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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for nkx2.2b
Z-value: 0.94
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Transcription factors associated with nkx2.2b
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| nkx2.2b | dr11_v1_chr20_+_48782068_48782068 | -0.50 | 3.4e-02 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr13_+_47710434 Show fit | 1.95 |
ENSDART00000188724
|
transmembrane protein 87B |
|
| chr4_-_837768 Show fit | 1.93 |
ENSDART00000185280
ENSDART00000135618 |
sine oculis binding protein homolog (Drosophila) b |
|
| chr4_-_20081621 Show fit | 1.74 |
ENSDART00000024647
|
DENN/MADD domain containing 6B |
|
| chr22_-_17631675 Show fit | 1.73 |
ENSDART00000132565
|
histocompatibility (minor) HA-1 b |
|
| chr24_-_33308045 Show fit | 1.72 |
ENSDART00000149711
|
solute carrier family 4 (anion exchanger), member 2b |
|
| chr10_+_41945890 Show fit | 1.67 |
ENSDART00000063013
ENSDART00000128313 |
transmembrane protein 120B |
|
| chr11_+_42422371 Show fit | 1.67 |
ENSDART00000163780
|
DENN/MADD domain containing 6Aa |
|
| chr17_+_12075805 Show fit | 1.60 |
ENSDART00000155329
|
consortin, connexin sorting protein a |
|
| chr6_-_49547680 Show fit | 1.54 |
ENSDART00000169678
|
protein phosphatase 4, regulatory subunit 1-like |
|
| chr7_-_71585065 Show fit | 1.49 |
ENSDART00000128678
|
methyltransferase like 4 |
Network of associatons between targets according to the STRING database.
First level regulatory network of nkx2.2b
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 2.0 | GO:0070897 | DNA-templated transcriptional preinitiation complex assembly(GO:0070897) |
| 0.0 | 1.9 | GO:0000079 | regulation of cyclin-dependent protein serine/threonine kinase activity(GO:0000079) regulation of cyclin-dependent protein kinase activity(GO:1904029) |
| 0.2 | 1.7 | GO:0045444 | fat cell differentiation(GO:0045444) |
| 0.1 | 1.7 | GO:0015701 | bicarbonate transport(GO:0015701) |
| 0.5 | 1.6 | GO:0090004 | positive regulation of Golgi to plasma membrane protein transport(GO:0042998) positive regulation of establishment of protein localization to plasma membrane(GO:0090004) |
| 0.0 | 1.6 | GO:0046856 | phosphatidylinositol dephosphorylation(GO:0046856) |
| 0.0 | 1.6 | GO:0031101 | fin regeneration(GO:0031101) |
| 0.1 | 1.5 | GO:0080111 | DNA demethylation(GO:0080111) |
| 0.1 | 1.5 | GO:0006506 | GPI anchor biosynthetic process(GO:0006506) |
| 0.1 | 1.5 | GO:0006446 | regulation of translational initiation(GO:0006446) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 4.6 | GO:0055037 | recycling endosome(GO:0055037) |
| 0.0 | 3.3 | GO:0016323 | basolateral plasma membrane(GO:0016323) |
| 0.0 | 2.6 | GO:0005802 | trans-Golgi network(GO:0005802) |
| 0.1 | 2.3 | GO:0005876 | spindle microtubule(GO:0005876) |
| 0.0 | 2.3 | GO:1903293 | protein serine/threonine phosphatase complex(GO:0008287) phosphatase complex(GO:1903293) |
| 0.0 | 2.1 | GO:0043296 | apical junction complex(GO:0043296) |
| 0.3 | 2.0 | GO:0000126 | transcription factor TFIIIB complex(GO:0000126) |
| 0.0 | 1.9 | GO:0000307 | cyclin-dependent protein kinase holoenzyme complex(GO:0000307) |
| 0.0 | 1.7 | GO:0016607 | nuclear speck(GO:0016607) |
| 0.1 | 1.6 | GO:0016581 | NuRD complex(GO:0016581) CHD-type complex(GO:0090545) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 2.3 | GO:0003697 | single-stranded DNA binding(GO:0003697) |
| 0.3 | 2.2 | GO:0000995 | transcription factor activity, core RNA polymerase III binding(GO:0000995) |
| 0.0 | 2.0 | GO:0003713 | transcription coactivator activity(GO:0003713) |
| 0.0 | 1.9 | GO:0016538 | cyclin-dependent protein serine/threonine kinase regulator activity(GO:0016538) |
| 0.1 | 1.7 | GO:0005452 | inorganic anion exchanger activity(GO:0005452) |
| 0.4 | 1.6 | GO:0071253 | connexin binding(GO:0071253) |
| 0.1 | 1.6 | GO:0001103 | RNA polymerase II repressing transcription factor binding(GO:0001103) |
| 0.1 | 1.6 | GO:0004438 | phosphatidylinositol-3-phosphatase activity(GO:0004438) |
| 0.3 | 1.5 | GO:0008311 | double-stranded DNA exodeoxyribonuclease activity(GO:0008309) double-stranded DNA 3'-5' exodeoxyribonuclease activity(GO:0008311) |
| 0.2 | 1.5 | GO:0017176 | phosphatidylinositol N-acetylglucosaminyltransferase activity(GO:0017176) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 2.6 | PID HIF2PATHWAY | HIF-2-alpha transcription factor network |
| 0.0 | 1.9 | PID P53 REGULATION PATHWAY | p53 pathway |
| 0.1 | 1.4 | PID RAS PATHWAY | Regulation of Ras family activation |
| 0.1 | 1.1 | PID TCR RAS PATHWAY | Ras signaling in the CD4+ TCR pathway |
| 0.1 | 1.1 | PID INSULIN GLUCOSE PATHWAY | Insulin-mediated glucose transport |
| 0.0 | 1.1 | PID PLK1 PATHWAY | PLK1 signaling events |
| 0.0 | 0.9 | PID ATM PATHWAY | ATM pathway |
| 0.0 | 0.9 | PID MTOR 4PATHWAY | mTOR signaling pathway |
| 0.0 | 0.9 | PID P53 DOWNSTREAM PATHWAY | Direct p53 effectors |
| 0.0 | 0.7 | PID MAPK TRK PATHWAY | Trk receptor signaling mediated by the MAPK pathway |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 2.0 | REACTOME MRNA SPLICING | Genes involved in mRNA Splicing |
| 0.1 | 1.5 | REACTOME BASE FREE SUGAR PHOSPHATE REMOVAL VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY | Genes involved in Base-free sugar-phosphate removal via the single-nucleotide replacement pathway |
| 0.1 | 1.5 | REACTOME RNA POL III CHAIN ELONGATION | Genes involved in RNA Polymerase III Chain Elongation |
| 0.1 | 1.5 | REACTOME SYNTHESIS OF GLYCOSYLPHOSPHATIDYLINOSITOL GPI | Genes involved in Synthesis of glycosylphosphatidylinositol (GPI) |
| 0.0 | 1.5 | REACTOME MRNA 3 END PROCESSING | Genes involved in mRNA 3'-end processing |
| 0.1 | 1.3 | REACTOME REGULATION OF HYPOXIA INDUCIBLE FACTOR HIF BY OXYGEN | Genes involved in Regulation of Hypoxia-inducible Factor (HIF) by Oxygen |
| 0.1 | 1.2 | REACTOME NOTCH HLH TRANSCRIPTION PATHWAY | Genes involved in Notch-HLH transcription pathway |
| 0.0 | 1.2 | REACTOME ACTIVATION OF THE PRE REPLICATIVE COMPLEX | Genes involved in Activation of the pre-replicative complex |
| 0.3 | 1.1 | REACTOME REGULATION OF COMPLEMENT CASCADE | Genes involved in Regulation of Complement cascade |
| 0.1 | 1.1 | REACTOME REGULATION OF INSULIN SECRETION BY ACETYLCHOLINE | Genes involved in Regulation of Insulin Secretion by Acetylcholine |