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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for rfx1a+rfx1b
Z-value: 2.17
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Transcription factors associated with rfx1a+rfx1b
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| rfx1a | dr11_v1_chr3_-_19200571_19200651 | 0.99 | 1.2e-14 | Click! |
| rfx1b | dr11_v1_chr1_-_54107321_54107321 | 0.94 | 4.4e-09 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr9_+_48219111 Show fit | 10.17 |
ENSDART00000111225
ENSDART00000145972 |
coiled-coil domain containing 173 |
|
| chr5_+_61919217 Show fit | 9.46 |
ENSDART00000097340
|
radial spoke head 4 homolog A |
|
| chr6_-_8264751 Show fit | 9.20 |
ENSDART00000091628
|
coiled-coil domain containing 151 |
|
| chr4_+_15819728 Show fit | 8.80 |
ENSDART00000101613
|
leucine-rich repeats and guanylate kinase domain containing |
|
| chr25_+_21895182 Show fit | 8.46 |
ENSDART00000152075
|
si:ch211-147k9.8 |
|
| chr1_+_22002649 Show fit | 8.40 |
ENSDART00000141317
|
dynein, axonemal, heavy chain 6 |
|
| chr5_-_29671586 Show fit | 8.01 |
ENSDART00000098336
|
sperm acrosome associated 9 |
|
| chr14_+_6954579 Show fit | 7.96 |
ENSDART00000060998
|
NME/NM23 family member 5 |
|
| chr5_+_39563301 Show fit | 7.94 |
ENSDART00000131245
ENSDART00000097872 |
si:ch211-57h10.1 |
|
| chr1_-_6225285 Show fit | 7.90 |
ENSDART00000141653
|
malate dehydrogenase 1B, NAD (soluble) |
Network of associatons between targets according to the STRING database.
First level regulatory network of rfx1a+rfx1b
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.1 | 22.5 | GO:0060287 | epithelial cilium movement involved in determination of left/right asymmetry(GO:0060287) |
| 0.0 | 19.4 | GO:0006397 | mRNA processing(GO:0006397) |
| 0.6 | 16.1 | GO:0070286 | axonemal dynein complex assembly(GO:0070286) |
| 0.4 | 14.0 | GO:0042073 | intraciliary transport(GO:0042073) |
| 0.2 | 11.7 | GO:0009142 | nucleoside triphosphate biosynthetic process(GO:0009142) |
| 1.0 | 11.5 | GO:0060294 | cilium movement involved in cell motility(GO:0060294) |
| 0.2 | 10.9 | GO:0003341 | cilium movement(GO:0003341) |
| 2.7 | 8.0 | GO:1902176 | regulation of oxidative stress-induced intrinsic apoptotic signaling pathway(GO:1902175) negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway(GO:1902176) |
| 1.6 | 7.9 | GO:0006107 | oxaloacetate metabolic process(GO:0006107) |
| 0.7 | 7.8 | GO:0001881 | receptor recycling(GO:0001881) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 18.5 | GO:0030286 | dynein complex(GO:0030286) |
| 0.3 | 17.1 | GO:0031514 | motile cilium(GO:0031514) |
| 0.0 | 15.1 | GO:0005829 | cytosol(GO:0005829) |
| 0.8 | 14.1 | GO:0030992 | intraciliary transport particle B(GO:0030992) |
| 0.3 | 12.9 | GO:0097014 | axoneme(GO:0005930) ciliary plasm(GO:0097014) |
| 3.2 | 9.5 | GO:0001534 | radial spoke(GO:0001534) |
| 0.8 | 8.0 | GO:0001669 | acrosomal vesicle(GO:0001669) |
| 0.1 | 7.7 | GO:0036064 | ciliary basal body(GO:0036064) |
| 2.0 | 6.1 | GO:0032998 | Fc receptor complex(GO:0032997) Fc-epsilon receptor I complex(GO:0032998) |
| 0.4 | 5.9 | GO:0031209 | SCAR complex(GO:0031209) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 28.1 | GO:0061630 | ubiquitin protein ligase activity(GO:0061630) |
| 0.4 | 12.4 | GO:0045505 | dynein intermediate chain binding(GO:0045505) |
| 2.3 | 11.7 | GO:0004127 | cytidylate kinase activity(GO:0004127) |
| 0.0 | 10.9 | GO:0003924 | GTPase activity(GO:0003924) |
| 0.3 | 9.2 | GO:0008574 | ATP-dependent microtubule motor activity, plus-end-directed(GO:0008574) |
| 1.8 | 8.8 | GO:0004385 | guanylate kinase activity(GO:0004385) |
| 0.3 | 8.0 | GO:0004550 | nucleoside diphosphate kinase activity(GO:0004550) |
| 1.6 | 7.9 | GO:0030060 | L-malate dehydrogenase activity(GO:0030060) |
| 0.1 | 6.6 | GO:0005212 | structural constituent of eye lens(GO:0005212) |
| 0.0 | 6.3 | GO:0008017 | microtubule binding(GO:0008017) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 4.3 | PID CD8 TCR DOWNSTREAM PATHWAY | Downstream signaling in naïve CD8+ T cells |
| 0.0 | 1.8 | PID E2F PATHWAY | E2F transcription factor network |
| 0.0 | 1.1 | PID CASPASE PATHWAY | Caspase cascade in apoptosis |
| 0.1 | 1.0 | ST GRANULE CELL SURVIVAL PATHWAY | Granule Cell Survival Pathway is a specific case of more general PAC1 Receptor Pathway. |
| 0.0 | 0.9 | PID LKB1 PATHWAY | LKB1 signaling events |
| 0.0 | 0.9 | PID ERBB1 DOWNSTREAM PATHWAY | ErbB1 downstream signaling |
| 0.0 | 0.6 | PID ERB GENOMIC PATHWAY | Validated nuclear estrogen receptor beta network |
| 0.0 | 0.3 | PID SYNDECAN 1 PATHWAY | Syndecan-1-mediated signaling events |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.9 | 4.3 | REACTOME ENDOSOMAL VACUOLAR PATHWAY | Genes involved in Endosomal/Vacuolar pathway |
| 0.1 | 3.5 | REACTOME G0 AND EARLY G1 | Genes involved in G0 and Early G1 |
| 0.1 | 1.7 | REACTOME BRANCHED CHAIN AMINO ACID CATABOLISM | Genes involved in Branched-chain amino acid catabolism |
| 0.0 | 1.5 | REACTOME LOSS OF NLP FROM MITOTIC CENTROSOMES | Genes involved in Loss of Nlp from mitotic centrosomes |
| 0.1 | 1.4 | REACTOME FORMATION OF TUBULIN FOLDING INTERMEDIATES BY CCT TRIC | Genes involved in Formation of tubulin folding intermediates by CCT/TriC |
| 0.1 | 1.1 | REACTOME MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE | Genes involved in mRNA Decay by 5' to 3' Exoribonuclease |
| 0.1 | 1.0 | REACTOME ACTIVATION OF THE AP1 FAMILY OF TRANSCRIPTION FACTORS | Genes involved in Activation of the AP-1 family of transcription factors |
| 0.0 | 0.6 | REACTOME CS DS DEGRADATION | Genes involved in CS/DS degradation |
| 0.0 | 0.6 | REACTOME YAP1 AND WWTR1 TAZ STIMULATED GENE EXPRESSION | Genes involved in YAP1- and WWTR1 (TAZ)-stimulated gene expression |
| 0.0 | 0.3 | REACTOME SYNTHESIS SECRETION AND DEACYLATION OF GHRELIN | Genes involved in Synthesis, Secretion, and Deacylation of Ghrelin |