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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for rxraa+rxrab+rxrba+rxrgb
Z-value: 0.99
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Transcription factors associated with rxraa+rxrab+rxrba+rxrgb
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| rxrgb | dr11_v1_chr20_+_33875256_33875256 | -0.68 | 1.8e-03 | Click! |
| rxrba | dr11_v1_chr19_-_7272921_7273057 | 0.38 | 1.2e-01 | Click! |
| rxrab | dr11_v1_chr5_-_64511428_64511428 | 0.20 | 4.3e-01 | Click! |
| rxraa | dr11_v1_chr21_+_17880511_17880511 | -0.10 | 7.1e-01 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr6_+_154556 Show fit | 3.93 |
ENSDART00000193153
|
zinc finger, GATA-like protein 1 |
|
| chr11_+_18175893 Show fit | 3.41 |
ENSDART00000177625
|
zgc:173545 |
|
| chr11_+_18037729 Show fit | 3.35 |
ENSDART00000111624
|
zgc:175135 |
|
| chr11_+_18130300 Show fit | 3.31 |
ENSDART00000169146
|
zgc:175135 |
|
| chr11_+_18157260 Show fit | 3.27 |
ENSDART00000144659
|
zgc:173545 |
|
| chr11_+_18053333 Show fit | 3.27 |
ENSDART00000075750
|
zgc:175135 |
|
| chr20_+_54304800 Show fit | 2.90 |
ENSDART00000121661
|
zona pellucida glycoprotein 2, tandem duplicate 6 |
|
| chr20_+_54295213 Show fit | 2.52 |
ENSDART00000074085
|
zona pellucida glycoprotein 2, tandem duplicate 3 |
|
| chr20_+_54312970 Show fit | 2.51 |
ENSDART00000024598
ENSDART00000193172 |
zona pellucida glycoprotein 2, tandem duplicate 5 |
|
| chr20_+_54309148 Show fit | 2.48 |
ENSDART00000099360
|
zona pellucida glycoprotein 2, tandem duplicate 1 |
Network of associatons between targets according to the STRING database.
First level regulatory network of rxraa+rxrab+rxrba+rxrgb
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 9.3 | GO:0048545 | response to steroid hormone(GO:0048545) |
| 0.1 | 6.7 | GO:0070098 | chemokine-mediated signaling pathway(GO:0070098) |
| 0.1 | 5.6 | GO:0048599 | oocyte development(GO:0048599) |
| 0.5 | 2.3 | GO:0016338 | calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules(GO:0016338) |
| 0.1 | 2.3 | GO:0006635 | fatty acid beta-oxidation(GO:0006635) |
| 0.2 | 2.0 | GO:0040038 | meiotic cytokinesis(GO:0033206) polar body extrusion after meiotic divisions(GO:0040038) |
| 0.6 | 1.7 | GO:0050787 | response to mercury ion(GO:0046689) detoxification of mercury ion(GO:0050787) |
| 0.2 | 1.6 | GO:0031998 | regulation of fatty acid beta-oxidation(GO:0031998) |
| 0.1 | 1.5 | GO:0000463 | maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)(GO:0000463) |
| 0.0 | 1.4 | GO:0006891 | intra-Golgi vesicle-mediated transport(GO:0006891) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 3.2 | GO:0072686 | mitotic spindle(GO:0072686) |
| 0.3 | 2.3 | GO:0035517 | PR-DUB complex(GO:0035517) |
| 0.0 | 2.0 | GO:0005762 | organellar large ribosomal subunit(GO:0000315) mitochondrial large ribosomal subunit(GO:0005762) |
| 0.0 | 1.9 | GO:0005759 | mitochondrial matrix(GO:0005759) |
| 0.4 | 1.2 | GO:0097189 | apoptotic body(GO:0097189) |
| 0.3 | 1.2 | GO:1904423 | dehydrodolichyl diphosphate synthase complex(GO:1904423) |
| 0.1 | 1.2 | GO:0017119 | Golgi transport complex(GO:0017119) |
| 0.4 | 1.1 | GO:1990072 | TRAPPIII protein complex(GO:1990072) |
| 0.0 | 1.0 | GO:0032156 | septin ring(GO:0005940) septin complex(GO:0031105) septin cytoskeleton(GO:0032156) |
| 0.0 | 1.0 | GO:0000781 | chromosome, telomeric region(GO:0000781) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 8.7 | GO:0030246 | carbohydrate binding(GO:0030246) |
| 0.4 | 6.7 | GO:0031729 | CCR1 chemokine receptor binding(GO:0031726) CCR4 chemokine receptor binding(GO:0031729) |
| 0.0 | 2.4 | GO:0001227 | transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding(GO:0001227) |
| 0.5 | 2.3 | GO:0042975 | peroxisome proliferator activated receptor binding(GO:0042975) |
| 0.3 | 2.3 | GO:0004300 | enoyl-CoA hydratase activity(GO:0004300) |
| 0.0 | 2.2 | GO:0016811 | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides(GO:0016811) |
| 0.5 | 1.4 | GO:0003985 | acetyl-CoA C-acetyltransferase activity(GO:0003985) |
| 0.0 | 1.4 | GO:0043492 | hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances(GO:0016820) ATPase activity, coupled to transmembrane movement of substances(GO:0042626) ATPase activity, coupled to movement of substances(GO:0043492) |
| 0.0 | 1.3 | GO:0004993 | G-protein coupled serotonin receptor activity(GO:0004993) |
| 0.3 | 1.2 | GO:0045547 | dehydrodolichyl diphosphate synthase activity(GO:0045547) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 2.0 | PID AR PATHWAY | Coregulation of Androgen receptor activity |
| 0.0 | 1.2 | PID RHOA REG PATHWAY | Regulation of RhoA activity |
| 0.0 | 1.2 | WNT SIGNALING | Genes related to Wnt-mediated signal transduction |
| 0.0 | 0.6 | PID BETA CATENIN DEG PATHWAY | Degradation of beta catenin |
| 0.0 | 0.6 | PID HNF3B PATHWAY | FOXA2 and FOXA3 transcription factor networks |
| 0.0 | 0.6 | PID ERBB1 INTERNALIZATION PATHWAY | Internalization of ErbB1 |
| 0.0 | 0.4 | PID P38 MKK3 6PATHWAY | p38 MAPK signaling pathway |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 3.6 | REACTOME MITOCHONDRIAL FATTY ACID BETA OXIDATION | Genes involved in Mitochondrial Fatty Acid Beta-Oxidation |
| 0.1 | 1.7 | REACTOME ABC FAMILY PROTEINS MEDIATED TRANSPORT | Genes involved in ABC-family proteins mediated transport |
| 0.0 | 1.1 | REACTOME TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION | Genes involved in Transport to the Golgi and subsequent modification |
| 0.0 | 1.1 | REACTOME MITOCHONDRIAL PROTEIN IMPORT | Genes involved in Mitochondrial Protein Import |
| 0.0 | 1.1 | REACTOME PPARA ACTIVATES GENE EXPRESSION | Genes involved in PPARA Activates Gene Expression |
| 0.0 | 0.9 | REACTOME SIGNALING BY RHO GTPASES | Genes involved in Signaling by Rho GTPases |
| 0.0 | 0.8 | REACTOME RNA POL III CHAIN ELONGATION | Genes involved in RNA Polymerase III Chain Elongation |
| 0.0 | 0.7 | REACTOME NRAGE SIGNALS DEATH THROUGH JNK | Genes involved in NRAGE signals death through JNK |
| 0.0 | 0.6 | REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS | Genes involved in Apoptotic cleavage of cellular proteins |
| 0.0 | 0.4 | REACTOME ADVANCED GLYCOSYLATION ENDPRODUCT RECEPTOR SIGNALING | Genes involved in Advanced glycosylation endproduct receptor signaling |