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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for nfil3-4+si:dkey-172o19.2
Z-value: 1.04
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Transcription factors associated with nfil3-4+si:dkey-172o19.2
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| nfil3-4 | dr11_v1_chr22_+_20560041_20560041 | 0.66 | 3.0e-03 | Click! |
| si:dkey-172o19.2 | dr11_v1_chr22_+_20546612_20546612 | 0.64 | 4.5e-03 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr9_-_1702648 Show fit | 3.64 |
ENSDART00000102934
|
heterogeneous nuclear ribonucleoprotein A3 |
|
| chr25_-_19584735 Show fit | 3.47 |
ENSDART00000137930
|
synaptonemal complex protein 3 |
|
| chr22_-_15562933 Show fit | 3.39 |
ENSDART00000141528
|
ankyrin repeat and MYND domain containing 1 |
|
| chr25_-_19585010 Show fit | 3.08 |
ENSDART00000021340
|
synaptonemal complex protein 3 |
|
| chr12_-_23128746 Show fit | 3.00 |
ENSDART00000170018
|
armadillo repeat containing 4 |
|
| chr24_-_26310854 Show fit | 2.96 |
ENSDART00000080113
|
apolipoprotein Db |
|
| chr16_+_34523515 Show fit | 2.92 |
ENSDART00000041007
|
stathmin 1b |
|
| chr9_-_48736388 Show fit | 2.91 |
ENSDART00000022074
|
dehydrogenase/reductase (SDR family) member 9 |
|
| chr16_+_43139504 Show fit | 2.86 |
ENSDART00000065643
|
DBF4 zinc finger |
|
| chr5_-_41494831 Show fit | 2.75 |
ENSDART00000051081
|
eukaryotic translation elongation factor 2, like 2 |
Network of associatons between targets according to the STRING database.
First level regulatory network of nfil3-4+si:dkey-172o19.2
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 20.3 | GO:0046777 | protein autophosphorylation(GO:0046777) |
| 0.2 | 6.5 | GO:0007286 | spermatid development(GO:0007286) |
| 0.1 | 4.9 | GO:0006096 | glycolytic process(GO:0006096) |
| 0.1 | 4.8 | GO:0007568 | aging(GO:0007568) |
| 1.5 | 4.6 | GO:0044821 | telomere localization(GO:0034397) telomere tethering at nuclear periphery(GO:0034398) meiotic telomere tethering at nuclear periphery(GO:0044821) meiotic telomere clustering(GO:0045141) meiotic attachment of telomere to nuclear envelope(GO:0070197) chromosome localization to nuclear envelope involved in homologous chromosome segregation(GO:0090220) chromosome attachment to the nuclear envelope(GO:0097240) |
| 0.1 | 4.5 | GO:0042737 | drug metabolic process(GO:0017144) drug catabolic process(GO:0042737) exogenous drug catabolic process(GO:0042738) |
| 0.3 | 3.9 | GO:0042572 | retinol metabolic process(GO:0042572) |
| 0.1 | 3.8 | GO:0006414 | translational elongation(GO:0006414) |
| 0.5 | 3.6 | GO:2000105 | positive regulation of DNA-dependent DNA replication(GO:2000105) |
| 0.0 | 3.6 | GO:0071560 | transforming growth factor beta receptor signaling pathway(GO:0007179) response to transforming growth factor beta(GO:0071559) cellular response to transforming growth factor beta stimulus(GO:0071560) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 17.4 | GO:0005615 | extracellular space(GO:0005615) |
| 0.3 | 8.0 | GO:0000795 | synaptonemal complex(GO:0000795) |
| 0.0 | 6.3 | GO:0005576 | extracellular region(GO:0005576) |
| 0.1 | 4.4 | GO:0099501 | synaptic vesicle membrane(GO:0030672) exocytic vesicle membrane(GO:0099501) |
| 0.3 | 3.9 | GO:0070187 | telosome(GO:0070187) |
| 0.1 | 3.3 | GO:0044447 | axoneme part(GO:0044447) |
| 1.0 | 2.9 | GO:0032839 | dendrite cytoplasm(GO:0032839) |
| 0.2 | 2.7 | GO:0036038 | MKS complex(GO:0036038) |
| 0.3 | 2.4 | GO:0036156 | inner dynein arm(GO:0036156) |
| 0.1 | 2.4 | GO:0071144 | SMAD2-SMAD3 protein complex(GO:0071144) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 4.6 | GO:0043022 | ribosome binding(GO:0043022) |
| 0.1 | 4.5 | GO:0016712 | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen(GO:0016712) |
| 0.1 | 3.3 | GO:0045505 | dynein intermediate chain binding(GO:0045505) |
| 0.1 | 3.0 | GO:0004693 | cyclin-dependent protein serine/threonine kinase activity(GO:0004693) cyclin-dependent protein kinase activity(GO:0097472) |
| 0.1 | 3.0 | GO:0004181 | metallocarboxypeptidase activity(GO:0004181) |
| 0.0 | 3.0 | GO:0004222 | metalloendopeptidase activity(GO:0004222) |
| 0.4 | 2.9 | GO:0004745 | retinol dehydrogenase activity(GO:0004745) |
| 0.2 | 2.9 | GO:0043539 | protein serine/threonine kinase activator activity(GO:0043539) |
| 0.1 | 2.6 | GO:0008483 | transaminase activity(GO:0008483) |
| 0.4 | 2.5 | GO:0004392 | heme oxygenase (decyclizing) activity(GO:0004392) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 2.9 | NABA ECM REGULATORS | Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix |
| 0.2 | 2.5 | PID ALK2 PATHWAY | ALK2 signaling events |
| 0.0 | 2.0 | NABA ECM AFFILIATED | Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins |
| 0.0 | 1.7 | PID ATR PATHWAY | ATR signaling pathway |
| 0.1 | 1.6 | PID P38 MKK3 6PATHWAY | p38 MAPK signaling pathway |
| 0.0 | 1.6 | PID HNF3B PATHWAY | FOXA2 and FOXA3 transcription factor networks |
| 0.1 | 1.4 | SA G2 AND M PHASES | Cdc25 activates the cdc2/cyclin B complex to induce the G2/M transition. |
| 0.1 | 1.3 | PID INTEGRIN2 PATHWAY | Beta2 integrin cell surface interactions |
| 0.0 | 1.3 | PID MYC PATHWAY | C-MYC pathway |
| 0.0 | 0.9 | PID CD40 PATHWAY | CD40/CD40L signaling |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 7.7 | REACTOME MEIOTIC SYNAPSIS | Genes involved in Meiotic Synapsis |
| 0.1 | 5.1 | REACTOME ACTIVATION OF ATR IN RESPONSE TO REPLICATION STRESS | Genes involved in Activation of ATR in response to replication stress |
| 0.2 | 3.5 | REACTOME GLYCOLYSIS | Genes involved in Glycolysis |
| 0.0 | 3.1 | REACTOME PEPTIDE CHAIN ELONGATION | Genes involved in Peptide chain elongation |
| 0.2 | 2.5 | REACTOME AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION | Genes involved in Amino acid synthesis and interconversion (transamination) |
| 0.2 | 2.5 | REACTOME SIGNALING BY BMP | Genes involved in Signaling by BMP |
| 0.0 | 2.4 | REACTOME RESPIRATORY ELECTRON TRANSPORT ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING AND HEAT PRODUCTION BY UNCOUPLING PROTEINS | Genes involved in Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. |
| 0.0 | 2.2 | REACTOME DESTABILIZATION OF MRNA BY AUF1 HNRNP D0 | Genes involved in Destabilization of mRNA by AUF1 (hnRNP D0) |
| 0.4 | 2.1 | REACTOME THE NLRP3 INFLAMMASOME | Genes involved in The NLRP3 inflammasome |
| 0.0 | 1.8 | REACTOME LOSS OF NLP FROM MITOTIC CENTROSOMES | Genes involved in Loss of Nlp from mitotic centrosomes |