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GSE130291:vernalization in Arabidopsis thaliana
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Results for AT3G47500
Z-value: 2.21
Transcription factors associated with AT3G47500
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
|
AT3G47500
|
AT3G47500 | cycling DOF factor 3 |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| CDF3 | arTal_v1_Chr3_-_17506124_17506124 | 0.77 | 1.4e-03 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| arTal_v1_Chr4_-_7401951_7401951 Show fit | 4.87 |
AT4G12470.1
|
azelaic acid induced 1 |
|
| arTal_v1_Chr5_-_17199793_17199910 Show fit | 4.87 |
AT5G42900.1
AT5G42900.3 AT5G42900.2 |
cold regulated protein 27 |
|
| arTal_v1_Chr5_+_5206156_5206156 Show fit | 4.68 |
AT5G15950.2
|
Adenosylmethionine decarboxylase family protein |
|
| arTal_v1_Chr5_+_5205869_5205869 Show fit | 4.65 |
AT5G15950.1
|
Adenosylmethionine decarboxylase family protein |
|
| arTal_v1_Chr5_-_14753088_14753088 Show fit | 4.63 |
AT5G37260.1
|
Homeodomain-like superfamily protein |
|
| arTal_v1_Chr1_-_9275193_9275193 Show fit | 4.29 |
AT1G26790.1
|
Dof-type zinc finger DNA-binding family protein |
|
| arTal_v1_Chr3_+_18940643_18940643 Show fit | 3.97 |
AT3G50970.1
|
dehydrin family protein |
|
| arTal_v1_Chr5_-_5692920_5692992 Show fit | 3.71 |
AT5G17300.2
AT5G17300.1 |
Homeodomain-like superfamily protein |
|
| arTal_v1_Chr3_-_489467_489467 Show fit | 3.66 |
AT3G02380.1
|
CONSTANS-like 2 |
|
| arTal_v1_Chr2_+_19245591_19245684 Show fit | 3.58 |
AT2G46830.1
AT2G46830.2 |
circadian clock associated 1 |
Network of associatons between targets according to the STRING database.
First level regulatory network of AT3G47500
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 2.0 | 11.8 | GO:0042754 | negative regulation of circadian rhythm(GO:0042754) |
| 0.1 | 11.6 | GO:0007623 | circadian rhythm(GO:0007623) rhythmic process(GO:0048511) |
| 0.7 | 9.7 | GO:0010100 | negative regulation of photomorphogenesis(GO:0010100) |
| 0.0 | 9.4 | GO:0006412 | translation(GO:0006412) |
| 0.0 | 9.2 | GO:0006468 | protein phosphorylation(GO:0006468) |
| 1.6 | 8.1 | GO:0072708 | response to sorbitol(GO:0072708) |
| 0.1 | 7.9 | GO:0009658 | chloroplast organization(GO:0009658) |
| 0.2 | 7.2 | GO:0006730 | one-carbon metabolic process(GO:0006730) |
| 0.1 | 6.6 | GO:0042752 | regulation of circadian rhythm(GO:0042752) |
| 0.2 | 6.5 | GO:0070417 | cellular response to cold(GO:0070417) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 75.2 | GO:0005829 | cytosol(GO:0005829) |
| 0.0 | 51.5 | GO:0005886 | plasma membrane(GO:0005886) |
| 0.0 | 31.5 | GO:0009506 | cell-cell junction(GO:0005911) plasmodesma(GO:0009506) cell junction(GO:0030054) symplast(GO:0055044) |
| 0.1 | 9.3 | GO:0016604 | nuclear body(GO:0016604) |
| 0.2 | 9.0 | GO:0009707 | chloroplast outer membrane(GO:0009707) |
| 0.0 | 8.9 | GO:0005774 | vacuolar membrane(GO:0005774) |
| 0.1 | 8.2 | GO:0000138 | Golgi trans cisterna(GO:0000138) |
| 0.1 | 7.7 | GO:0000325 | plant-type vacuole(GO:0000325) |
| 0.0 | 7.6 | GO:0005802 | trans-Golgi network(GO:0005802) |
| 0.1 | 7.3 | GO:0022625 | cytosolic large ribosomal subunit(GO:0022625) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 27.6 | GO:0000975 | regulatory region DNA binding(GO:0000975) transcription regulatory region sequence-specific DNA binding(GO:0000976) regulatory region nucleic acid binding(GO:0001067) transcription regulatory region DNA binding(GO:0044212) |
| 0.0 | 25.7 | GO:0003700 | nucleic acid binding transcription factor activity(GO:0001071) transcription factor activity, sequence-specific DNA binding(GO:0003700) |
| 0.1 | 12.8 | GO:0043492 | hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances(GO:0016820) ATPase activity, coupled to transmembrane movement of substances(GO:0042626) ATPase activity, coupled to movement of substances(GO:0043492) |
| 0.1 | 12.8 | GO:0003735 | structural constituent of ribosome(GO:0003735) |
| 1.6 | 9.8 | GO:0019904 | protein domain specific binding(GO:0019904) |
| 0.6 | 9.5 | GO:0016157 | sucrose synthase activity(GO:0016157) |
| 0.3 | 7.3 | GO:0005388 | calcium-transporting ATPase activity(GO:0005388) |
| 0.0 | 6.4 | GO:0005524 | ATP binding(GO:0005524) |
| 0.3 | 6.3 | GO:0005199 | structural constituent of cell wall(GO:0005199) |
| 0.0 | 6.2 | GO:0043531 | ADP binding(GO:0043531) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.8 | 2.4 | SIG PIP3 SIGNALING IN CARDIAC MYOCTES | Genes related to PIP3 signaling in cardiac myocytes |
| 0.3 | 1.7 | PID CIRCADIAN PATHWAY | Circadian rhythm pathway |
| 0.5 | 1.5 | ST G ALPHA I PATHWAY | G alpha i Pathway |
| 0.2 | 1.3 | PID AP1 PATHWAY | AP-1 transcription factor network |
| 0.2 | 1.3 | PID HIF1 TFPATHWAY | HIF-1-alpha transcription factor network |
| 0.3 | 1.2 | PID PDGFRA PATHWAY | PDGFR-alpha signaling pathway |
| 0.2 | 1.2 | PID MTOR 4PATHWAY | mTOR signaling pathway |
| 0.4 | 1.1 | PID TAP63 PATHWAY | Validated transcriptional targets of TAp63 isoforms |
| 0.2 | 1.1 | PID S1P S1P1 PATHWAY | S1P1 pathway |
| 0.3 | 1.0 | PID EPO PATHWAY | EPO signaling pathway |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.2 | 4.9 | REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES | Genes involved in Recruitment of mitotic centrosome proteins and complexes |
| 0.9 | 3.4 | REACTOME SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 7ALPHA HYDROXYCHOLESTEROL | Genes involved in Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol |
| 0.5 | 3.2 | REACTOME LIPID DIGESTION MOBILIZATION AND TRANSPORT | Genes involved in Lipid digestion, mobilization, and transport |
| 0.3 | 1.8 | REACTOME E2F ENABLED INHIBITION OF PRE REPLICATION COMPLEX FORMATION | Genes involved in E2F-enabled inhibition of pre-replication complex formation |
| 0.4 | 1.7 | REACTOME BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION | Genes involved in BMAL1:CLOCK/NPAS2 Activates Circadian Expression |
| 0.3 | 1.6 | REACTOME INTERFERON SIGNALING | Genes involved in Interferon Signaling |
| 0.1 | 1.6 | REACTOME FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION | Genes involved in Factors involved in megakaryocyte development and platelet production |
| 0.1 | 1.6 | REACTOME INFLUENZA LIFE CYCLE | Genes involved in Influenza Life Cycle |
| 0.4 | 1.2 | REACTOME DEADENYLATION OF MRNA | Genes involved in Deadenylation of mRNA |
| 0.3 | 1.2 | REACTOME CITRIC ACID CYCLE TCA CYCLE | Genes involved in Citric acid cycle (TCA cycle) |