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GSE130291:vernalization in Arabidopsis thaliana
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Results for AT3G50060
Z-value: 1.84
Transcription factors associated with AT3G50060
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
|
AT3G50060
|
AT3G50060 | myb domain protein 77 |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| MYB77 | arTal_v1_Chr3_-_18559326_18559326 | -0.21 | 4.7e-01 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| arTal_v1_Chr5_+_5209717_5209717 Show fit | 2.96 |
AT5G15960.1
|
stress-responsive protein (KIN1) / stress-induced protein (KIN1) |
|
| arTal_v1_Chr2_-_17710433_17710433 Show fit | 2.89 |
AT2G42530.1
|
cold regulated 15b |
|
| arTal_v1_Chr1_+_28975255_28975255 Show fit | 2.80 |
AT1G77120.1
|
alcohol dehydrogenase 1 |
|
| arTal_v1_Chr5_-_22712441_22712441 Show fit | 2.51 |
AT5G56080.1
|
nicotianamine synthase 2 |
|
| arTal_v1_Chr5_+_21240717_21240717 Show fit | 2.42 |
AT5G52310.1
|
low-temperature-responsive protein 78 (LTI78) / desiccation-responsive protein 29A (RD29A) |
|
| arTal_v1_Chr2_+_538250_538250 Show fit | 2.40 |
AT2G02120.1
|
Scorpion toxin-like knottin superfamily protein |
|
| arTal_v1_Chr1_+_3019639_3019639 Show fit | 2.27 |
AT1G09350.1
|
galactinol synthase 3 |
|
| arTal_v1_Chr1_-_10289666_10289666 Show fit | 2.17 |
AT1G29395.1
|
COLD REGULATED 314 INNER MEMBRANE 1 |
|
| arTal_v1_Chr5_-_17199793_17199910 Show fit | 2.14 |
AT5G42900.1
AT5G42900.3 AT5G42900.2 |
cold regulated protein 27 |
|
| arTal_v1_Chr4_+_10707344_10707378 Show fit | 2.14 |
AT4G19690.2
AT4G19690.1 |
iron-regulated transporter 1 |
Network of associatons between targets according to the STRING database.
First level regulatory network of AT3G50060
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 22.6 | GO:0006412 | translation(GO:0006412) |
| 0.2 | 14.6 | GO:0009631 | cold acclimation(GO:0009631) |
| 0.1 | 11.6 | GO:0042254 | ribosome biogenesis(GO:0042254) |
| 0.3 | 10.4 | GO:0055072 | iron ion homeostasis(GO:0055072) |
| 0.3 | 9.3 | GO:0045036 | protein targeting to chloroplast(GO:0045036) establishment of protein localization to chloroplast(GO:0072596) |
| 0.2 | 9.1 | GO:0006749 | glutathione metabolic process(GO:0006749) |
| 0.3 | 8.5 | GO:0000027 | ribosomal large subunit assembly(GO:0000027) |
| 0.1 | 8.2 | GO:0006457 | protein folding(GO:0006457) |
| 0.2 | 8.1 | GO:0015995 | chlorophyll biosynthetic process(GO:0015995) |
| 0.1 | 7.7 | GO:0009658 | chloroplast organization(GO:0009658) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 165.7 | GO:0005829 | cytosol(GO:0005829) |
| 0.1 | 58.0 | GO:0009570 | chloroplast stroma(GO:0009570) |
| 0.0 | 41.8 | GO:0009536 | plastid(GO:0009536) |
| 0.1 | 37.9 | GO:0005730 | nucleolus(GO:0005730) |
| 0.0 | 32.8 | GO:0005886 | plasma membrane(GO:0005886) |
| 0.1 | 23.1 | GO:0031976 | plastid thylakoid(GO:0031976) |
| 0.2 | 20.1 | GO:0022625 | cytosolic large ribosomal subunit(GO:0022625) |
| 0.0 | 17.2 | GO:0030054 | cell-cell junction(GO:0005911) plasmodesma(GO:0009506) cell junction(GO:0030054) symplast(GO:0055044) |
| 0.1 | 15.6 | GO:0000790 | nuclear chromatin(GO:0000790) |
| 0.2 | 13.6 | GO:0009707 | chloroplast outer membrane(GO:0009707) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 37.1 | GO:0044822 | mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822) |
| 0.1 | 26.1 | GO:0003735 | structural constituent of ribosome(GO:0003735) |
| 0.0 | 16.5 | GO:0008270 | zinc ion binding(GO:0008270) |
| 0.1 | 14.5 | GO:0051082 | unfolded protein binding(GO:0051082) |
| 0.3 | 11.6 | GO:0050135 | NAD(P)+ nucleosidase activity(GO:0050135) |
| 0.1 | 11.5 | GO:0003724 | RNA helicase activity(GO:0003724) |
| 0.1 | 10.0 | GO:0015631 | tubulin binding(GO:0015631) |
| 0.2 | 9.6 | GO:0003755 | peptidyl-prolyl cis-trans isomerase activity(GO:0003755) |
| 0.1 | 9.4 | 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) |
| 0.2 | 9.3 | GO:0004364 | glutathione transferase activity(GO:0004364) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.5 | 2.7 | ST DIFFERENTIATION PATHWAY IN PC12 CELLS | Differentiation Pathway in PC12 Cells; this is a specific case of PAC1 Receptor Pathway. |
| 0.2 | 2.1 | PID HIF1 TFPATHWAY | HIF-1-alpha transcription factor network |
| 0.2 | 1.9 | PID P53 DOWNSTREAM PATHWAY | Direct p53 effectors |
| 0.6 | 1.8 | PID BCR 5PATHWAY | BCR signaling pathway |
| 0.4 | 1.8 | PID CIRCADIAN PATHWAY | Circadian rhythm pathway |
| 0.6 | 1.7 | SIG PIP3 SIGNALING IN CARDIAC MYOCTES | Genes related to PIP3 signaling in cardiac myocytes |
| 0.2 | 1.7 | PID MTOR 4PATHWAY | mTOR signaling pathway |
| 0.5 | 1.6 | ST INTEGRIN SIGNALING PATHWAY | Integrin Signaling Pathway |
| 0.4 | 1.5 | SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES | Genes related to regulation of the actin cytoskeleton |
| 0.5 | 1.4 | PID HNF3B PATHWAY | FOXA2 and FOXA3 transcription factor networks |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 6.0 | REACTOME TRANSLATION | Genes involved in Translation |
| 0.7 | 2.6 | REACTOME LOSS OF NLP FROM MITOTIC CENTROSOMES | Genes involved in Loss of Nlp from mitotic centrosomes |
| 0.6 | 2.3 | REACTOME PROLONGED ERK ACTIVATION EVENTS | Genes involved in Prolonged ERK activation events |
| 0.5 | 2.1 | REACTOME SYNTHESIS OF BILE ACIDS AND BILE SALTS | Genes involved in Synthesis of bile acids and bile salts |
| 0.6 | 1.8 | REACTOME PHOSPHORYLATION OF CD3 AND TCR ZETA CHAINS | Genes involved in Phosphorylation of CD3 and TCR zeta chains |
| 0.5 | 1.8 | REACTOME BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION | Genes involved in BMAL1:CLOCK/NPAS2 Activates Circadian Expression |
| 0.4 | 1.8 | REACTOME L1CAM INTERACTIONS | Genes involved in L1CAM interactions |
| 0.2 | 1.7 | REACTOME SIGNALING BY RHO GTPASES | Genes involved in Signaling by Rho GTPases |
| 0.3 | 1.6 | REACTOME SLC MEDIATED TRANSMEMBRANE TRANSPORT | Genes involved in SLC-mediated transmembrane transport |
| 0.4 | 1.3 | REACTOME ABACAVIR TRANSPORT AND METABOLISM | Genes involved in Abacavir transport and metabolism |