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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for lhx3+lhx4
Z-value: 1.58
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Transcription factors associated with lhx3+lhx4
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| LHX3 | dr11_v1_chr5_+_71802014_71802014 | 0.87 | 3.2e-06 | Click! |
| lhx4 | dr11_v1_chr8_-_14484599_14484599 | 0.87 | 3.2e-06 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr10_-_17083180 Show fit | 6.77 |
ENSDART00000170083
|
family with sequence similarity 166, member B |
|
| chr8_+_43340995 Show fit | 6.17 |
ENSDART00000038566
|
refilin A |
|
| chr2_+_49799470 Show fit | 5.64 |
ENSDART00000146325
|
si:ch211-190k17.19 |
|
| chr9_-_48407408 Show fit | 5.50 |
ENSDART00000058248
|
zgc:172182 |
|
| chr24_+_35787629 Show fit | 4.67 |
ENSDART00000136721
|
si:dkeyp-7a3.1 |
|
| chr18_+_25752592 Show fit | 4.58 |
ENSDART00000111767
|
si:ch211-39k3.2 |
|
| chr7_-_28148310 Show fit | 4.47 |
ENSDART00000044208
|
LIM domain only 1 |
|
| chr5_+_69747417 Show fit | 4.42 |
ENSDART00000153717
|
si:ch211-275j6.5 |
|
| chr8_-_13046089 Show fit | 4.41 |
ENSDART00000137784
|
si:dkey-208b23.5 |
|
| chr5_+_6954162 Show fit | 4.34 |
ENSDART00000086666
|
sperm-tail PG-rich repeat containing 2 |
Network of associatons between targets according to the STRING database.
First level regulatory network of lhx3+lhx4
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 19.1 | GO:0046777 | protein autophosphorylation(GO:0046777) |
| 2.1 | 6.2 | GO:0061037 | negative regulation of chondrocyte differentiation(GO:0032331) negative regulation of cartilage development(GO:0061037) negative regulation of chondrocyte development(GO:0061182) regulation of bone mineralization involved in bone maturation(GO:1900157) negative regulation of bone mineralization involved in bone maturation(GO:1900158) negative regulation of bone development(GO:1903011) |
| 0.1 | 5.6 | GO:0033339 | pectoral fin development(GO:0033339) |
| 0.0 | 5.4 | GO:0016579 | protein deubiquitination(GO:0016579) |
| 0.5 | 5.3 | GO:0034605 | cellular response to heat(GO:0034605) |
| 0.2 | 5.0 | GO:0006695 | cholesterol biosynthetic process(GO:0006695) secondary alcohol biosynthetic process(GO:1902653) |
| 1.5 | 4.4 | GO:1904158 | axonemal central apparatus assembly(GO:1904158) |
| 0.2 | 4.4 | GO:0006415 | translational termination(GO:0006415) |
| 0.1 | 4.2 | GO:0060122 | inner ear receptor stereocilium organization(GO:0060122) |
| 0.2 | 4.1 | GO:0086010 | membrane depolarization during action potential(GO:0086010) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 6.2 | GO:0032432 | actin filament bundle(GO:0032432) |
| 0.0 | 4.8 | GO:0005769 | early endosome(GO:0005769) |
| 0.1 | 4.5 | GO:0010494 | cytoplasmic stress granule(GO:0010494) |
| 0.1 | 4.4 | GO:0044447 | axoneme part(GO:0044447) |
| 0.1 | 4.4 | GO:0000315 | organellar large ribosomal subunit(GO:0000315) mitochondrial large ribosomal subunit(GO:0005762) |
| 0.2 | 4.1 | GO:0034706 | voltage-gated sodium channel complex(GO:0001518) sodium channel complex(GO:0034706) |
| 0.2 | 4.0 | GO:0005903 | brush border(GO:0005903) |
| 0.1 | 4.0 | GO:0005637 | nuclear inner membrane(GO:0005637) |
| 0.1 | 3.9 | GO:0016605 | PML body(GO:0016605) |
| 0.9 | 3.6 | GO:0031673 | H zone(GO:0031673) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 14.3 | GO:0004674 | protein serine/threonine kinase activity(GO:0004674) |
| 0.5 | 6.8 | GO:0005504 | fatty acid binding(GO:0005504) |
| 1.5 | 6.2 | GO:0031005 | filamin binding(GO:0031005) |
| 0.0 | 5.8 | GO:0004843 | thiol-dependent ubiquitin-specific protease activity(GO:0004843) thiol-dependent ubiquitinyl hydrolase activity(GO:0036459) ubiquitinyl hydrolase activity(GO:0101005) |
| 0.4 | 4.4 | GO:0003747 | translation release factor activity(GO:0003747) translation termination factor activity(GO:0008079) |
| 0.6 | 4.1 | GO:0008332 | low voltage-gated calcium channel activity(GO:0008332) |
| 0.7 | 4.0 | GO:0005436 | sodium:phosphate symporter activity(GO:0005436) |
| 0.2 | 4.0 | GO:0016628 | oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor(GO:0016628) |
| 0.5 | 3.8 | GO:0036122 | BMP binding(GO:0036122) |
| 0.2 | 3.6 | GO:0008553 | hydrogen-exporting ATPase activity, phosphorylative mechanism(GO:0008553) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 4.1 | NABA ECM GLYCOPROTEINS | Genes encoding structural ECM glycoproteins |
| 0.1 | 1.6 | PID PDGFRA PATHWAY | PDGFR-alpha signaling pathway |
| 0.0 | 1.3 | PID HIF1 TFPATHWAY | HIF-1-alpha transcription factor network |
| 0.0 | 1.3 | NABA ECM AFFILIATED | Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins |
| 0.0 | 0.9 | PID RHOA PATHWAY | RhoA signaling pathway |
| 0.0 | 0.8 | PID VEGFR1 2 PATHWAY | Signaling events mediated by VEGFR1 and VEGFR2 |
| 0.0 | 0.7 | PID NCADHERIN PATHWAY | N-cadherin signaling events |
| 0.0 | 0.6 | PID AURORA A PATHWAY | Aurora A signaling |
| 0.0 | 0.6 | PID REG GR PATHWAY | Glucocorticoid receptor regulatory network |
| 0.0 | 0.5 | PID INTEGRIN2 PATHWAY | Beta2 integrin cell surface interactions |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 5.0 | REACTOME CHOLESTEROL BIOSYNTHESIS | Genes involved in Cholesterol biosynthesis |
| 0.2 | 3.6 | REACTOME PRE NOTCH PROCESSING IN GOLGI | Genes involved in Pre-NOTCH Processing in Golgi |
| 0.2 | 3.0 | REACTOME AMINE COMPOUND SLC TRANSPORTERS | Genes involved in Amine compound SLC transporters |
| 0.1 | 1.9 | REACTOME GRB2 SOS PROVIDES LINKAGE TO MAPK SIGNALING FOR INTERGRINS | Genes involved in GRB2:SOS provides linkage to MAPK signaling for Intergrins |
| 0.0 | 1.9 | REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES | Genes involved in Cross-presentation of soluble exogenous antigens (endosomes) |
| 0.0 | 1.6 | REACTOME VOLTAGE GATED POTASSIUM CHANNELS | Genes involved in Voltage gated Potassium channels |
| 0.1 | 1.3 | REACTOME ALPHA LINOLENIC ACID ALA METABOLISM | Genes involved in alpha-linolenic acid (ALA) metabolism |
| 0.1 | 1.3 | REACTOME MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE | Genes involved in mRNA Decay by 5' to 3' Exoribonuclease |
| 0.1 | 1.3 | REACTOME METAL ION SLC TRANSPORTERS | Genes involved in Metal ion SLC transporters |
| 0.1 | 1.1 | REACTOME VIRAL MESSENGER RNA SYNTHESIS | Genes involved in Viral Messenger RNA Synthesis |