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GSE130291:vernalization in Arabidopsis thaliana
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Results for AT5G39760
Z-value: 1.37
Transcription factors associated with AT5G39760
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
|
AT5G39760
|
AT5G39760 | homeobox protein 23 |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| HB23 | arTal_v1_Chr5_+_15911350_15911350 | -0.06 | 8.4e-01 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| arTal_v1_Chr4_-_13317640_13317640 Show fit | 2.30 |
AT4G26320.1
|
arabinogalactan protein 13 |
|
| arTal_v1_Chr4_-_7421828_7421828 Show fit | 1.89 |
AT4G12520.1
|
Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein |
|
| arTal_v1_Chr1_-_10164452_10164452 Show fit | 1.86 |
AT1G29090.1
|
Cysteine proteinases superfamily protein |
|
| arTal_v1_Chr4_-_993039_993039 Show fit | 1.82 |
AT4G02270.1
|
root hair specific 13 |
|
| arTal_v1_Chr4_-_7417873_7417873 Show fit | 1.80 |
AT4G12510.1
|
Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein |
|
| arTal_v1_Chr1_-_1527360_1527360 Show fit | 1.78 |
AT1G05250.1
|
Peroxidase superfamily protein |
|
| arTal_v1_Chr4_-_14542565_14542565 Show fit | 1.71 |
AT4G29690.1
|
Alkaline-phosphatase-like family protein |
|
| arTal_v1_Chr4_-_13016235_13016235 Show fit | 1.69 |
AT4G25470.1
|
C-repeat/DRE binding factor 2 |
|
| arTal_v1_Chr5_+_1461786_1461786 Show fit | 1.66 |
AT5G04960.1
|
Plant invertase/pectin methylesterase inhibitor superfamily |
|
| arTal_v1_Chr4_+_10703348_10703348 Show fit | 1.66 |
AT4G19680.1
AT4G19680.2 |
iron regulated transporter 2 |
Network of associatons between targets according to the STRING database.
First level regulatory network of AT5G39760
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 7.8 | GO:0010411 | xyloglucan metabolic process(GO:0010411) |
| 0.1 | 7.2 | GO:0045490 | pectin catabolic process(GO:0045490) |
| 0.4 | 4.4 | GO:0010106 | cellular response to iron ion starvation(GO:0010106) |
| 0.1 | 4.2 | GO:0045168 | cell-cell signaling involved in cell fate commitment(GO:0045168) |
| 0.1 | 4.1 | GO:0009631 | cold acclimation(GO:0009631) |
| 0.0 | 3.3 | GO:1902600 | hydrogen ion transmembrane transport(GO:1902600) |
| 0.2 | 3.2 | GO:0048766 | root hair initiation(GO:0048766) |
| 0.1 | 3.2 | GO:0045492 | xylan biosynthetic process(GO:0045492) |
| 0.1 | 3.1 | GO:0006099 | tricarboxylic acid cycle(GO:0006099) citrate metabolic process(GO:0006101) |
| 0.2 | 3.0 | GO:0016998 | cell wall macromolecule catabolic process(GO:0016998) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 64.1 | GO:0005576 | extracellular region(GO:0005576) |
| 0.1 | 38.4 | GO:0031225 | anchored component of membrane(GO:0031225) |
| 0.1 | 15.8 | GO:0009505 | plant-type cell wall(GO:0009505) |
| 0.0 | 14.8 | GO:0005794 | Golgi apparatus(GO:0005794) |
| 0.0 | 11.9 | GO:0005618 | cell wall(GO:0005618) external encapsulating structure(GO:0030312) |
| 0.1 | 7.3 | GO:0000138 | Golgi trans cisterna(GO:0000138) |
| 0.1 | 6.4 | GO:0022627 | cytosolic small ribosomal subunit(GO:0022627) |
| 0.0 | 5.4 | GO:0009705 | plant-type vacuole membrane(GO:0009705) |
| 0.0 | 4.5 | GO:0022625 | cytosolic large ribosomal subunit(GO:0022625) |
| 0.1 | 4.3 | GO:0005764 | lysosome(GO:0005764) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 9.8 | GO:0004601 | peroxidase activity(GO:0004601) |
| 0.1 | 7.9 | GO:0030599 | pectinesterase activity(GO:0030599) |
| 0.3 | 5.6 | GO:0052716 | hydroquinone:oxygen oxidoreductase activity(GO:0052716) |
| 0.1 | 5.4 | GO:0015171 | amino acid transmembrane transporter activity(GO:0015171) |
| 0.1 | 4.8 | GO:0001228 | transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding(GO:0001228) |
| 0.2 | 4.2 | GO:0005372 | water transmembrane transporter activity(GO:0005372) water channel activity(GO:0015250) |
| 0.2 | 4.2 | GO:0005199 | structural constituent of cell wall(GO:0005199) |
| 0.5 | 4.1 | GO:0033946 | xyloglucan-specific endo-beta-1,4-glucanase activity(GO:0033946) |
| 0.0 | 4.1 | GO:0005198 | structural molecule activity(GO:0005198) |
| 0.1 | 3.9 | GO:0016762 | xyloglucan:xyloglucosyl transferase activity(GO:0016762) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 2.5 | PID CASPASE PATHWAY | Caspase cascade in apoptosis |
| 0.1 | 1.2 | PID CXCR4 PATHWAY | CXCR4-mediated signaling events |
| 0.4 | 1.1 | PID AVB3 OPN PATHWAY | Osteopontin-mediated events |
| 0.3 | 0.9 | PID IL12 2PATHWAY | IL12-mediated signaling events |
| 0.2 | 0.9 | NABA ECM GLYCOPROTEINS | Genes encoding structural ECM glycoproteins |
| 0.2 | 0.9 | NABA SECRETED FACTORS | Genes encoding secreted soluble factors |
| 0.1 | 0.7 | PID HDAC CLASSII PATHWAY | Signaling events mediated by HDAC Class II |
| 0.2 | 0.6 | PID REG GR PATHWAY | Glucocorticoid receptor regulatory network |
| 0.2 | 0.6 | ST WNT BETA CATENIN PATHWAY | Wnt/beta-catenin Pathway |
| 0.2 | 0.5 | SA G2 AND M PHASES | Cdc25 activates the cdc2/cyclin B complex to induce the G2/M transition. |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.5 | 1.5 | REACTOME NUCLEOTIDE BINDING DOMAIN LEUCINE RICH REPEAT CONTAINING RECEPTOR NLR SIGNALING PATHWAYS | Genes involved in Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways |
| 0.3 | 1.4 | REACTOME INNATE IMMUNE SYSTEM | Genes involved in Innate Immune System |
| 0.1 | 1.3 | REACTOME HEMOSTASIS | Genes involved in Hemostasis |
| 0.2 | 1.2 | REACTOME SIGNALING BY PDGF | Genes involved in Signaling by PDGF |
| 0.4 | 1.1 | REACTOME INTEGRATION OF ENERGY METABOLISM | Genes involved in Integration of energy metabolism |
| 0.3 | 1.0 | REACTOME GLYCOSPHINGOLIPID METABOLISM | Genes involved in Glycosphingolipid metabolism |
| 0.2 | 0.9 | REACTOME MHC CLASS II ANTIGEN PRESENTATION | Genes involved in MHC class II antigen presentation |
| 0.3 | 0.7 | REACTOME APOPTOSIS INDUCED DNA FRAGMENTATION | Genes involved in Apoptosis induced DNA fragmentation |
| 0.1 | 0.7 | REACTOME E2F ENABLED INHIBITION OF PRE REPLICATION COMPLEX FORMATION | Genes involved in E2F-enabled inhibition of pre-replication complex formation |
| 0.2 | 0.6 | REACTOME HDL MEDIATED LIPID TRANSPORT | Genes involved in HDL-mediated lipid transport |