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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for foxd3
Z-value: 2.45
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Transcription factors associated with foxd3
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| foxd3 | dr11_v1_chr6_-_32093830_32093830 | -0.68 | 2.0e-03 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr12_+_28888975 Show fit | 10.09 |
ENSDART00000076362
|
phosphorylase kinase, gamma 2 (testis) |
|
| chr22_+_24559947 Show fit | 8.20 |
ENSDART00000169847
|
WD repeat domain 47b |
|
| chr6_-_25201810 Show fit | 6.52 |
ENSDART00000168683
|
leucine rich repeat containing 8 VRAC subunit C |
|
| chr17_+_14965570 Show fit | 6.51 |
ENSDART00000066604
|
G protein-coupled receptor 137c |
|
| chr15_+_38299385 Show fit | 6.36 |
ENSDART00000142403
|
si:dkey-24p1.6 |
|
| chr15_+_38299563 Show fit | 5.94 |
ENSDART00000099375
|
si:dkey-24p1.6 |
|
| chr1_-_33647138 Show fit | 5.60 |
ENSDART00000142111
ENSDART00000015547 |
claudin g |
|
| chr14_-_16082806 Show fit | 5.27 |
ENSDART00000165656
|
MAX dimerization protein 3 |
|
| chr17_-_4245902 Show fit | 5.23 |
ENSDART00000151851
|
growth differentiation factor 3 |
|
| chr14_+_32926385 Show fit | 4.96 |
ENSDART00000139159
|
ligand of numb-protein X 2b |
Network of associatons between targets according to the STRING database.
First level regulatory network of foxd3
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 14.9 | GO:0061640 | cytoskeleton-dependent cytokinesis(GO:0061640) |
| 1.9 | 9.3 | GO:0016338 | calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules(GO:0016338) |
| 0.0 | 8.9 | GO:0030029 | actin filament-based process(GO:0030029) |
| 0.2 | 8.7 | GO:0005978 | glycogen biosynthetic process(GO:0005978) glucan biosynthetic process(GO:0009250) |
| 0.4 | 7.5 | GO:0031442 | positive regulation of mRNA 3'-end processing(GO:0031442) |
| 0.0 | 6.7 | GO:1990778 | protein localization to plasma membrane(GO:0072659) protein localization to cell periphery(GO:1990778) |
| 0.1 | 6.6 | GO:0090504 | epiboly(GO:0090504) |
| 0.5 | 6.3 | GO:1904263 | positive regulation of TORC1 signaling(GO:1904263) |
| 2.1 | 6.2 | GO:0060623 | regulation of chromosome condensation(GO:0060623) |
| 0.2 | 6.2 | GO:0048268 | clathrin coat assembly(GO:0048268) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 24.8 | GO:0005764 | lysosome(GO:0005764) |
| 0.2 | 21.3 | GO:0005923 | bicellular tight junction(GO:0005923) occluding junction(GO:0070160) |
| 0.1 | 15.8 | GO:0005813 | centrosome(GO:0005813) |
| 0.1 | 15.4 | GO:0005730 | nucleolus(GO:0005730) |
| 0.2 | 11.3 | GO:0031901 | early endosome membrane(GO:0031901) |
| 0.3 | 11.0 | GO:0031105 | septin ring(GO:0005940) septin complex(GO:0031105) septin cytoskeleton(GO:0032156) |
| 0.8 | 10.1 | GO:0005964 | phosphorylase kinase complex(GO:0005964) |
| 0.0 | 9.4 | GO:0005794 | Golgi apparatus(GO:0005794) |
| 0.4 | 9.3 | GO:0071141 | SMAD protein complex(GO:0071141) |
| 0.1 | 8.7 | GO:0000118 | histone deacetylase complex(GO:0000118) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 18.4 | GO:0042393 | histone binding(GO:0042393) |
| 0.1 | 16.6 | GO:0005085 | guanyl-nucleotide exchange factor activity(GO:0005085) |
| 0.1 | 15.9 | GO:0004197 | cysteine-type endopeptidase activity(GO:0004197) |
| 0.1 | 13.9 | GO:0042802 | identical protein binding(GO:0042802) |
| 0.1 | 11.1 | GO:0050839 | cell adhesion molecule binding(GO:0050839) |
| 2.0 | 10.1 | GO:0004689 | phosphorylase kinase activity(GO:0004689) |
| 0.1 | 8.5 | GO:0060090 | binding, bridging(GO:0060090) |
| 0.3 | 6.9 | GO:0070411 | I-SMAD binding(GO:0070411) |
| 0.3 | 6.7 | GO:0015095 | magnesium ion transmembrane transporter activity(GO:0015095) |
| 0.3 | 6.5 | GO:0017136 | histone deacetylase activity(GO:0004407) NAD-dependent histone deacetylase activity(GO:0017136) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 12.2 | PID HDAC CLASSI PATHWAY | Signaling events mediated by HDAC Class I |
| 0.3 | 9.3 | PID AURORA B PATHWAY | Aurora B signaling |
| 0.5 | 8.8 | PID BETA CATENIN DEG PATHWAY | Degradation of beta catenin |
| 0.1 | 5.8 | PID AR PATHWAY | Coregulation of Androgen receptor activity |
| 0.1 | 5.7 | PID FANCONI PATHWAY | Fanconi anemia pathway |
| 0.1 | 5.3 | PID FOXM1 PATHWAY | FOXM1 transcription factor network |
| 0.3 | 4.8 | PID SMAD2 3PATHWAY | Regulation of cytoplasmic and nuclear SMAD2/3 signaling |
| 0.3 | 4.7 | PID ERB GENOMIC PATHWAY | Validated nuclear estrogen receptor beta network |
| 0.1 | 4.5 | PID CDC42 PATHWAY | CDC42 signaling events |
| 0.1 | 4.4 | PID RAC1 REG PATHWAY | Regulation of RAC1 activity |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.8 | 10.1 | REACTOME GLYCOGEN BREAKDOWN GLYCOGENOLYSIS | Genes involved in Glycogen breakdown (glycogenolysis) |
| 0.2 | 8.0 | REACTOME LOSS OF NLP FROM MITOTIC CENTROSOMES | Genes involved in Loss of Nlp from mitotic centrosomes |
| 0.2 | 8.0 | REACTOME METABOLISM OF VITAMINS AND COFACTORS | Genes involved in Metabolism of vitamins and cofactors |
| 0.4 | 6.3 | REACTOME GLUTATHIONE CONJUGATION | Genes involved in Glutathione conjugation |
| 0.3 | 6.3 | REACTOME KINESINS | Genes involved in Kinesins |
| 0.1 | 5.5 | REACTOME ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS | Genes involved in Association of TriC/CCT with target proteins during biosynthesis |
| 0.2 | 5.4 | REACTOME EGFR DOWNREGULATION | Genes involved in EGFR downregulation |
| 0.3 | 5.0 | REACTOME DEADENYLATION OF MRNA | Genes involved in Deadenylation of mRNA |
| 0.5 | 4.8 | REACTOME SIGNALING BY NODAL | Genes involved in Signaling by NODAL |
| 0.3 | 4.8 | REACTOME YAP1 AND WWTR1 TAZ STIMULATED GENE EXPRESSION | Genes involved in YAP1- and WWTR1 (TAZ)-stimulated gene expression |