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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for sox19a+sox2
Z-value: 2.32
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Transcription factors associated with sox19a+sox2
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| sox2 | dr11_v1_chr22_-_37349967_37349967 | -0.65 | 3.3e-03 | Click! |
| sox19a | dr11_v1_chr5_-_24201437_24201437 | -0.39 | 1.1e-01 | Click! |
Network of associatons between targets according to the STRING database.
First level regulatory network of sox19a+sox2
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 21.1 | GO:0032272 | negative regulation of actin filament polymerization(GO:0030837) negative regulation of protein polymerization(GO:0032272) |
| 0.2 | 20.2 | GO:0000380 | alternative mRNA splicing, via spliceosome(GO:0000380) |
| 0.9 | 18.5 | GO:0008078 | mesodermal cell migration(GO:0008078) |
| 1.0 | 15.1 | GO:0048096 | chromatin-mediated maintenance of transcription(GO:0048096) |
| 0.1 | 13.6 | GO:0000398 | RNA splicing, via transesterification reactions(GO:0000375) RNA splicing, via transesterification reactions with bulged adenosine as nucleophile(GO:0000377) mRNA splicing, via spliceosome(GO:0000398) |
| 1.2 | 13.0 | GO:0009263 | deoxyribonucleotide biosynthetic process(GO:0009263) |
| 0.1 | 12.5 | GO:0045930 | negative regulation of mitotic cell cycle(GO:0045930) |
| 0.2 | 11.6 | GO:0043044 | ATP-dependent chromatin remodeling(GO:0043044) |
| 0.1 | 10.8 | GO:0090630 | activation of GTPase activity(GO:0090630) |
| 0.3 | 10.5 | GO:0032007 | negative regulation of TOR signaling(GO:0032007) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 13.6 | GO:0016607 | nuclear speck(GO:0016607) |
| 0.0 | 13.0 | GO:0005794 | Golgi apparatus(GO:0005794) |
| 0.3 | 10.9 | GO:0090544 | BAF-type complex(GO:0090544) |
| 0.1 | 10.8 | GO:0005923 | bicellular tight junction(GO:0005923) occluding junction(GO:0070160) |
| 0.0 | 9.9 | GO:0005730 | nucleolus(GO:0005730) |
| 0.1 | 9.4 | GO:0001726 | ruffle(GO:0001726) |
| 0.1 | 8.3 | GO:0005871 | kinesin complex(GO:0005871) |
| 0.2 | 7.7 | GO:0000307 | cyclin-dependent protein kinase holoenzyme complex(GO:0000307) |
| 0.2 | 7.2 | GO:0032156 | septin ring(GO:0005940) septin complex(GO:0031105) septin cytoskeleton(GO:0032156) |
| 0.0 | 7.2 | GO:0005938 | cell cortex(GO:0005938) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 28.4 | GO:0042393 | histone binding(GO:0042393) |
| 0.1 | 21.4 | GO:0005096 | GTPase activator activity(GO:0005096) |
| 0.1 | 15.9 | GO:0000989 | transcription factor activity, transcription factor binding(GO:0000989) transcription cofactor activity(GO:0003712) |
| 0.0 | 13.7 | GO:0003723 | RNA binding(GO:0003723) |
| 0.2 | 13.6 | GO:0003730 | mRNA 3'-UTR binding(GO:0003730) |
| 0.1 | 12.2 | GO:0044822 | mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822) |
| 0.1 | 11.9 | GO:0004197 | cysteine-type endopeptidase activity(GO:0004197) |
| 1.6 | 11.5 | GO:0016728 | 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) |
| 1.0 | 10.4 | GO:0016504 | peptidase activator activity(GO:0016504) |
| 0.7 | 8.8 | GO:0015129 | lactate transmembrane transporter activity(GO:0015129) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.6 | 13.9 | PID ECADHERIN KERATINOCYTE PATHWAY | E-cadherin signaling in keratinocytes |
| 0.2 | 12.9 | PID MTOR 4PATHWAY | mTOR signaling pathway |
| 0.2 | 8.2 | PID RAC1 REG PATHWAY | Regulation of RAC1 activity |
| 0.5 | 7.8 | PID HEDGEHOG 2PATHWAY | Signaling events mediated by the Hedgehog family |
| 0.4 | 7.1 | PID SMAD2 3PATHWAY | Regulation of cytoplasmic and nuclear SMAD2/3 signaling |
| 0.1 | 7.1 | PID E2F PATHWAY | E2F transcription factor network |
| 0.3 | 5.5 | PID CIRCADIAN PATHWAY | Circadian rhythm pathway |
| 0.4 | 5.1 | PID REELIN PATHWAY | Reelin signaling pathway |
| 0.1 | 3.9 | PID ECADHERIN STABILIZATION PATHWAY | Stabilization and expansion of the E-cadherin adherens junction |
| 0.1 | 3.9 | PID AURORA B PATHWAY | Aurora B signaling |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 18.1 | REACTOME MRNA SPLICING | Genes involved in mRNA Splicing |
| 0.5 | 13.0 | REACTOME G1 S SPECIFIC TRANSCRIPTION | Genes involved in G1/S-Specific Transcription |
| 0.5 | 10.1 | REACTOME ADHERENS JUNCTIONS INTERACTIONS | Genes involved in Adherens junctions interactions |
| 0.5 | 8.3 | REACTOME BILE SALT AND ORGANIC ANION SLC TRANSPORTERS | Genes involved in Bile salt and organic anion SLC transporters |
| 0.1 | 7.7 | REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES | Genes involved in Antiviral mechanism by IFN-stimulated genes |
| 0.3 | 5.9 | REACTOME N GLYCAN ANTENNAE ELONGATION | Genes involved in N-Glycan antennae elongation |
| 0.0 | 4.9 | REACTOME SIGNALING BY RHO GTPASES | Genes involved in Signaling by Rho GTPases |
| 0.4 | 4.6 | 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 | 4.5 | REACTOME ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS | Genes involved in Association of TriC/CCT with target proteins during biosynthesis |
| 0.0 | 4.2 | REACTOME PPARA ACTIVATES GENE EXPRESSION | Genes involved in PPARA Activates Gene Expression |