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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for rfx3_rfx2+rfx4
Z-value: 15.64
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Transcription factors associated with rfx3_rfx2+rfx4
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
| ENSDARG00000014550 | regulatory factor X, 3 (influences HLA class II expression) | |
| ENSDARG00000013575 | regulatory factor X, 2 (influences HLA class II expression) | |
| ENSDARG00000026395 | regulatory factor X, 4 | |
| ENSDARG00000116861 | regulatory factor X, 4 |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| rfx3 | dr11_v1_chr10_-_641609_641609 | 0.99 | 1.2e-13 | Click! |
| rfx2 | dr11_v1_chr8_-_20138054_20138251 | 0.95 | 1.1e-09 | Click! |
| rfx4 | dr11_v1_chr18_-_15373620_15373620 | 0.17 | 5.0e-01 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr20_-_3915770 Show fit | 68.54 |
ENSDART00000159322
|
si:ch73-111k22.3 |
|
| chr3_-_1190132 Show fit | 66.60 |
ENSDART00000149709
|
single-pass membrane protein with aspartate-rich tail 1a |
|
| chr4_-_5652030 Show fit | 59.33 |
ENSDART00000010903
|
radial spoke head 9 homolog |
|
| chr4_-_13626831 Show fit | 58.00 |
ENSDART00000173077
|
si:dkeyp-81f3.4 |
|
| chr23_-_28692581 Show fit | 57.99 |
ENSDART00000078141
|
RIB43A domain with coiled-coils 1 |
|
| chr25_+_21895182 Show fit | 55.95 |
ENSDART00000152075
|
si:ch211-147k9.8 |
|
| chr10_-_36682509 Show fit | 55.34 |
ENSDART00000148093
ENSDART00000063365 |
DnaJ (Hsp40) homolog, subfamily B, member 13 |
|
| chr5_+_39563301 Show fit | 54.78 |
ENSDART00000131245
ENSDART00000097872 |
si:ch211-57h10.1 |
|
| chr19_-_4023050 Show fit | 54.15 |
ENSDART00000162883
|
sperm-tail PG-rich repeat containing 1 |
|
| chr16_+_4497302 Show fit | 53.67 |
ENSDART00000081826
ENSDART00000148096 |
tetratricopeptide repeat domain 29 |
Network of associatons between targets according to the STRING database.
First level regulatory network of rfx3_rfx2+rfx4
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 2.6 | 929.8 | GO:0046777 | protein autophosphorylation(GO:0046777) |
| 1.3 | 749.6 | GO:0006397 | mRNA processing(GO:0006397) |
| 8.2 | 238.5 | GO:0070286 | axonemal dynein complex assembly(GO:0070286) |
| 22.2 | 155.5 | GO:0007288 | sperm axoneme assembly(GO:0007288) |
| 3.5 | 145.0 | GO:0003341 | cilium movement(GO:0003341) |
| 5.0 | 95.3 | GO:0060287 | epithelial cilium movement involved in determination of left/right asymmetry(GO:0060287) |
| 0.4 | 86.0 | GO:0060271 | cilium morphogenesis(GO:0060271) |
| 1.0 | 77.4 | GO:0006165 | nucleoside diphosphate phosphorylation(GO:0006165) |
| 5.7 | 68.5 | GO:0001881 | receptor recycling(GO:0001881) |
| 0.9 | 68.4 | GO:0044782 | cilium organization(GO:0044782) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 537.4 | GO:0005634 | nucleus(GO:0005634) |
| 0.1 | 536.6 | GO:0005737 | cytoplasm(GO:0005737) |
| 5.2 | 382.2 | GO:0031514 | motile cilium(GO:0031514) |
| 1.1 | 213.7 | GO:0005929 | cilium(GO:0005929) |
| 4.2 | 163.3 | GO:0005930 | axoneme(GO:0005930) |
| 2.6 | 162.2 | GO:0036064 | ciliary basal body(GO:0036064) |
| 8.5 | 102.4 | GO:0036157 | outer dynein arm(GO:0036157) |
| 32.0 | 95.9 | GO:0001534 | radial spoke(GO:0001534) |
| 0.1 | 93.6 | GO:0005829 | cytosol(GO:0005829) |
| 0.3 | 78.9 | GO:0005874 | microtubule(GO:0005874) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.0 | 934.6 | GO:0004674 | protein serine/threonine kinase activity(GO:0004674) |
| 1.9 | 807.2 | GO:0061630 | ubiquitin protein ligase activity(GO:0061630) |
| 0.3 | 135.6 | GO:0003924 | GTPase activity(GO:0003924) |
| 6.9 | 130.3 | GO:0045504 | dynein heavy chain binding(GO:0045504) |
| 2.5 | 80.3 | GO:0045505 | dynein intermediate chain binding(GO:0045505) |
| 5.7 | 74.7 | GO:0004017 | adenylate kinase activity(GO:0004017) |
| 1.2 | 71.9 | GO:0005200 | structural constituent of cytoskeleton(GO:0005200) |
| 2.7 | 67.4 | GO:0097472 | cyclin-dependent protein serine/threonine kinase activity(GO:0004693) cyclin-dependent protein kinase activity(GO:0097472) |
| 0.5 | 67.3 | GO:0005516 | calmodulin binding(GO:0005516) |
| 6.5 | 58.2 | GO:0016286 | small conductance calcium-activated potassium channel activity(GO:0016286) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.9 | 52.6 | PID NOTCH PATHWAY | Notch signaling pathway |
| 1.1 | 39.2 | ST GA13 PATHWAY | G alpha 13 Pathway |
| 1.4 | 36.1 | PID LIS1 PATHWAY | Lissencephaly gene (LIS1) in neuronal migration and development |
| 1.0 | 36.0 | ST DIFFERENTIATION PATHWAY IN PC12 CELLS | Differentiation Pathway in PC12 Cells; this is a specific case of PAC1 Receptor Pathway. |
| 0.2 | 26.1 | NABA SECRETED FACTORS | Genes encoding secreted soluble factors |
| 1.2 | 21.1 | PID TOLL ENDOGENOUS PATHWAY | Endogenous TLR signaling |
| 0.8 | 16.7 | PID ARF6 PATHWAY | Arf6 signaling events |
| 0.5 | 15.2 | PID VEGFR1 2 PATHWAY | Signaling events mediated by VEGFR1 and VEGFR2 |
| 0.1 | 10.5 | NABA ECM REGULATORS | Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix |
| 0.2 | 8.6 | PID AR TF PATHWAY | Regulation of Androgen receptor activity |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 2.1 | 43.4 | REACTOME GLYCOLYSIS | Genes involved in Glycolysis |
| 2.0 | 41.4 | REACTOME SYNTHESIS AND INTERCONVERSION OF NUCLEOTIDE DI AND TRIPHOSPHATES | Genes involved in Synthesis and interconversion of nucleotide di- and triphosphates |
| 1.4 | 39.2 | REACTOME SPHINGOLIPID DE NOVO BIOSYNTHESIS | Genes involved in Sphingolipid de novo biosynthesis |
| 1.0 | 34.2 | REACTOME G1 PHASE | Genes involved in G1 Phase |
| 3.6 | 32.6 | REACTOME NFKB IS ACTIVATED AND SIGNALS SURVIVAL | Genes involved in NF-kB is activated and signals survival |
| 1.9 | 31.1 | REACTOME POST CHAPERONIN TUBULIN FOLDING PATHWAY | Genes involved in Post-chaperonin tubulin folding pathway |
| 1.9 | 16.7 | REACTOME HORMONE LIGAND BINDING RECEPTORS | Genes involved in Hormone ligand-binding receptors |
| 0.3 | 16.4 | REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX | Genes involved in Formation of the ternary complex, and subsequently, the 43S complex |
| 2.5 | 15.2 | REACTOME REGULATION OF RHEB GTPASE ACTIVITY BY AMPK | Genes involved in Regulation of Rheb GTPase activity by AMPK |
| 0.8 | 13.6 | REACTOME INHIBITION OF INSULIN SECRETION BY ADRENALINE NORADRENALINE | Genes involved in Inhibition of Insulin Secretion by Adrenaline/Noradrenaline |