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GSE130291:vernalization in Arabidopsis thaliana
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Results for AT1G06280
Z-value: 2.05
Transcription factors associated with AT1G06280
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
|
AT1G06280
|
AT1G06280 | LOB domain-containing protein 2 |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| LBD2 | arTal_v1_Chr1_-_1920949_1920949 | 0.33 | 2.4e-01 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| arTal_v1_Chr4_+_10707344_10707378 Show fit | 2.00 |
AT4G19690.2
AT4G19690.1 |
iron-regulated transporter 1 |
|
| arTal_v1_Chr5_-_16252434_16252434 Show fit | 1.78 |
AT5G40590.1
|
Cysteine/Histidine-rich C1 domain family protein |
|
| arTal_v1_Chr3_+_4104463_4104463 Show fit | 1.77 |
AT3G12900.1
|
2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein |
|
| arTal_v1_Chr3_+_18940643_18940643 Show fit | 1.73 |
AT3G50970.1
|
dehydrin family protein |
|
| arTal_v1_Chr2_-_17712290_17712330 Show fit | 1.51 |
AT2G42540.2
AT2G42540.4 AT2G42540.1 AT2G42540.3 |
cold-regulated 15a |
|
| arTal_v1_Chr4_-_15954803_15954803 Show fit | 1.43 |
AT4G33070.1
|
Thiamine pyrophosphate dependent pyruvate decarboxylase family protein |
|
| arTal_v1_Chr3_+_21749966_21749966 Show fit | 1.42 |
AT3G58810.1
AT3G58810.2 |
metal tolerance protein A2 |
|
| arTal_v1_Chr5_-_1459039_1459039 Show fit | 1.40 |
AT5G04950.1
|
nicotianamine synthase 1 |
|
| arTal_v1_Chr2_+_2015624_2015706 Show fit | 1.27 |
AT2G05510.1
AT2G05510.3 AT2G05510.4 AT2G05510.2 AT2G05510.6 AT2G05510.5 |
Glycine-rich protein family |
|
| arTal_v1_Chr4_-_18472048_18472048 Show fit | 1.26 |
AT4G39800.1
|
myo-inositol-1-phosphate synthase 1 |
Network of associatons between targets according to the STRING database.
First level regulatory network of AT1G06280
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 14.5 | GO:0006412 | translation(GO:0006412) peptide biosynthetic process(GO:0043043) |
| 0.1 | 6.4 | GO:0045036 | protein targeting to chloroplast(GO:0045036) establishment of protein localization to chloroplast(GO:0072596) |
| 0.0 | 6.3 | GO:0046686 | response to cadmium ion(GO:0046686) |
| 0.0 | 5.4 | GO:0042254 | ribosome biogenesis(GO:0042254) |
| 0.1 | 5.0 | GO:0006457 | protein folding(GO:0006457) |
| 0.0 | 4.8 | GO:0008380 | RNA splicing(GO:0008380) |
| 0.1 | 4.4 | GO:0000027 | ribosomal large subunit assembly(GO:0000027) |
| 0.9 | 3.8 | GO:0015675 | nickel cation transport(GO:0015675) |
| 0.1 | 3.8 | GO:0006099 | tricarboxylic acid cycle(GO:0006099) citrate metabolic process(GO:0006101) |
| 0.1 | 3.8 | GO:0015995 | chlorophyll biosynthetic process(GO:0015995) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 80.0 | GO:0005829 | cytosol(GO:0005829) |
| 0.0 | 32.5 | GO:0055044 | cell-cell junction(GO:0005911) plasmodesma(GO:0009506) cell junction(GO:0030054) symplast(GO:0055044) |
| 0.1 | 26.9 | GO:0009570 | chloroplast stroma(GO:0009570) |
| 0.1 | 17.5 | GO:0048046 | apoplast(GO:0048046) |
| 0.1 | 17.2 | GO:0005768 | endosome(GO:0005768) |
| 0.1 | 16.8 | GO:0005730 | nucleolus(GO:0005730) |
| 0.0 | 10.6 | GO:0009941 | chloroplast envelope(GO:0009941) |
| 0.1 | 10.3 | GO:0022625 | cytosolic large ribosomal subunit(GO:0022625) |
| 0.1 | 8.1 | GO:0022627 | cytosolic small ribosomal subunit(GO:0022627) |
| 0.1 | 6.8 | GO:0009295 | nucleoid(GO:0009295) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 24.8 | GO:0003729 | mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822) |
| 0.1 | 20.7 | GO:0003735 | structural constituent of ribosome(GO:0003735) |
| 0.1 | 11.4 | GO:0051082 | unfolded protein binding(GO:0051082) |
| 0.0 | 7.5 | GO:0004674 | protein serine/threonine kinase activity(GO:0004674) |
| 0.1 | 6.1 | GO:0003724 | RNA helicase activity(GO:0003724) |
| 0.0 | 6.0 | GO:0008270 | zinc ion binding(GO:0008270) |
| 0.1 | 5.8 | GO:0004601 | peroxidase activity(GO:0004601) |
| 0.1 | 5.7 | GO:0043621 | protein self-association(GO:0043621) |
| 0.0 | 5.6 | GO:0043531 | ADP binding(GO:0043531) |
| 0.0 | 5.0 | GO:0016820 | 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) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 1.3 | NABA CORE MATRISOME | Ensemble of genes encoding core extracellular matrix including ECM glycoproteins, collagens and proteoglycans |
| 0.2 | 1.2 | PID CIRCADIAN PATHWAY | Circadian rhythm pathway |
| 0.3 | 1.0 | PID NECTIN PATHWAY | Nectin adhesion pathway |
| 0.3 | 1.0 | SIG PIP3 SIGNALING IN CARDIAC MYOCTES | Genes related to PIP3 signaling in cardiac myocytes |
| 0.2 | 0.8 | PID ATF2 PATHWAY | ATF-2 transcription factor network |
| 0.1 | 0.8 | PID ATR PATHWAY | ATR signaling pathway |
| 0.1 | 0.8 | ST FAS SIGNALING PATHWAY | Fas Signaling Pathway |
| 0.2 | 0.7 | PID AP1 PATHWAY | AP-1 transcription factor network |
| 0.3 | 0.6 | ST ERK1 ERK2 MAPK PATHWAY | ERK1/ERK2 MAPK Pathway |
| 0.1 | 0.6 | PID MTOR 4PATHWAY | mTOR signaling pathway |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 2.7 | REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION | Genes involved in 3' -UTR-mediated translational regulation |
| 0.8 | 2.4 | REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION | Genes involved in GABA synthesis, release, reuptake and degradation |
| 0.3 | 1.9 | REACTOME CIRCADIAN CLOCK | Genes involved in Circadian Clock |
| 0.2 | 1.5 | REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE | Genes involved in Pyruvate metabolism and Citric Acid (TCA) cycle |
| 0.2 | 1.5 | REACTOME UNWINDING OF DNA | Genes involved in Unwinding of DNA |
| 0.2 | 1.4 | REACTOME LIPID DIGESTION MOBILIZATION AND TRANSPORT | Genes involved in Lipid digestion, mobilization, and transport |
| 0.1 | 1.2 | REACTOME ABCA TRANSPORTERS IN LIPID HOMEOSTASIS | Genes involved in ABCA transporters in lipid homeostasis |
| 0.3 | 1.0 | REACTOME P130CAS LINKAGE TO MAPK SIGNALING FOR INTEGRINS | Genes involved in p130Cas linkage to MAPK signaling for integrins |
| 0.1 | 1.0 | REACTOME PPARA ACTIVATES GENE EXPRESSION | Genes involved in PPARA Activates Gene Expression |
| 0.3 | 0.9 | REACTOME ABACAVIR TRANSPORT AND METABOLISM | Genes involved in Abacavir transport and metabolism |