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GSE130291:vernalization in Arabidopsis thaliana
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Results for AT5G62000
Z-value: 2.39
Transcription factors associated with AT5G62000
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
|
AT5G62000
|
AT5G62000 | auxin response factor 2 |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| ARF2 | arTal_v1_Chr5_+_24910191_24910358 | 0.37 | 1.9e-01 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| arTal_v1_Chr2_-_17712290_17712330 Show fit | 4.71 |
AT2G42540.2
AT2G42540.4 AT2G42540.1 AT2G42540.3 |
cold-regulated 15a |
|
| arTal_v1_Chr5_-_21992812_21992814 Show fit | 2.73 |
AT5G54190.2
AT5G54190.1 |
protochlorophyllide oxidoreductase A |
|
| arTal_v1_Chr5_+_21240717_21240717 Show fit | 2.67 |
AT5G52310.1
|
low-temperature-responsive protein 78 (LTI78) / desiccation-responsive protein 29A (RD29A) |
|
| arTal_v1_Chr4_-_7406994_7406994 Show fit | 2.55 |
AT4G12480.1
|
Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein |
|
| arTal_v1_Chr1_-_9275193_9275193 Show fit | 2.50 |
AT1G26790.1
|
Dof-type zinc finger DNA-binding family protein |
|
| arTal_v1_Chr2_+_1966806_1966816 Show fit | 2.16 |
AT2G05380.1
AT2G05380.2 |
glycine-rich protein 3 short isoform |
|
| arTal_v1_Chr3_-_489467_489467 Show fit | 2.14 |
AT3G02380.1
|
CONSTANS-like 2 |
|
| arTal_v1_Chr2_+_1966610_1966610 Show fit | 2.13 |
AT2G05380.3
|
glycine-rich protein 3 short isoform |
|
| arTal_v1_Chr1_-_4651549_4651549 Show fit | 1.91 |
AT1G13600.1
|
basic leucine-zipper 58 |
|
| arTal_v1_Chr5_-_14753088_14753088 Show fit | 1.89 |
AT5G37260.1
|
Homeodomain-like superfamily protein |
Network of associatons between targets according to the STRING database.
First level regulatory network of AT5G62000
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 8.7 | GO:0009658 | chloroplast organization(GO:0009658) |
| 0.1 | 6.3 | GO:0015995 | chlorophyll biosynthetic process(GO:0015995) |
| 0.4 | 5.8 | GO:0010100 | negative regulation of photomorphogenesis(GO:0010100) |
| 0.5 | 4.9 | GO:0009819 | drought recovery(GO:0009819) |
| 0.1 | 4.6 | GO:0055072 | iron ion homeostasis(GO:0055072) |
| 0.3 | 4.5 | GO:0009608 | response to symbiont(GO:0009608) |
| 0.0 | 4.5 | GO:0043043 | translation(GO:0006412) peptide biosynthetic process(GO:0043043) |
| 0.1 | 3.8 | GO:0031146 | SCF-dependent proteasomal ubiquitin-dependent protein catabolic process(GO:0031146) |
| 0.0 | 3.5 | GO:0006366 | transcription from RNA polymerase II promoter(GO:0006366) |
| 0.1 | 3.4 | GO:0009911 | positive regulation of flower development(GO:0009911) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 15.2 | GO:0009941 | chloroplast envelope(GO:0009941) |
| 0.0 | 14.4 | GO:0044434 | chloroplast part(GO:0044434) |
| 0.0 | 7.6 | GO:0022626 | cytosolic ribosome(GO:0022626) |
| 0.1 | 7.0 | GO:0009707 | chloroplast outer membrane(GO:0009707) |
| 0.1 | 5.7 | GO:0015935 | small ribosomal subunit(GO:0015935) |
| 0.1 | 5.5 | GO:0031977 | thylakoid lumen(GO:0031977) |
| 0.0 | 5.1 | GO:0000790 | nuclear chromatin(GO:0000790) |
| 0.0 | 4.5 | GO:0080008 | Cul4-RING E3 ubiquitin ligase complex(GO:0080008) |
| 0.1 | 3.1 | GO:0031969 | chloroplast membrane(GO:0031969) |
| 0.0 | 3.1 | GO:0019005 | SCF ubiquitin ligase complex(GO:0019005) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 21.9 | GO:0001071 | nucleic acid binding transcription factor activity(GO:0001071) transcription factor activity, sequence-specific DNA binding(GO:0003700) |
| 0.0 | 9.3 | GO:0003735 | structural constituent of ribosome(GO:0003735) |
| 0.0 | 6.0 | GO:0000978 | RNA polymerase II core promoter proximal region sequence-specific DNA binding(GO:0000978) |
| 0.2 | 5.5 | GO:0048029 | monosaccharide binding(GO:0048029) |
| 1.4 | 4.1 | GO:0016630 | protochlorophyllide reductase activity(GO:0016630) |
| 0.0 | 4.1 | GO:0015631 | tubulin binding(GO:0015631) |
| 0.1 | 3.8 | GO:0003713 | transcription coactivator activity(GO:0003713) |
| 0.3 | 3.7 | GO:0004430 | 1-phosphatidylinositol 4-kinase activity(GO:0004430) |
| 0.1 | 3.6 | GO:0050135 | NAD(P)+ nucleosidase activity(GO:0050135) |
| 0.3 | 3.4 | GO:0008453 | alanine-glyoxylate transaminase activity(GO:0008453) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 1.2 | SIG PIP3 SIGNALING IN CARDIAC MYOCTES | Genes related to PIP3 signaling in cardiac myocytes |
| 0.2 | 0.9 | PID PDGFRA PATHWAY | PDGFR-alpha signaling pathway |
| 0.2 | 0.7 | PID INTEGRIN3 PATHWAY | Beta3 integrin cell surface interactions |
| 0.2 | 0.7 | PID S1P S1P1 PATHWAY | S1P1 pathway |
| 0.1 | 0.7 | NABA CORE MATRISOME | Ensemble of genes encoding core extracellular matrix including ECM glycoproteins, collagens and proteoglycans |
| 0.2 | 0.6 | PID HNF3B PATHWAY | FOXA2 and FOXA3 transcription factor networks |
| 0.1 | 0.6 | PID HIF1 TFPATHWAY | HIF-1-alpha transcription factor network |
| 0.2 | 0.5 | PID BCR 5PATHWAY | BCR signaling pathway |
| 0.1 | 0.5 | PID SMAD2 3NUCLEAR PATHWAY | Regulation of nuclear SMAD2/3 signaling |
| 0.2 | 0.4 | PID TCPTP PATHWAY | Signaling events mediated by TCPTP |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 1.9 | REACTOME TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES | Genes involved in Transmembrane transport of small molecules |
| 0.1 | 1.8 | REACTOME FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION | Genes involved in Factors involved in megakaryocyte development and platelet production |
| 0.4 | 1.4 | REACTOME SYNTHESIS OF BILE ACIDS AND BILE SALTS | Genes involved in Synthesis of bile acids and bile salts |
| 0.1 | 1.4 | REACTOME NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX | Genes involved in Nonsense Mediated Decay Enhanced by the Exon Junction Complex |
| 0.3 | 1.3 | REACTOME FANCONI ANEMIA PATHWAY | Genes involved in Fanconi Anemia pathway |
| 0.3 | 1.3 | REACTOME INTEGRIN ALPHAIIB BETA3 SIGNALING | Genes involved in Integrin alphaIIb beta3 signaling |
| 0.2 | 1.1 | REACTOME LIPID DIGESTION MOBILIZATION AND TRANSPORT | Genes involved in Lipid digestion, mobilization, and transport |
| 0.2 | 0.7 | REACTOME TRNA AMINOACYLATION | Genes involved in tRNA Aminoacylation |
| 0.2 | 0.7 | REACTOME GLYCOSPHINGOLIPID METABOLISM | Genes involved in Glycosphingolipid metabolism |
| 0.1 | 0.7 | REACTOME TRANSCRIPTIONAL REGULATION OF WHITE ADIPOCYTE DIFFERENTIATION | Genes involved in Transcriptional Regulation of White Adipocyte Differentiation |