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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for arid3a+arid3b+arid3c
Z-value: 1.39
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Transcription factors associated with arid3a+arid3b+arid3c
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
| ENSDARG00000067729 | AT rich interactive domain 3C (BRIGHT-like) | |
| ENSDARG00000070843 | AT rich interactive domain 3A (BRIGHT-like) | |
| ENSDARG00000104034 | AT rich interactive domain 3B (BRIGHT-like) | |
| ENSDARG00000114447 | AT rich interactive domain 3C (BRIGHT-like) |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| arid3b | dr11_v1_chr25_-_29074064_29074064 | 0.89 | 6.5e-07 | Click! |
| arid3c | dr11_v1_chr5_+_41322783_41322783 | -0.77 | 2.0e-04 | Click! |
| arid3a | dr11_v1_chr11_+_5681762_5681762 | 0.71 | 8.8e-04 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr10_+_45031398 Show fit | 7.77 |
ENSDART00000160536
|
glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID), b |
|
| chr21_-_42831033 Show fit | 7.51 |
ENSDART00000160998
|
serine/threonine kinase 10 |
|
| chr17_-_1174960 Show fit | 5.03 |
ENSDART00000161202
|
DnaJ (Hsp40) homolog, subfamily C, member 17 |
|
| chr17_-_4245902 Show fit | 4.76 |
ENSDART00000151851
|
growth differentiation factor 3 |
|
| chr14_+_46342882 Show fit | 4.31 |
ENSDART00000193707
ENSDART00000060577 |
transmembrane protein 33 |
|
| chr15_-_31109760 Show fit | 3.47 |
ENSDART00000154254
|
kinase suppressor of ras 1b |
|
| chr5_+_69650148 Show fit | 3.41 |
ENSDART00000097244
|
general transcription factor IIH, polypeptide 3 |
|
| chr8_-_29930821 Show fit | 3.40 |
ENSDART00000125173
|
excision repair cross-complementation group 6-like 2 |
|
| chr12_+_1609563 Show fit | 3.03 |
ENSDART00000163559
|
solute carrier family 39 member 11 |
|
| chr21_+_43172506 Show fit | 2.98 |
ENSDART00000121725
|
zinc finger, CCHC domain containing 10 |
Network of associatons between targets according to the STRING database.
First level regulatory network of arid3a+arid3b+arid3c
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 7.2 | GO:2000401 | regulation of lymphocyte migration(GO:2000401) |
| 0.1 | 6.9 | GO:0030203 | glycosaminoglycan metabolic process(GO:0030203) |
| 0.1 | 5.1 | GO:0032272 | negative regulation of actin filament polymerization(GO:0030837) negative regulation of protein polymerization(GO:0032272) |
| 0.9 | 4.5 | GO:1900145 | nodal signaling pathway involved in determination of left/right asymmetry(GO:0038107) regulation of nodal signaling pathway involved in determination of left/right asymmetry(GO:1900145) |
| 0.5 | 4.3 | GO:1901339 | regulation of store-operated calcium channel activity(GO:1901339) |
| 0.2 | 3.4 | GO:0070816 | phosphorylation of RNA polymerase II C-terminal domain(GO:0070816) |
| 0.4 | 3.3 | GO:0070933 | histone H4 deacetylation(GO:0070933) |
| 0.5 | 2.8 | GO:0060397 | JAK-STAT cascade involved in growth hormone signaling pathway(GO:0060397) |
| 0.2 | 2.8 | GO:0016486 | peptide hormone processing(GO:0016486) |
| 0.2 | 2.6 | GO:0045453 | bone resorption(GO:0045453) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 10.3 | GO:0005764 | lysosome(GO:0005764) |
| 0.0 | 3.9 | GO:0000118 | histone deacetylase complex(GO:0000118) |
| 0.1 | 3.6 | GO:0055038 | recycling endosome membrane(GO:0055038) |
| 0.0 | 3.6 | GO:0030173 | integral component of Golgi membrane(GO:0030173) intrinsic component of Golgi membrane(GO:0031228) |
| 0.5 | 3.4 | GO:0000439 | core TFIIH complex(GO:0000439) |
| 0.1 | 3.1 | GO:0030014 | CCR4-NOT complex(GO:0030014) |
| 0.1 | 3.0 | GO:0016592 | mediator complex(GO:0016592) |
| 0.4 | 2.5 | GO:0070695 | FHF complex(GO:0070695) |
| 0.2 | 2.5 | GO:0071564 | npBAF complex(GO:0071564) |
| 0.1 | 2.5 | GO:0030131 | clathrin adaptor complex(GO:0030131) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.5 | 7.8 | GO:0008449 | N-acetylglucosamine-6-sulfatase activity(GO:0008449) |
| 0.0 | 6.5 | GO:0042803 | protein homodimerization activity(GO:0042803) |
| 0.0 | 4.9 | GO:0017171 | serine-type peptidase activity(GO:0008236) serine hydrolase activity(GO:0017171) |
| 0.0 | 4.2 | GO:0005125 | cytokine activity(GO:0005125) |
| 0.0 | 3.9 | GO:0008017 | microtubule binding(GO:0008017) |
| 0.2 | 3.3 | GO:0031078 | histone deacetylase activity (H3-K14 specific)(GO:0031078) NAD-dependent histone deacetylase activity (H3-K14 specific)(GO:0032041) |
| 0.0 | 3.1 | GO:0031490 | chromatin DNA binding(GO:0031490) |
| 0.0 | 2.8 | GO:0030674 | protein binding, bridging(GO:0030674) |
| 0.3 | 2.6 | GO:0003993 | acid phosphatase activity(GO:0003993) |
| 0.1 | 2.6 | GO:0051959 | dynein light intermediate chain binding(GO:0051959) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 4.3 | NABA ECM REGULATORS | Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix |
| 0.0 | 4.2 | NABA SECRETED FACTORS | Genes encoding secreted soluble factors |
| 0.0 | 3.3 | PID HDAC CLASSI PATHWAY | Signaling events mediated by HDAC Class I |
| 0.2 | 2.8 | PID IL5 PATHWAY | IL5-mediated signaling events |
| 0.2 | 2.5 | PID SMAD2 3PATHWAY | Regulation of cytoplasmic and nuclear SMAD2/3 signaling |
| 0.1 | 2.1 | PID MAPK TRK PATHWAY | Trk receptor signaling mediated by the MAPK pathway |
| 0.1 | 1.7 | PID PI3KCI AKT PATHWAY | Class I PI3K signaling events mediated by Akt |
| 0.0 | 1.4 | PID TGFBR PATHWAY | TGF-beta receptor signaling |
| 0.1 | 1.3 | PID NETRIN PATHWAY | Netrin-mediated signaling events |
| 0.1 | 1.2 | PID HIF1A PATHWAY | Hypoxic and oxygen homeostasis regulation of HIF-1-alpha |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 6.3 | REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION | Genes involved in NOTCH1 Intracellular Domain Regulates Transcription |
| 0.4 | 4.0 | REACTOME SIGNALING BY NODAL | Genes involved in Signaling by NODAL |
| 0.1 | 3.5 | REACTOME ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS | Genes involved in Association of TriC/CCT with target proteins during biosynthesis |
| 0.1 | 3.4 | REACTOME FORMATION OF INCISION COMPLEX IN GG NER | Genes involved in Formation of incision complex in GG-NER |
| 0.3 | 2.8 | REACTOME IL 7 SIGNALING | Genes involved in Interleukin-7 signaling |
| 0.1 | 2.3 | REACTOME MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE | Genes involved in mRNA Decay by 5' to 3' Exoribonuclease |
| 0.2 | 2.0 | REACTOME TRYPTOPHAN CATABOLISM | Genes involved in Tryptophan catabolism |
| 0.0 | 1.9 | REACTOME ION TRANSPORT BY P TYPE ATPASES | Genes involved in Ion transport by P-type ATPases |
| 0.1 | 1.7 | REACTOME CD28 DEPENDENT PI3K AKT SIGNALING | Genes involved in CD28 dependent PI3K/Akt signaling |
| 0.1 | 1.7 | REACTOME CONVERSION FROM APC C CDC20 TO APC C CDH1 IN LATE ANAPHASE | Genes involved in Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase |