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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for sox13
Z-value: 1.27
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Transcription factors associated with sox13
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| sox13 | dr11_v1_chr11_+_37803773_37803773 | 0.92 | 9.2e-08 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr13_-_24448278 Show fit | 1.38 |
ENSDART00000057584
|
solute carrier family 1 (glutamate/neutral amino acid transporter), member 4 |
|
| chr17_+_12075805 Show fit | 1.36 |
ENSDART00000155329
|
consortin, connexin sorting protein a |
|
| chr20_-_14718801 Show fit | 1.35 |
ENSDART00000137605
|
SUN domain containing ossification factor |
|
| chr14_-_12071679 Show fit | 1.35 |
ENSDART00000165581
|
thymosin beta 1 |
|
| chr4_-_20108833 Show fit | 1.34 |
ENSDART00000100867
|
family with sequence similarity 3, member C |
|
| chr12_+_48674381 Show fit | 1.32 |
ENSDART00000105309
|
uroporphyrinogen III synthase |
|
| chr1_+_6646529 Show fit | 1.31 |
ENSDART00000144641
ENSDART00000103701 ENSDART00000138919 |
ubiquitin-conjugating enzyme E2F (putative) |
|
| chr22_-_29906764 Show fit | 1.11 |
ENSDART00000019786
|
structural maintenance of chromosomes 3 |
|
| chr10_-_8434816 Show fit | 1.11 |
ENSDART00000108643
|
tectonic family member 1 |
|
| chr1_-_338445 Show fit | 1.06 |
ENSDART00000010092
|
growth arrest-specific 6 |
Network of associatons between targets according to the STRING database.
First level regulatory network of sox13
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 1.8 | GO:0051568 | histone H3-K4 methylation(GO:0051568) |
| 0.0 | 1.6 | GO:0007492 | endoderm development(GO:0007492) |
| 0.1 | 1.5 | GO:0007064 | mitotic sister chromatid cohesion(GO:0007064) |
| 0.5 | 1.4 | GO:0042998 | positive regulation of Golgi to plasma membrane protein transport(GO:0042998) positive regulation of establishment of protein localization to plasma membrane(GO:0090004) |
| 0.1 | 1.4 | GO:0042989 | sequestering of actin monomers(GO:0042989) |
| 0.1 | 1.4 | GO:0046850 | regulation of bone remodeling(GO:0046850) |
| 0.1 | 1.4 | GO:0045116 | protein neddylation(GO:0045116) |
| 0.2 | 1.3 | GO:0045721 | negative regulation of gluconeogenesis(GO:0045721) |
| 0.1 | 1.3 | GO:0045199 | maintenance of apical/basal cell polarity(GO:0035090) maintenance of epithelial cell apical/basal polarity(GO:0045199) |
| 0.1 | 1.3 | GO:0006782 | protoporphyrinogen IX biosynthetic process(GO:0006782) protoporphyrinogen IX metabolic process(GO:0046501) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 1.6 | GO:0035097 | histone methyltransferase complex(GO:0035097) |
| 0.1 | 1.5 | GO:0030893 | meiotic cohesin complex(GO:0030893) |
| 0.0 | 1.4 | GO:0048786 | presynaptic active zone(GO:0048786) |
| 0.0 | 1.4 | GO:0036064 | ciliary basal body(GO:0036064) |
| 0.1 | 1.3 | GO:0048188 | Set1C/COMPASS complex(GO:0048188) |
| 0.0 | 1.3 | GO:0000307 | cyclin-dependent protein kinase holoenzyme complex(GO:0000307) |
| 0.1 | 1.2 | GO:0070775 | H3 histone acetyltransferase complex(GO:0070775) MOZ/MORF histone acetyltransferase complex(GO:0070776) |
| 0.0 | 1.2 | GO:0016592 | mediator complex(GO:0016592) |
| 0.1 | 1.1 | GO:0048179 | activin receptor complex(GO:0048179) |
| 0.1 | 1.1 | GO:0036038 | MKS complex(GO:0036038) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 1.6 | GO:0016504 | peptidase activator activity(GO:0016504) |
| 0.0 | 1.6 | GO:0061650 | ubiquitin-like protein conjugating enzyme activity(GO:0061650) |
| 0.1 | 1.4 | GO:0003785 | actin monomer binding(GO:0003785) |
| 0.3 | 1.3 | GO:0071253 | connexin binding(GO:0071253) |
| 0.0 | 1.3 | GO:0004438 | phosphatidylinositol-3-phosphatase activity(GO:0004438) |
| 0.3 | 1.2 | GO:0031151 | histone methyltransferase activity (H3-K79 specific)(GO:0031151) |
| 0.1 | 1.2 | GO:0010484 | H3 histone acetyltransferase activity(GO:0010484) histone acetyltransferase activity (H3-K23 specific)(GO:0043994) |
| 0.1 | 1.2 | GO:0004767 | sphingomyelin phosphodiesterase activity(GO:0004767) |
| 0.0 | 1.2 | GO:0019003 | GDP binding(GO:0019003) |
| 0.1 | 1.1 | GO:0017002 | activin-activated receptor activity(GO:0017002) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 1.8 | PID EPHB FWD PATHWAY | EPHB forward signaling |
| 0.2 | 1.5 | ST TYPE I INTERFERON PATHWAY | Type I Interferon (alpha/beta IFN) Pathway |
| 0.0 | 1.1 | PID ATM PATHWAY | ATM pathway |
| 0.0 | 0.9 | PID DELTA NP63 PATHWAY | Validated transcriptional targets of deltaNp63 isoforms |
| 0.0 | 0.8 | PID MYC PATHWAY | C-MYC pathway |
| 0.1 | 0.7 | SA PROGRAMMED CELL DEATH | Programmed cell death, or apoptosis, eliminates damaged or unneeded cells. |
| 0.0 | 0.7 | SA G1 AND S PHASES | Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition. |
| 0.0 | 0.7 | PID HNF3A PATHWAY | FOXA1 transcription factor network |
| 0.0 | 0.6 | PID IL2 PI3K PATHWAY | IL2 signaling events mediated by PI3K |
| 0.0 | 0.6 | PID FAK PATHWAY | Signaling events mediated by focal adhesion kinase |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 1.5 | REACTOME REGULATION OF IFNA SIGNALING | Genes involved in Regulation of IFNA signaling |
| 0.1 | 1.4 | REACTOME AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE | Genes involved in Amino acid transport across the plasma membrane |
| 0.1 | 1.3 | REACTOME SEMA3A PLEXIN REPULSION SIGNALING BY INHIBITING INTEGRIN ADHESION | Genes involved in SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion |
| 0.1 | 1.3 | REACTOME METABOLISM OF PORPHYRINS | Genes involved in Metabolism of porphyrins |
| 0.0 | 1.3 | REACTOME MEIOTIC SYNAPSIS | Genes involved in Meiotic Synapsis |
| 0.1 | 0.9 | REACTOME VITAMIN B5 PANTOTHENATE METABOLISM | Genes involved in Vitamin B5 (pantothenate) metabolism |
| 0.0 | 0.9 | REACTOME CHOLESTEROL BIOSYNTHESIS | Genes involved in Cholesterol biosynthesis |
| 0.1 | 0.8 | REACTOME MEMBRANE BINDING AND TARGETTING OF GAG PROTEINS | Genes involved in Membrane binding and targetting of GAG proteins |
| 0.0 | 0.8 | REACTOME SYNTHESIS OF PIPS AT THE GOLGI MEMBRANE | Genes involved in Synthesis of PIPs at the Golgi membrane |
| 0.0 | 0.7 | REACTOME LYSOSOME VESICLE BIOGENESIS | Genes involved in Lysosome Vesicle Biogenesis |