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GSE130291:vernalization in Arabidopsis thaliana
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Results for AT3G60530
Z-value: 2.88
Transcription factors associated with AT3G60530
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
|
AT3G60530
|
AT3G60530 | GATA transcription factor 4 |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| GATA4 | arTal_v1_Chr3_+_22373013_22373013 | 0.31 | 2.7e-01 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| arTal_v1_Chr4_-_14542565_14542565 Show fit | 3.47 |
AT4G29690.1
|
Alkaline-phosphatase-like family protein |
|
| arTal_v1_Chr1_-_24703041_24703166 Show fit | 3.44 |
AT1G66270.2
AT1G66270.1 |
Glycosyl hydrolase superfamily protein |
|
| arTal_v1_Chr4_+_8929031_8929031 Show fit | 2.55 |
AT4G15670.1
|
Thioredoxin superfamily protein |
|
| arTal_v1_Chr5_+_15742543_15742543 Show fit | 2.45 |
AT5G39320.1
|
UDP-glucose 6-dehydrogenase family protein |
|
| arTal_v1_Chr1_-_28453820_28453820 Show fit | 2.41 |
AT1G75780.1
|
tubulin beta-1 chain |
|
| arTal_v1_Chr3_-_20142763_20142763 Show fit | 2.36 |
AT3G54400.1
|
Eukaryotic aspartyl protease family protein |
|
| arTal_v1_Chr5_-_1861656_1861703 Show fit | 2.36 |
AT5G06150.2
AT5G06150.1 |
Cyclin family protein |
|
| arTal_v1_Chr1_-_24709996_24709996 Show fit | 2.26 |
AT1G66280.1
|
Glycosyl hydrolase superfamily protein |
|
| arTal_v1_Chr3_+_9409160_9409160 Show fit | 2.25 |
AT3G25780.1
|
allene oxide cyclase 3 |
|
| arTal_v1_Chr1_-_1043887_1043887 Show fit | 2.18 |
AT1G04040.1
|
HAD superfamily, subfamily IIIB acid phosphatase |
Network of associatons between targets according to the STRING database.
First level regulatory network of AT3G60530
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 6.6 | GO:0009834 | plant-type secondary cell wall biogenesis(GO:0009834) |
| 0.3 | 6.3 | GO:0006890 | retrograde vesicle-mediated transport, Golgi to ER(GO:0006890) |
| 1.6 | 6.2 | GO:0006023 | aminoglycan biosynthetic process(GO:0006023) glycosaminoglycan biosynthetic process(GO:0006024) UDP-glucuronate biosynthetic process(GO:0006065) glycosaminoglycan metabolic process(GO:0030203) |
| 0.1 | 5.1 | GO:0006888 | ER to Golgi vesicle-mediated transport(GO:0006888) |
| 0.1 | 5.1 | GO:0045454 | cell redox homeostasis(GO:0045454) |
| 0.1 | 4.4 | GO:0072657 | protein localization to membrane(GO:0072657) |
| 0.2 | 4.3 | GO:0033356 | UDP-L-arabinose metabolic process(GO:0033356) |
| 0.8 | 4.2 | GO:0006556 | S-adenosylmethionine biosynthetic process(GO:0006556) |
| 1.3 | 3.9 | GO:0071258 | cellular response to gravity(GO:0071258) |
| 0.8 | 3.9 | GO:1903175 | fatty alcohol biosynthetic process(GO:1903175) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 40.0 | GO:0005794 | Golgi apparatus(GO:0005794) |
| 0.0 | 22.9 | GO:0005886 | plasma membrane(GO:0005886) |
| 0.0 | 20.8 | GO:0009506 | cell-cell junction(GO:0005911) plasmodesma(GO:0009506) cell junction(GO:0030054) symplast(GO:0055044) |
| 0.1 | 17.9 | GO:0048046 | apoplast(GO:0048046) |
| 0.0 | 13.9 | GO:0005773 | vacuole(GO:0005773) |
| 0.1 | 11.2 | GO:0005802 | trans-Golgi network(GO:0005802) |
| 0.1 | 10.8 | GO:0000138 | Golgi trans cisterna(GO:0000138) |
| 0.1 | 7.5 | GO:0099503 | secretory vesicle(GO:0099503) |
| 0.5 | 6.8 | GO:0045298 | tubulin complex(GO:0045298) |
| 0.0 | 6.1 | GO:0005783 | endoplasmic reticulum(GO:0005783) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 12.5 | GO:0003924 | GTPase activity(GO:0003924) |
| 0.3 | 9.8 | GO:0005200 | structural constituent of cytoskeleton(GO:0005200) |
| 0.0 | 8.0 | GO:0005198 | structural molecule activity(GO:0005198) |
| 1.2 | 6.2 | GO:0003979 | UDP-glucose 6-dehydrogenase activity(GO:0003979) |
| 1.0 | 4.9 | GO:0003871 | 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity(GO:0003871) methionine synthase activity(GO:0008705) 5-methyltetrahydrofolate-dependent methyltransferase activity(GO:0042084) 5-methyltetrahydropteroyltri-L-glutamate-dependent methyltransferase activity(GO:0042085) |
| 0.1 | 4.8 | GO:0102483 | scopolin beta-glucosidase activity(GO:0102483) |
| 0.1 | 4.7 | GO:0022884 | protein transmembrane transporter activity(GO:0008320) macromolecule transmembrane transporter activity(GO:0022884) |
| 0.4 | 4.4 | GO:0048040 | UDP-glucuronate decarboxylase activity(GO:0048040) |
| 0.7 | 4.3 | GO:0052691 | UDP-arabinopyranose mutase activity(GO:0052691) |
| 1.1 | 4.2 | GO:0036218 | dTTP diphosphatase activity(GO:0036218) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 1.3 | SA CASPASE CASCADE | Apoptosis is mediated by caspases, cysteine proteases arranged in a proteolytic cascade. |
| 0.3 | 1.0 | SIG CHEMOTAXIS | Genes related to chemotaxis |
| 0.1 | 0.5 | PID BETA CATENIN NUC PATHWAY | Regulation of nuclear beta catenin signaling and target gene transcription |
| 0.1 | 0.4 | PID PLK1 PATHWAY | PLK1 signaling events |
| 0.2 | 0.2 | SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES | Genes related to regulation of the actin cytoskeleton |
| 0.1 | 0.2 | PID PI3KCI PATHWAY | Class I PI3K signaling events |
| 0.0 | 0.1 | SA G1 AND S PHASES | Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition. |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 1.5 | REACTOME G1 S SPECIFIC TRANSCRIPTION | Genes involved in G1/S-Specific Transcription |
| 0.3 | 1.3 | REACTOME MITOCHONDRIAL PROTEIN IMPORT | Genes involved in Mitochondrial Protein Import |
| 0.3 | 1.3 | REACTOME BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN | Genes involved in Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein |
| 0.1 | 1.1 | REACTOME MEIOTIC RECOMBINATION | Genes involved in Meiotic Recombination |
| 0.0 | 1.0 | REACTOME INFLUENZA VIRAL RNA TRANSCRIPTION AND REPLICATION | Genes involved in Influenza Viral RNA Transcription and Replication |
| 0.3 | 0.8 | REACTOME PURINE METABOLISM | Genes involved in Purine metabolism |
| 0.3 | 0.8 | REACTOME INTRINSIC PATHWAY FOR APOPTOSIS | Genes involved in Intrinsic Pathway for Apoptosis |
| 0.1 | 0.7 | REACTOME ASPARAGINE N LINKED GLYCOSYLATION | Genes involved in Asparagine N-linked glycosylation |
| 0.1 | 0.7 | REACTOME SIGNALING BY RHO GTPASES | Genes involved in Signaling by Rho GTPases |
| 0.3 | 0.6 | REACTOME PRE NOTCH EXPRESSION AND PROCESSING | Genes involved in Pre-NOTCH Expression and Processing |