Project
PRJNA438478: RNAseq of wild type zebrafish germline
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Results for SPDEF
Z-value: 1.24
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Transcription factors associated with SPDEF
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| SPDEF | dr11_v1_chr6_-_54290227_54290227 | -0.72 | 6.8e-04 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr3_-_3398383 Show fit | 4.39 |
ENSDART00000047865
|
si:dkey-46g23.2 |
|
| chr3_-_3413669 Show fit | 4.08 |
ENSDART00000113517
ENSDART00000179861 ENSDART00000115331 |
zgc:171446 |
|
| chr22_-_5171362 Show fit | 3.15 |
ENSDART00000124889
|
tumor necrosis factor, alpha-induced protein 8-like 1 |
|
| chr21_-_43636595 Show fit | 3.12 |
ENSDART00000151115
ENSDART00000151486 ENSDART00000151778 |
si:ch1073-263o8.2 |
|
| chr15_+_38299385 Show fit | 2.97 |
ENSDART00000142403
|
si:dkey-24p1.6 |
|
| chr15_+_38299563 Show fit | 2.82 |
ENSDART00000099375
|
si:dkey-24p1.6 |
|
| chr25_+_8921425 Show fit | 2.68 |
ENSDART00000128591
|
1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional) |
|
| chr20_-_23254876 Show fit | 2.65 |
ENSDART00000141510
|
OCIA domain containing 1 |
|
| chr21_-_30994577 Show fit | 2.42 |
ENSDART00000065503
|
post-GPI attachment to proteins 2 |
|
| chr3_-_36440705 Show fit | 2.39 |
ENSDART00000162875
|
rogdi homolog (Drosophila) |
Network of associatons between targets according to the STRING database.
First level regulatory network of SPDEF
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 7.7 | GO:0010466 | negative regulation of peptidase activity(GO:0010466) |
| 0.0 | 5.6 | GO:0070085 | glycosylation(GO:0070085) |
| 0.1 | 4.1 | GO:0000462 | maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)(GO:0000462) |
| 0.1 | 4.1 | GO:0032007 | negative regulation of TOR signaling(GO:0032007) |
| 0.9 | 3.7 | GO:0042779 | tRNA 3'-trailer cleavage(GO:0042779) |
| 0.3 | 3.5 | GO:0071850 | mitotic cell cycle arrest(GO:0071850) |
| 0.1 | 3.4 | GO:0006515 | misfolded or incompletely synthesized protein catabolic process(GO:0006515) |
| 0.2 | 3.2 | GO:0036353 | histone H2A-K119 monoubiquitination(GO:0036353) |
| 0.2 | 3.2 | GO:0045747 | positive regulation of Notch signaling pathway(GO:0045747) regulation of clathrin-mediated endocytosis(GO:2000369) |
| 0.1 | 3.0 | GO:0018231 | peptidyl-L-cysteine S-palmitoylation(GO:0018230) peptidyl-S-diacylglycerol-L-cysteine biosynthetic process from peptidyl-cysteine(GO:0018231) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 9.3 | GO:0005794 | Golgi apparatus(GO:0005794) |
| 0.0 | 3.4 | GO:0072686 | mitotic spindle(GO:0072686) |
| 0.0 | 3.4 | GO:0016607 | nuclear speck(GO:0016607) |
| 0.1 | 3.2 | GO:0035102 | PRC1 complex(GO:0035102) |
| 0.4 | 2.6 | GO:0034388 | Pwp2p-containing subcomplex of 90S preribosome(GO:0034388) |
| 0.6 | 2.4 | GO:0043291 | RAVE complex(GO:0043291) |
| 0.8 | 2.3 | GO:0031465 | Cul4B-RING E3 ubiquitin ligase complex(GO:0031465) |
| 0.1 | 2.3 | GO:0030867 | rough endoplasmic reticulum membrane(GO:0030867) |
| 0.1 | 2.2 | GO:0032040 | small-subunit processome(GO:0032040) |
| 0.0 | 1.9 | GO:0031901 | early endosome membrane(GO:0031901) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 8.0 | GO:0004867 | serine-type endopeptidase inhibitor activity(GO:0004867) |
| 0.0 | 4.8 | GO:0004197 | cysteine-type endopeptidase activity(GO:0004197) |
| 0.0 | 4.2 | GO:0004722 | protein serine/threonine phosphatase activity(GO:0004722) |
| 0.9 | 3.8 | GO:0004534 | 5'-3' exoribonuclease activity(GO:0004534) |
| 1.2 | 3.7 | GO:0042781 | 3'-tRNA processing endoribonuclease activity(GO:0042781) |
| 0.2 | 3.5 | GO:0008239 | dipeptidyl-peptidase activity(GO:0008239) |
| 0.4 | 3.4 | GO:0004176 | ATP-dependent peptidase activity(GO:0004176) |
| 0.3 | 3.2 | GO:0035612 | AP-2 adaptor complex binding(GO:0035612) |
| 0.1 | 3.2 | GO:1990841 | promoter-specific chromatin binding(GO:1990841) |
| 0.1 | 3.0 | GO:0019707 | protein-cysteine S-palmitoyltransferase activity(GO:0019706) protein-cysteine S-acyltransferase activity(GO:0019707) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 4.8 | PID PLK1 PATHWAY | PLK1 signaling events |
| 0.1 | 2.4 | PID RET PATHWAY | Signaling events regulated by Ret tyrosine kinase |
| 0.0 | 1.9 | NABA ECM REGULATORS | Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix |
| 0.1 | 1.6 | SA G2 AND M PHASES | Cdc25 activates the cdc2/cyclin B complex to induce the G2/M transition. |
| 0.1 | 1.5 | PID IL12 STAT4 PATHWAY | IL12 signaling mediated by STAT4 |
| 0.0 | 1.4 | PID FAK PATHWAY | Signaling events mediated by focal adhesion kinase |
| 0.2 | 1.2 | ST INTERFERON GAMMA PATHWAY | Interferon gamma pathway. |
| 0.0 | 1.2 | PID IL12 2PATHWAY | IL12-mediated signaling events |
| 0.0 | 0.8 | PID BARD1 PATHWAY | BARD1 signaling events |
| 0.0 | 0.8 | PID SMAD2 3NUCLEAR PATHWAY | Regulation of nuclear SMAD2/3 signaling |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 3.8 | REACTOME ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS | Genes involved in Association of TriC/CCT with target proteins during biosynthesis |
| 0.0 | 1.9 | REACTOME ACTIVATION OF CHAPERONE GENES BY XBP1S | Genes involved in Activation of Chaperone Genes by XBP1(S) |
| 0.0 | 1.8 | REACTOME MRNA SPLICING MINOR PATHWAY | Genes involved in mRNA Splicing - Minor Pathway |
| 0.0 | 1.8 | REACTOME O LINKED GLYCOSYLATION OF MUCINS | Genes involved in O-linked glycosylation of mucins |
| 0.1 | 1.6 | REACTOME CYCLIN A B1 ASSOCIATED EVENTS DURING G2 M TRANSITION | Genes involved in Cyclin A/B1 associated events during G2/M transition |
| 0.0 | 1.6 | REACTOME GOLGI ASSOCIATED VESICLE BIOGENESIS | Genes involved in Golgi Associated Vesicle Biogenesis |
| 0.1 | 1.5 | REACTOME PHASE II CONJUGATION | Genes involved in Phase II conjugation |
| 0.1 | 1.4 | REACTOME NOTCH HLH TRANSCRIPTION PATHWAY | Genes involved in Notch-HLH transcription pathway |
| 0.2 | 1.3 | REACTOME CD28 DEPENDENT VAV1 PATHWAY | Genes involved in CD28 dependent Vav1 pathway |
| 0.1 | 1.2 | REACTOME SULFUR AMINO ACID METABOLISM | Genes involved in Sulfur amino acid metabolism |