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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for nrf1
Z-value: 1.88
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Transcription factors associated with nrf1
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| nrf1 | dr11_v1_chr4_-_15103646_15103696 | 0.98 | 2.4e-13 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr15_-_45538773 Show fit | 5.75 |
ENSDART00000113494
|
Mab-21 domain containing 2 |
|
| chr15_-_28587147 Show fit | 5.14 |
ENSDART00000156049
|
slingshot protein phosphatase 2a |
|
| chr25_+_22320738 Show fit | 4.30 |
ENSDART00000073566
|
cytochrome P450, family 11, subfamily A, polypeptide 1 |
|
| chr25_+_22319940 Show fit | 4.16 |
ENSDART00000154065
ENSDART00000153492 ENSDART00000024866 ENSDART00000154376 |
cytochrome P450, family 11, subfamily A, polypeptide 1 |
|
| chr3_+_48473346 Show fit | 3.95 |
ENSDART00000166294
|
meteorin, glial cell differentiation regulator-like |
|
| chr20_-_182841 Show fit | 3.94 |
ENSDART00000064546
|
si:ch211-241j12.3 |
|
| chr1_+_51615672 Show fit | 3.92 |
ENSDART00000165117
|
zgc:165656 |
|
| chr17_+_33415319 Show fit | 3.71 |
ENSDART00000140805
ENSDART00000025501 ENSDART00000146447 |
synaptosomal-associated protein 23.1 |
|
| chr8_+_7875110 Show fit | 3.63 |
ENSDART00000167423
ENSDART00000160267 ENSDART00000180490 |
methyl-CpG binding domain protein 1a |
|
| chr24_-_42072886 Show fit | 3.58 |
ENSDART00000171389
|
|
Network of associatons between targets according to the STRING database.
First level regulatory network of nrf1
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.7 | 8.5 | GO:0006700 | C21-steroid hormone biosynthetic process(GO:0006700) |
| 0.0 | 7.9 | GO:0043087 | regulation of GTPase activity(GO:0043087) |
| 0.2 | 7.0 | GO:0031629 | synaptic vesicle fusion to presynaptic active zone membrane(GO:0031629) vesicle fusion to plasma membrane(GO:0099500) |
| 0.1 | 6.9 | GO:0032272 | negative regulation of actin filament polymerization(GO:0030837) negative regulation of protein polymerization(GO:0032272) |
| 1.1 | 6.8 | GO:0060251 | regulation of glial cell proliferation(GO:0060251) |
| 1.3 | 6.4 | GO:0070986 | left/right axis specification(GO:0070986) |
| 0.9 | 5.3 | GO:0015910 | peroxisomal long-chain fatty acid import(GO:0015910) |
| 0.5 | 5.3 | GO:0006659 | phosphatidylserine biosynthetic process(GO:0006659) |
| 0.2 | 4.8 | GO:0006446 | regulation of translational initiation(GO:0006446) |
| 0.1 | 4.6 | GO:0006413 | translational initiation(GO:0006413) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 10.3 | GO:0005789 | endoplasmic reticulum membrane(GO:0005789) |
| 0.0 | 6.8 | GO:0010008 | endosome membrane(GO:0010008) |
| 0.1 | 6.5 | GO:0005811 | lipid particle(GO:0005811) |
| 1.0 | 5.8 | GO:0031428 | box C/D snoRNP complex(GO:0031428) |
| 0.3 | 5.8 | GO:0032588 | trans-Golgi network membrane(GO:0032588) |
| 0.0 | 5.3 | GO:0031227 | intrinsic component of endoplasmic reticulum membrane(GO:0031227) |
| 0.1 | 4.8 | GO:0031201 | SNARE complex(GO:0031201) |
| 0.2 | 4.3 | GO:0071004 | U2-type prespliceosome(GO:0071004) prespliceosome(GO:0071010) |
| 0.2 | 4.0 | GO:0071565 | nBAF complex(GO:0071565) |
| 0.1 | 3.9 | GO:0016605 | PML body(GO:0016605) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 12.3 | GO:0005096 | GTPase activator activity(GO:0005096) |
| 0.0 | 10.7 | GO:0008270 | zinc ion binding(GO:0008270) |
| 0.1 | 9.0 | GO:0005484 | SNAP receptor activity(GO:0005484) |
| 0.0 | 8.9 | GO:0035091 | phosphatidylinositol binding(GO:0035091) |
| 2.8 | 8.5 | GO:0008386 | cholesterol monooxygenase (side-chain-cleaving) activity(GO:0008386) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen(GO:0016713) |
| 0.0 | 7.2 | GO:0005085 | guanyl-nucleotide exchange factor activity(GO:0005085) |
| 0.0 | 7.0 | GO:0042393 | histone binding(GO:0042393) |
| 0.1 | 6.9 | GO:0008138 | protein tyrosine/serine/threonine phosphatase activity(GO:0008138) |
| 0.1 | 5.8 | GO:0019208 | phosphatase regulator activity(GO:0019208) |
| 1.1 | 5.7 | GO:0047184 | 1-acylglycerophosphocholine O-acyltransferase activity(GO:0047184) 1-alkylglycerophosphocholine O-acetyltransferase activity(GO:0047192) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 5.0 | PID BARD1 PATHWAY | BARD1 signaling events |
| 0.1 | 3.6 | ST B CELL ANTIGEN RECEPTOR | B Cell Antigen Receptor |
| 0.1 | 3.6 | ST INTEGRIN SIGNALING PATHWAY | Integrin Signaling Pathway |
| 0.1 | 3.3 | PID ERA GENOMIC PATHWAY | Validated nuclear estrogen receptor alpha network |
| 0.1 | 3.2 | PID TELOMERASE PATHWAY | Regulation of Telomerase |
| 0.2 | 3.1 | PID TOLL ENDOGENOUS PATHWAY | Endogenous TLR signaling |
| 0.1 | 1.8 | PID P38 MKK3 6PATHWAY | p38 MAPK signaling pathway |
| 0.0 | 1.4 | PID P53 DOWNSTREAM PATHWAY | Direct p53 effectors |
| 0.2 | 1.3 | SA MMP CYTOKINE CONNECTION | Cytokines can induce activation of matrix metalloproteinases, which degrade extracellular matrix. |
| 0.1 | 1.2 | PID SMAD2 3PATHWAY | Regulation of cytoplasmic and nuclear SMAD2/3 signaling |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.9 | 8.5 | REACTOME ENDOGENOUS STEROLS | Genes involved in Endogenous sterols |
| 0.7 | 5.7 | REACTOME ACYL CHAIN REMODELLING OF PG | Genes involved in Acyl chain remodelling of PG |
| 0.1 | 5.2 | REACTOME GLYCEROPHOSPHOLIPID BIOSYNTHESIS | Genes involved in Glycerophospholipid biosynthesis |
| 0.2 | 4.9 | REACTOME SULFUR AMINO ACID METABOLISM | Genes involved in Sulfur amino acid metabolism |
| 0.1 | 3.9 | REACTOME GOLGI ASSOCIATED VESICLE BIOGENESIS | Genes involved in Golgi Associated Vesicle Biogenesis |
| 0.2 | 3.3 | REACTOME RNA POL III TRANSCRIPTION INITIATION FROM TYPE 2 PROMOTER | Genes involved in RNA Polymerase III Transcription Initiation From Type 2 Promoter |
| 0.1 | 3.2 | REACTOME ACTIVATION OF CHAPERONE GENES BY XBP1S | Genes involved in Activation of Chaperone Genes by XBP1(S) |
| 0.1 | 3.2 | REACTOME METABOLISM OF VITAMINS AND COFACTORS | Genes involved in Metabolism of vitamins and cofactors |
| 0.3 | 3.1 | REACTOME IKK COMPLEX RECRUITMENT MEDIATED BY RIP1 | Genes involved in IKK complex recruitment mediated by RIP1 |
| 0.1 | 2.5 | REACTOME MICRORNA MIRNA BIOGENESIS | Genes involved in MicroRNA (miRNA) Biogenesis |