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GSE53960: rat RNA-Seq transcriptomic Bodymap
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Results for Vdr
Z-value: 0.84
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Transcription factors associated with Vdr
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| Vdr | rn6_v1_chr7_-_139394166_139394166 | -0.27 | 6.6e-07 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr1_+_248723397 Show fit | 33.55 |
ENSRNOT00000072188
|
mannose-binding protein C-like |
|
| chr16_-_7007287 Show fit | 28.58 |
ENSRNOT00000041216
|
inter-alpha trypsin inhibitor, heavy chain 3 |
|
| chr16_-_7007051 Show fit | 28.19 |
ENSRNOT00000023984
|
inter-alpha trypsin inhibitor, heavy chain 3 |
|
| chr10_+_64952119 Show fit | 24.25 |
ENSRNOT00000012154
|
pipecolic acid and sarcosine oxidase |
|
| chr6_+_128050250 Show fit | 24.05 |
ENSRNOT00000077517
ENSRNOT00000013961 |
Ab1-233 |
|
| chr12_-_11733099 Show fit | 22.26 |
ENSRNOT00000051244
ENSRNOT00000087257 |
cytochrome P450, family 3, subfamily a, polypeptide 23/polypeptide 1 |
|
| chr7_-_123621102 Show fit | 21.08 |
ENSRNOT00000046024
|
cytochrome P450, family 2, subfamily d, polypeptide 5 |
|
| chr2_-_23256158 Show fit | 18.87 |
ENSRNOT00000015336
|
betaine-homocysteine S-methyltransferase |
|
| chr10_+_65767930 Show fit | 18.84 |
ENSRNOT00000039954
|
vitronectin |
|
| chr1_+_83711251 Show fit | 18.30 |
ENSRNOT00000028237
ENSRNOT00000092008 |
cytochrome P450, family 2, subfamily a, polypeptide 1 |
Network of associatons between targets according to the STRING database.
First level regulatory network of Vdr
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.7 | 56.8 | GO:0030212 | hyaluronan metabolic process(GO:0030212) |
| 5.2 | 36.2 | GO:0009804 | coumarin metabolic process(GO:0009804) |
| 2.4 | 33.6 | GO:0001867 | complement activation, lectin pathway(GO:0001867) |
| 0.0 | 33.6 | GO:0050911 | detection of chemical stimulus involved in sensory perception of smell(GO:0050911) |
| 6.1 | 24.3 | GO:0006554 | lysine catabolic process(GO:0006554) L-lysine catabolic process to acetyl-CoA(GO:0019474) L-lysine catabolic process(GO:0019477) L-lysine metabolic process(GO:0046440) |
| 1.9 | 22.3 | GO:0070989 | oxidative demethylation(GO:0070989) |
| 1.2 | 21.2 | GO:0045603 | positive regulation of endothelial cell differentiation(GO:0045603) |
| 0.4 | 21.1 | GO:0019369 | arachidonic acid metabolic process(GO:0019369) |
| 6.3 | 18.9 | GO:0006579 | amino-acid betaine catabolic process(GO:0006579) |
| 1.7 | 18.8 | GO:0061302 | smooth muscle cell-matrix adhesion(GO:0061302) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 74.9 | GO:0042175 | nuclear outer membrane-endoplasmic reticulum membrane network(GO:0042175) |
| 0.2 | 31.0 | GO:0005777 | peroxisome(GO:0005777) microbody(GO:0042579) |
| 0.4 | 27.6 | GO:0005581 | collagen trimer(GO:0005581) |
| 0.0 | 26.9 | GO:0005615 | extracellular space(GO:0005615) |
| 0.0 | 24.8 | GO:0070062 | extracellular exosome(GO:0070062) |
| 0.2 | 20.7 | GO:0072562 | blood microparticle(GO:0072562) |
| 3.1 | 18.8 | GO:0048237 | rough endoplasmic reticulum lumen(GO:0048237) |
| 0.8 | 17.0 | GO:0005922 | connexon complex(GO:0005922) |
| 0.5 | 11.8 | GO:0030057 | desmosome(GO:0030057) |
| 0.1 | 11.0 | GO:0043197 | dendritic spine(GO:0043197) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 2.1 | 58.5 | GO:0008395 | steroid hydroxylase activity(GO:0008395) |
| 0.5 | 54.7 | GO:0004867 | serine-type endopeptidase inhibitor activity(GO:0004867) |
| 0.0 | 27.0 | GO:0004984 | olfactory receptor activity(GO:0004984) |
| 6.1 | 24.3 | GO:0016647 | oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor(GO:0016647) |
| 0.8 | 21.1 | GO:0070330 | aromatase activity(GO:0070330) |
| 2.4 | 18.9 | GO:0008172 | S-methyltransferase activity(GO:0008172) |
| 0.8 | 18.8 | GO:0001871 | pattern binding(GO:0001871) polysaccharide binding(GO:0030247) |
| 1.4 | 17.2 | GO:0004499 | N,N-dimethylaniline monooxygenase activity(GO:0004499) |
| 0.3 | 17.1 | GO:0005160 | transforming growth factor beta receptor binding(GO:0005160) |
| 1.2 | 17.0 | GO:0005243 | gap junction channel activity(GO:0005243) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 65.6 | NABA ECM REGULATORS | Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix |
| 0.9 | 18.8 | PID INTEGRIN5 PATHWAY | Beta5 beta6 beta7 and beta8 integrin cell surface interactions |
| 0.2 | 17.4 | PID NOTCH PATHWAY | Notch signaling pathway |
| 0.4 | 12.9 | PID ALK1 PATHWAY | ALK1 signaling events |
| 0.2 | 12.6 | PID LYSOPHOSPHOLIPID PATHWAY | LPA receptor mediated events |
| 0.2 | 10.5 | PID IL6 7 PATHWAY | IL6-mediated signaling events |
| 0.1 | 8.0 | PID IL4 2PATHWAY | IL4-mediated signaling events |
| 0.2 | 6.8 | PID HES HEY PATHWAY | Notch-mediated HES/HEY network |
| 0.1 | 5.6 | PID REG GR PATHWAY | Glucocorticoid receptor regulatory network |
| 0.2 | 4.7 | PID ERBB NETWORK PATHWAY | ErbB receptor signaling network |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 26.8 | REACTOME INTEGRIN CELL SURFACE INTERACTIONS | Genes involved in Integrin cell surface interactions |
| 0.7 | 18.9 | REACTOME SULFUR AMINO ACID METABOLISM | Genes involved in Sulfur amino acid metabolism |
| 0.5 | 18.1 | REACTOME AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE | Genes involved in Amino acid transport across the plasma membrane |
| 0.9 | 17.0 | REACTOME GAP JUNCTION ASSEMBLY | Genes involved in Gap junction assembly |
| 0.4 | 15.0 | REACTOME AMINE LIGAND BINDING RECEPTORS | Genes involved in Amine ligand-binding receptors |
| 0.3 | 14.0 | REACTOME CHEMOKINE RECEPTORS BIND CHEMOKINES | Genes involved in Chemokine receptors bind chemokines |
| 0.3 | 13.8 | REACTOME PHASE1 FUNCTIONALIZATION OF COMPOUNDS | Genes involved in Phase 1 - Functionalization of compounds |
| 0.8 | 11.8 | REACTOME APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS | Genes involved in Apoptotic cleavage of cell adhesion proteins |
| 0.1 | 7.5 | REACTOME RESPIRATORY ELECTRON TRANSPORT | Genes involved in Respiratory electron transport |
| 0.5 | 6.9 | REACTOME BILE SALT AND ORGANIC ANION SLC TRANSPORTERS | Genes involved in Bile salt and organic anion SLC transporters |