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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for lef1
Z-value: 1.32
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Transcription factors associated with lef1
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| lef1 | dr11_v1_chr1_+_49814942_49814942 | 0.91 | 1.6e-07 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr23_-_10175898 Show fit | 5.02 |
ENSDART00000146185
|
keratin 5 |
|
| chr1_+_44173245 Show fit | 3.80 |
ENSDART00000159450
ENSDART00000106048 ENSDART00000157763 |
catenin (cadherin-associated protein), delta 1 |
|
| chr3_-_55650771 Show fit | 3.44 |
ENSDART00000162413
|
axin 2 (conductin, axil) |
|
| chr20_-_29498178 Show fit | 3.35 |
ENSDART00000152986
ENSDART00000027851 ENSDART00000152954 |
ribonucleotide reductase M2 polypeptide |
|
| chr1_+_44173506 Show fit | 3.09 |
ENSDART00000170512
|
catenin (cadherin-associated protein), delta 1 |
|
| chr11_-_26832685 Show fit | 2.52 |
ENSDART00000153519
|
IQ motif and Sec7 domain 1b |
|
| chr5_-_28149767 Show fit | 2.49 |
ENSDART00000051515
|
zgc:110329 |
|
| chr1_+_36772348 Show fit | 2.39 |
ENSDART00000109314
|
Rho GTPase activating protein 10 |
|
| chr12_+_48340133 Show fit | 2.34 |
ENSDART00000152899
ENSDART00000153335 ENSDART00000054788 |
DNA-damage-inducible transcript 4 |
|
| chr19_+_43523690 Show fit | 2.32 |
ENSDART00000113031
|
WAS protein family, member 2 |
Network of associatons between targets according to the STRING database.
First level regulatory network of lef1
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 6.1 | GO:0008078 | mesodermal cell migration(GO:0008078) |
| 0.1 | 5.7 | GO:0045930 | negative regulation of mitotic cell cycle(GO:0045930) |
| 0.5 | 5.4 | GO:0009263 | deoxyribonucleotide biosynthetic process(GO:0009263) |
| 0.0 | 5.0 | GO:0008360 | regulation of cell shape(GO:0008360) |
| 0.3 | 4.4 | GO:2000054 | negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification(GO:2000054) |
| 0.0 | 4.4 | GO:0043484 | regulation of RNA splicing(GO:0043484) |
| 0.2 | 3.9 | GO:0060541 | respiratory system development(GO:0060541) |
| 0.2 | 3.5 | GO:0060287 | epithelial cilium movement involved in determination of left/right asymmetry(GO:0060287) |
| 0.6 | 3.2 | GO:1900145 | nodal signaling pathway involved in determination of left/right asymmetry(GO:0038107) regulation of nodal signaling pathway involved in determination of left/right asymmetry(GO:1900145) |
| 0.0 | 3.2 | GO:0031101 | fin regeneration(GO:0031101) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 9.3 | GO:0005912 | adherens junction(GO:0005912) anchoring junction(GO:0070161) |
| 0.1 | 6.1 | GO:0032432 | actin filament bundle(GO:0032432) |
| 0.5 | 5.0 | GO:0045095 | keratin filament(GO:0045095) |
| 0.0 | 3.8 | GO:0000922 | spindle pole(GO:0000922) |
| 0.0 | 3.6 | GO:0005730 | nucleolus(GO:0005730) |
| 0.0 | 3.2 | GO:0016607 | nuclear speck(GO:0016607) |
| 0.1 | 2.9 | GO:0000307 | cyclin-dependent protein kinase holoenzyme complex(GO:0000307) |
| 0.0 | 2.9 | GO:0043296 | apical junction complex(GO:0043296) |
| 0.2 | 2.5 | GO:0016602 | CCAAT-binding factor complex(GO:0016602) |
| 0.1 | 2.3 | GO:0031209 | SCAR complex(GO:0031209) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 7.3 | GO:0045296 | cadherin binding(GO:0045296) |
| 0.0 | 6.2 | GO:0003682 | chromatin binding(GO:0003682) |
| 0.0 | 5.9 | GO:0051015 | actin filament binding(GO:0051015) |
| 0.1 | 5.5 | GO:0003730 | mRNA 3'-UTR binding(GO:0003730) |
| 0.8 | 5.4 | GO:0004748 | ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor(GO:0004748) oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor(GO:0016728) ribonucleoside-diphosphate reductase activity(GO:0061731) |
| 0.0 | 5.3 | GO:0042393 | histone binding(GO:0042393) |
| 0.0 | 4.7 | GO:0003714 | transcription corepressor activity(GO:0003714) |
| 0.1 | 3.7 | GO:0030374 | ligand-dependent nuclear receptor transcription coactivator activity(GO:0030374) |
| 0.2 | 3.6 | GO:0008301 | DNA binding, bending(GO:0008301) |
| 0.0 | 2.8 | GO:0008138 | protein tyrosine/serine/threonine phosphatase activity(GO:0008138) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 7.2 | PID E2F PATHWAY | E2F transcription factor network |
| 0.4 | 7.0 | PID BETA CATENIN DEG PATHWAY | Degradation of beta catenin |
| 0.3 | 6.9 | PID ECADHERIN KERATINOCYTE PATHWAY | E-cadherin signaling in keratinocytes |
| 0.1 | 4.5 | PID DELTA NP63 PATHWAY | Validated transcriptional targets of deltaNp63 isoforms |
| 0.1 | 4.0 | PID ECADHERIN NASCENT AJ PATHWAY | E-cadherin signaling in the nascent adherens junction |
| 0.1 | 3.2 | PID MTOR 4PATHWAY | mTOR signaling pathway |
| 0.2 | 2.4 | PID INTEGRIN4 PATHWAY | Alpha6 beta4 integrin-ligand interactions |
| 0.1 | 2.1 | PID ERB GENOMIC PATHWAY | Validated nuclear estrogen receptor beta network |
| 0.1 | 2.1 | PID RB 1PATHWAY | Regulation of retinoblastoma protein |
| 0.1 | 2.0 | PID CIRCADIAN PATHWAY | Circadian rhythm pathway |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 7.3 | REACTOME ADHERENS JUNCTIONS INTERACTIONS | Genes involved in Adherens junctions interactions |
| 0.3 | 6.6 | REACTOME G1 S SPECIFIC TRANSCRIPTION | Genes involved in G1/S-Specific Transcription |
| 0.1 | 3.8 | REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES | Genes involved in Antiviral mechanism by IFN-stimulated genes |
| 0.1 | 3.6 | REACTOME REGULATION OF APOPTOSIS | Genes involved in Regulation of Apoptosis |
| 0.1 | 2.9 | REACTOME CIRCADIAN REPRESSION OF EXPRESSION BY REV ERBA | Genes involved in Circadian Repression of Expression by REV-ERBA |
| 0.2 | 2.3 | REACTOME INHIBITION OF REPLICATION INITIATION OF DAMAGED DNA BY RB1 E2F1 | Genes involved in Inhibition of replication initiation of damaged DNA by RB1/E2F1 |
| 0.1 | 2.3 | REACTOME CIRCADIAN CLOCK | Genes involved in Circadian Clock |
| 0.1 | 2.2 | REACTOME CELL JUNCTION ORGANIZATION | Genes involved in Cell junction organization |
| 0.2 | 1.9 | REACTOME SEMA3A PLEXIN REPULSION SIGNALING BY INHIBITING INTEGRIN ADHESION | Genes involved in SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion |
| 0.1 | 1.9 | REACTOME N GLYCAN ANTENNAE ELONGATION | Genes involved in N-Glycan antennae elongation |