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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for tfdp1a+tfdp1b
Z-value: 1.61
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Transcription factors associated with tfdp1a+tfdp1b
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| tfdp1a | dr11_v1_chr9_+_34952203_34952269 | 0.75 | 3.1e-04 | Click! |
| tfdp1b | dr11_v1_chr1_+_227241_227241 | -0.50 | 3.5e-02 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr8_-_1219815 Show fit | 4.20 |
ENSDART00000016800
ENSDART00000149969 |
zinc finger protein 367 |
|
| chr19_-_31007417 Show fit | 3.70 |
ENSDART00000048144
|
retinoblastoma binding protein 4 |
|
| chr13_-_36844945 Show fit | 3.64 |
ENSDART00000129562
ENSDART00000150899 |
ninein (GSK3B interacting protein) |
|
| chr10_-_76352 Show fit | 3.49 |
ENSDART00000186560
ENSDART00000144722 |
dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A, a |
|
| chr7_+_24881680 Show fit | 3.38 |
ENSDART00000058843
|
kelch repeat-containing protein |
|
| chr4_+_9279515 Show fit | 3.29 |
ENSDART00000048707
|
SLIT-ROBO Rho GTPase activating protein 1b |
|
| chr3_-_36364903 Show fit | 3.29 |
ENSDART00000028883
|
guanine nucleotide binding protein (G protein), alpha 13b |
|
| chr19_-_11846958 Show fit | 3.21 |
ENSDART00000148516
|
CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1 |
|
| chr12_-_41759686 Show fit | 3.12 |
ENSDART00000172175
ENSDART00000165152 |
protein phosphatase 2, regulatory subunit B, delta |
|
| chr12_-_26538823 Show fit | 3.09 |
ENSDART00000143213
|
acyl-CoA synthetase family member 2 |
Network of associatons between targets according to the STRING database.
First level regulatory network of tfdp1a+tfdp1b
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 14.2 | GO:0008380 | RNA splicing(GO:0008380) |
| 0.1 | 8.1 | GO:0018107 | peptidyl-threonine phosphorylation(GO:0018107) |
| 0.1 | 7.4 | GO:0030336 | negative regulation of cell migration(GO:0030336) |
| 0.4 | 5.1 | GO:0036089 | cleavage furrow formation(GO:0036089) |
| 0.0 | 5.1 | GO:0006338 | chromatin remodeling(GO:0006338) |
| 0.2 | 4.5 | GO:0030330 | DNA damage response, signal transduction by p53 class mediator(GO:0030330) |
| 0.4 | 4.2 | GO:0009263 | deoxyribonucleotide biosynthetic process(GO:0009263) |
| 0.8 | 4.1 | GO:0031174 | lifelong otolith mineralization(GO:0031174) |
| 0.1 | 4.1 | GO:0006303 | double-strand break repair via nonhomologous end joining(GO:0006303) |
| 1.3 | 3.9 | GO:0055109 | invagination involved in gastrulation with mouth forming second(GO:0055109) morphogenesis of an epithelial fold(GO:0060571) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 6.0 | GO:0016605 | PML body(GO:0016605) |
| 0.1 | 4.6 | GO:0000159 | protein phosphatase type 2A complex(GO:0000159) |
| 1.0 | 4.2 | GO:0033186 | CAF-1 complex(GO:0033186) |
| 0.0 | 3.9 | GO:0005938 | cell cortex(GO:0005938) |
| 0.0 | 3.8 | GO:0016607 | nuclear speck(GO:0016607) |
| 0.3 | 3.6 | GO:0097431 | mitotic spindle pole(GO:0097431) |
| 0.3 | 3.4 | GO:0005956 | protein kinase CK2 complex(GO:0005956) |
| 0.4 | 3.3 | GO:0031526 | brush border membrane(GO:0031526) |
| 0.3 | 3.3 | GO:0035145 | exon-exon junction complex(GO:0035145) |
| 0.2 | 2.9 | GO:0071565 | nBAF complex(GO:0071565) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 14.0 | GO:0005096 | GTPase activator activity(GO:0005096) |
| 0.1 | 12.0 | GO:0004197 | cysteine-type endopeptidase activity(GO:0004197) |
| 0.0 | 9.8 | GO:0004674 | protein serine/threonine kinase activity(GO:0004674) |
| 0.0 | 8.0 | GO:0003712 | transcription factor activity, transcription factor binding(GO:0000989) transcription cofactor activity(GO:0003712) |
| 0.1 | 6.1 | GO:0001227 | transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding(GO:0001227) |
| 0.0 | 5.9 | GO:0042393 | histone binding(GO:0042393) |
| 0.2 | 5.1 | GO:0003887 | DNA-directed DNA polymerase activity(GO:0003887) |
| 0.0 | 5.0 | GO:0051015 | actin filament binding(GO:0051015) |
| 0.0 | 4.9 | GO:0019208 | phosphatase regulator activity(GO:0019208) |
| 0.1 | 4.7 | GO:0004712 | protein serine/threonine/tyrosine kinase activity(GO:0004712) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 10.1 | PID AURORA B PATHWAY | Aurora B signaling |
| 0.1 | 7.9 | PID E2F PATHWAY | E2F transcription factor network |
| 0.2 | 5.3 | PID UPA UPAR PATHWAY | Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling |
| 0.2 | 4.1 | PID DNA PK PATHWAY | DNA-PK pathway in nonhomologous end joining |
| 0.1 | 3.5 | PID HIF2PATHWAY | HIF-2-alpha transcription factor network |
| 0.1 | 3.4 | PID PLK1 PATHWAY | PLK1 signaling events |
| 0.0 | 3.1 | PID BETA CATENIN NUC PATHWAY | Regulation of nuclear beta catenin signaling and target gene transcription |
| 0.0 | 2.4 | PID AR PATHWAY | Coregulation of Androgen receptor activity |
| 0.2 | 2.0 | SA PROGRAMMED CELL DEATH | Programmed cell death, or apoptosis, eliminates damaged or unneeded cells. |
| 0.0 | 2.0 | PID TELOMERASE PATHWAY | Regulation of Telomerase |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 10.3 | REACTOME ELONGATION ARREST AND RECOVERY | Genes involved in Elongation arrest and recovery |
| 0.3 | 7.4 | REACTOME G1 S SPECIFIC TRANSCRIPTION | Genes involved in G1/S-Specific Transcription |
| 0.1 | 5.4 | REACTOME TRANSPORT OF RIBONUCLEOPROTEINS INTO THE HOST NUCLEUS | Genes involved in Transport of Ribonucleoproteins into the Host Nucleus |
| 0.2 | 4.8 | REACTOME G0 AND EARLY G1 | Genes involved in G0 and Early G1 |
| 0.2 | 3.7 | REACTOME SMOOTH MUSCLE CONTRACTION | Genes involved in Smooth Muscle Contraction |
| 0.2 | 3.5 | REACTOME DESTABILIZATION OF MRNA BY KSRP | Genes involved in Destabilization of mRNA by KSRP |
| 0.1 | 3.4 | REACTOME APC C CDH1 MEDIATED DEGRADATION OF CDC20 AND OTHER APC C CDH1 TARGETED PROTEINS IN LATE MITOSIS EARLY G1 | Genes involved in APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 |
| 0.2 | 2.9 | REACTOME RNA POL III TRANSCRIPTION TERMINATION | Genes involved in RNA Polymerase III Transcription Termination |
| 0.3 | 2.8 | REACTOME REMOVAL OF THE FLAP INTERMEDIATE FROM THE C STRAND | Genes involved in Removal of the Flap Intermediate from the C-strand |
| 0.1 | 2.7 | REACTOME ION TRANSPORT BY P TYPE ATPASES | Genes involved in Ion transport by P-type ATPases |