATHWAY | Notch-mediated HES/HEY network |
| 0.0 | 0.1 | PID ARF6 DOWNSTREAM PATHWAY | Arf6 downstream pathway |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.5 | 1.6 | REACTOME TRNA AMINOACYLATION | Genes involved in tRNA Aminoacylation |
| 0.1 | 1.6 | REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE | Genes involved in SRP-dependent cotranslational protein targeting to membrane |
| 0.4 | 1.2 | REACTOME APOPTOSIS INDUCED DNA FRAGMENTATION | Genes involved in Apoptosis induced DNA fragmentation |
| 0.1 | 1.0 | REACTOME METABOLISM OF VITAMINS AND COFACTORS | Genes involved in Metabolism of vitamins and cofactors |
| 0.3 | 0.8 | REACTOME ABACAVIR TRANSPORT AND METABOLISM | Genes involved in Abacavir transport and metabolism |
| 0.2 | 0.8 | REACTOME PI METABOLISM | Genes involved in PI Metabolism |
| 0.1 | 0.6 | REACTOME DOUBLE STRAND BREAK REPAIR | Genes involved in Double-Strand Break Repair |
| 0.1 | 0.4 | REACTOME BASE EXCISION REPAIR | Genes involved in Base Excision Repair |
| 0.1 | 0.4 | REACTOME LIPID DIGESTION MOBILIZATION AND TRANSPORT | Genes involved in Lipid digestion, mobilization, and transport |
| 0.1 | 0.3 | REACTOME FORMATION OF INCISION COMPLEX IN GG NER | Genes involved in Formation of incision complex in GG-NER |