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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for msx1a
Z-value: 1.01
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Transcription factors associated with msx1a
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| msx1a | dr11_v1_chr14_-_12822_12847 | -0.61 | 7.5e-03 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr11_-_6452444 Show fit | 4.98 |
ENSDART00000137879
ENSDART00000134957 ENSDART00000004483 |
La ribonucleoprotein domain family, member 6b |
|
| chr10_-_21362071 Show fit | 4.97 |
ENSDART00000125167
|
avidin |
|
| chr10_-_21362320 Show fit | 4.64 |
ENSDART00000189789
|
avidin |
|
| chr21_+_25777425 Show fit | 3.78 |
ENSDART00000021620
|
claudin d |
|
| chr9_-_35633827 Show fit | 3.75 |
ENSDART00000077745
|
zona pellucida glycoprotein 2, like 1 |
|
| chr20_-_23426339 Show fit | 3.52 |
ENSDART00000004625
|
zygote arrest 1 |
|
| chr14_+_34490445 Show fit | 3.49 |
ENSDART00000132193
ENSDART00000148044 |
wingless-type MMTV integration site family, member 8a |
|
| chr18_-_40708537 Show fit | 3.30 |
ENSDART00000077577
|
si:ch211-132b12.8 |
|
| chr10_-_25217347 Show fit | 3.10 |
ENSDART00000036906
|
karyopherin alpha 7 (importin alpha 8) |
|
| chr8_+_45334255 Show fit | 2.93 |
ENSDART00000126848
ENSDART00000134161 ENSDART00000142322 ENSDART00000145011 ENSDART00000183560 |
poly(A) binding protein, cytoplasmic 1-like |
Network of associatons between targets according to the STRING database.
First level regulatory network of msx1a
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 4.0 | GO:1904029 | regulation of cyclin-dependent protein serine/threonine kinase activity(GO:0000079) regulation of cyclin-dependent protein kinase activity(GO:1904029) |
| 0.8 | 3.8 | GO:0016338 | calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules(GO:0016338) |
| 1.2 | 3.5 | GO:0039015 | spinal cord anterior/posterior patterning(GO:0021512) cell proliferation involved in pronephros development(GO:0039015) cell proliferation involved in kidney development(GO:0072111) |
| 0.3 | 3.1 | GO:0006607 | NLS-bearing protein import into nucleus(GO:0006607) |
| 0.0 | 2.6 | GO:0048545 | response to steroid hormone(GO:0048545) |
| 0.0 | 2.5 | GO:0017148 | negative regulation of translation(GO:0017148) |
| 0.5 | 2.4 | GO:0051145 | smooth muscle cell differentiation(GO:0051145) negative regulation of muscle cell differentiation(GO:0051148) |
| 0.6 | 2.3 | GO:0060074 | synapse maturation(GO:0060074) |
| 0.1 | 2.3 | GO:0006995 | cellular response to nitrogen starvation(GO:0006995) cellular response to nitrogen levels(GO:0043562) |
| 0.0 | 2.3 | GO:0070098 | chemokine-mediated signaling pathway(GO:0070098) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 4.2 | GO:0005923 | bicellular tight junction(GO:0005923) occluding junction(GO:0070160) |
| 1.3 | 4.0 | GO:0097124 | cyclin A2-CDK2 complex(GO:0097124) |
| 1.2 | 3.5 | GO:0097189 | apoptotic body(GO:0097189) |
| 0.0 | 2.4 | GO:0032432 | actin filament bundle(GO:0032432) |
| 0.1 | 2.3 | GO:0000421 | autophagosome membrane(GO:0000421) |
| 0.1 | 2.3 | GO:0005881 | cytoplasmic microtubule(GO:0005881) |
| 0.1 | 2.1 | GO:0010494 | cytoplasmic stress granule(GO:0010494) |
| 0.0 | 2.0 | GO:0031970 | mitochondrial intermembrane space(GO:0005758) organelle envelope lumen(GO:0031970) |
| 0.3 | 1.5 | GO:0000506 | glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex(GO:0000506) |
| 0.1 | 1.5 | GO:0035102 | PRC1 complex(GO:0035102) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.9 | 9.6 | GO:0009374 | biotin binding(GO:0009374) |
| 0.0 | 7.4 | GO:0042802 | identical protein binding(GO:0042802) |
| 0.0 | 4.7 | GO:0003729 | mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822) |
| 0.1 | 4.0 | GO:0016538 | cyclin-dependent protein serine/threonine kinase regulator activity(GO:0016538) |
| 0.2 | 3.8 | GO:0061608 | nuclear import signal receptor activity(GO:0061608) |
| 0.1 | 3.3 | GO:0005109 | frizzled binding(GO:0005109) |
| 0.2 | 2.9 | GO:0008266 | poly(U) RNA binding(GO:0008266) |
| 0.1 | 2.3 | GO:0031729 | CCR1 chemokine receptor binding(GO:0031726) CCR4 chemokine receptor binding(GO:0031729) |
| 0.1 | 2.3 | GO:0019894 | kinesin binding(GO:0019894) |
| 0.0 | 2.3 | GO:0031625 | ubiquitin protein ligase binding(GO:0031625) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 5.4 | WNT SIGNALING | Genes related to Wnt-mediated signal transduction |
| 0.3 | 4.0 | SA REG CASCADE OF CYCLIN EXPR | Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases. |
| 0.1 | 1.5 | PID PRL SIGNALING EVENTS PATHWAY | Signaling events mediated by PRL |
| 0.0 | 0.5 | PID RXR VDR PATHWAY | RXR and RAR heterodimerization with other nuclear receptor |
| 0.0 | 0.5 | PID RHOA PATHWAY | RhoA signaling pathway |
| 0.0 | 0.5 | PID AURORA B PATHWAY | Aurora B signaling |
| 0.0 | 0.4 | PID ECADHERIN KERATINOCYTE PATHWAY | E-cadherin signaling in keratinocytes |
| 0.0 | 0.2 | PID ARF 3PATHWAY | Arf1 pathway |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 4.0 | REACTOME CYCLIN A B1 ASSOCIATED EVENTS DURING G2 M TRANSITION | Genes involved in Cyclin A/B1 associated events during G2/M transition |
| 0.1 | 1.9 | REACTOME GLYCOLYSIS | Genes involved in Glycolysis |
| 0.1 | 1.8 | REACTOME BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN | Genes involved in Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein |
| 0.0 | 1.8 | REACTOME ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION | Genes involved in Antigen processing: Ubiquitination & Proteasome degradation |
| 0.1 | 1.5 | REACTOME SYNTHESIS OF GLYCOSYLPHOSPHATIDYLINOSITOL GPI | Genes involved in Synthesis of glycosylphosphatidylinositol (GPI) |
| 0.1 | 1.5 | REACTOME CYTOCHROME P450 ARRANGED BY SUBSTRATE TYPE | Genes involved in Cytochrome P450 - arranged by substrate type |
| 0.0 | 0.8 | REACTOME SIGNALING BY FGFR1 FUSION MUTANTS | Genes involved in Signaling by FGFR1 fusion mutants |
| 0.0 | 0.7 | REACTOME ION TRANSPORT BY P TYPE ATPASES | Genes involved in Ion transport by P-type ATPases |
| 0.1 | 0.5 | REACTOME TGF BETA RECEPTOR SIGNALING IN EMT EPITHELIAL TO MESENCHYMAL TRANSITION | Genes involved in TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) |
| 0.0 | 0.5 | REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES | Genes involved in Cross-presentation of soluble exogenous antigens (endosomes) |