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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for sox9a+sox9b
Z-value: 1.78
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Transcription factors associated with sox9a+sox9b
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| sox9a | dr11_v1_chr12_-_1951233_1951284 | -0.94 | 5.3e-09 | Click! |
| sox9b | dr11_v1_chr3_-_62527675_62527696 | 0.93 | 3.2e-08 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr8_-_32385989 Show fit | 7.15 |
ENSDART00000143716
ENSDART00000098850 |
lipase, endothelial |
|
| chr19_+_14109348 Show fit | 5.94 |
ENSDART00000159015
|
zgc:175136 |
|
| chr5_+_57924611 Show fit | 5.60 |
ENSDART00000050949
|
B-cell translocation gene 4 |
|
| chr18_+_45571378 Show fit | 5.36 |
ENSDART00000077251
|
kinesin family member C3 |
|
| chr24_-_2381143 Show fit | 5.25 |
ENSDART00000144307
|
ras responsive element binding protein 1a |
|
| chr7_+_58751504 Show fit | 4.89 |
ENSDART00000024185
|
zgc:56231 |
|
| chr16_+_35535375 Show fit | 4.66 |
ENSDART00000171675
|
Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4b |
|
| chr23_+_36308428 Show fit | 4.10 |
ENSDART00000134607
|
heterogeneous nuclear ribonucleoprotein A1b |
|
| chr20_+_54304800 Show fit | 4.05 |
ENSDART00000121661
|
zona pellucida glycoprotein 2, tandem duplicate 6 |
|
| chr24_-_41797681 Show fit | 4.02 |
ENSDART00000169643
|
Rho GTPase activating protein 28 |
Network of associatons between targets according to the STRING database.
First level regulatory network of sox9a+sox9b
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 9.4 | GO:0045930 | negative regulation of mitotic cell cycle(GO:0045930) |
| 0.4 | 8.8 | GO:0051098 | regulation of binding(GO:0051098) |
| 0.6 | 8.6 | GO:0035090 | maintenance of apical/basal cell polarity(GO:0035090) maintenance of epithelial cell apical/basal polarity(GO:0045199) |
| 0.9 | 7.9 | GO:0071539 | protein localization to centrosome(GO:0071539) |
| 0.4 | 7.2 | GO:0019433 | triglyceride catabolic process(GO:0019433) |
| 0.1 | 6.3 | GO:0030837 | negative regulation of actin filament polymerization(GO:0030837) negative regulation of protein polymerization(GO:0032272) |
| 0.0 | 5.1 | GO:0007018 | microtubule-based movement(GO:0007018) |
| 0.0 | 4.7 | GO:0000380 | alternative mRNA splicing, via spliceosome(GO:0000380) |
| 0.1 | 4.4 | GO:0008203 | cholesterol metabolic process(GO:0008203) |
| 0.1 | 4.2 | GO:0006383 | transcription from RNA polymerase III promoter(GO:0006383) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 29.5 | GO:0005576 | extracellular region(GO:0005576) |
| 0.1 | 9.3 | GO:0070160 | bicellular tight junction(GO:0005923) occluding junction(GO:0070160) |
| 0.1 | 8.5 | GO:0016607 | nuclear speck(GO:0016607) |
| 0.6 | 8.0 | GO:0034361 | very-low-density lipoprotein particle(GO:0034361) |
| 0.1 | 6.1 | GO:0005871 | kinesin complex(GO:0005871) |
| 0.0 | 4.0 | GO:0031201 | SNARE complex(GO:0031201) |
| 0.2 | 3.9 | GO:0032039 | integrator complex(GO:0032039) |
| 0.2 | 3.8 | GO:0034992 | microtubule organizing center attachment site(GO:0034992) LINC complex(GO:0034993) |
| 0.0 | 3.7 | GO:0005795 | Golgi stack(GO:0005795) |
| 0.5 | 3.6 | GO:0033018 | sarcoplasmic reticulum lumen(GO:0033018) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 9.7 | GO:0005096 | GTPase activator activity(GO:0005096) |
| 0.1 | 9.3 | GO:0003713 | transcription coactivator activity(GO:0003713) |
| 0.0 | 8.2 | GO:0003729 | mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822) |
| 2.0 | 8.0 | GO:0030228 | lipoprotein particle receptor activity(GO:0030228) |
| 0.7 | 7.2 | GO:0004465 | lipoprotein lipase activity(GO:0004465) |
| 0.2 | 7.0 | GO:0019003 | GDP binding(GO:0019003) |
| 0.0 | 6.3 | GO:0042393 | histone binding(GO:0042393) |
| 0.1 | 6.0 | GO:0003777 | microtubule motor activity(GO:0003777) |
| 0.2 | 4.3 | GO:0002039 | p53 binding(GO:0002039) |
| 0.6 | 4.2 | GO:0000995 | transcription factor activity, core RNA polymerase III binding(GO:0000995) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 8.0 | PID REELIN PATHWAY | Reelin signaling pathway |
| 0.5 | 7.5 | PID HEDGEHOG 2PATHWAY | Signaling events mediated by the Hedgehog family |
| 0.1 | 6.8 | PID TNF PATHWAY | TNF receptor signaling pathway |
| 0.2 | 5.8 | PID EPHB FWD PATHWAY | EPHB forward signaling |
| 0.1 | 5.4 | PID ECADHERIN STABILIZATION PATHWAY | Stabilization and expansion of the E-cadherin adherens junction |
| 0.1 | 5.4 | WNT SIGNALING | Genes related to Wnt-mediated signal transduction |
| 0.1 | 4.0 | PID RB 1PATHWAY | Regulation of retinoblastoma protein |
| 0.1 | 3.5 | PID HIF2PATHWAY | HIF-2-alpha transcription factor network |
| 0.1 | 3.5 | PID TRKR PATHWAY | Neurotrophic factor-mediated Trk receptor signaling |
| 0.1 | 3.0 | SIG INSULIN RECEPTOR PATHWAY IN CARDIAC MYOCYTES | Genes related to the insulin receptor pathway |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.7 | 6.5 | REACTOME SEMA3A PLEXIN REPULSION SIGNALING BY INHIBITING INTEGRIN ADHESION | Genes involved in SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion |
| 0.1 | 6.0 | REACTOME ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS | Genes involved in Association of TriC/CCT with target proteins during biosynthesis |
| 0.4 | 5.0 | REACTOME RESOLUTION OF AP SITES VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY | Genes involved in Resolution of AP sites via the single-nucleotide replacement pathway |
| 0.2 | 3.6 | REACTOME SIGNALING BY HIPPO | Genes involved in Signaling by Hippo |
| 0.1 | 3.4 | REACTOME METABOLISM OF VITAMINS AND COFACTORS | Genes involved in Metabolism of vitamins and cofactors |
| 0.1 | 3.3 | REACTOME MRNA 3 END PROCESSING | Genes involved in mRNA 3'-end processing |
| 0.3 | 3.1 | REACTOME AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION | Genes involved in Amino acid synthesis and interconversion (transamination) |
| 0.1 | 2.4 | REACTOME E2F ENABLED INHIBITION OF PRE REPLICATION COMPLEX FORMATION | Genes involved in E2F-enabled inhibition of pre-replication complex formation |
| 0.0 | 2.3 | REACTOME SIGNALING BY RHO GTPASES | Genes involved in Signaling by Rho GTPases |
| 0.1 | 2.2 | REACTOME PROTEOLYTIC CLEAVAGE OF SNARE COMPLEX PROTEINS | Genes involved in Proteolytic cleavage of SNARE complex proteins |