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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for nkx2.3+nkx2.7
Z-value: 1.08
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Transcription factors associated with nkx2.3+nkx2.7
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| nkx2.3 | dr11_v1_chr13_-_40411908_40411917 | -0.88 | 1.4e-06 | Click! |
| nkx2.7 | dr11_v1_chr8_-_50287949_50287949 | -0.51 | 2.9e-02 | Click! |
Network of associatons between targets according to the STRING database.
First level regulatory network of nkx2.3+nkx2.7
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 8.5 | GO:0000398 | RNA splicing, via transesterification reactions(GO:0000375) RNA splicing, via transesterification reactions with bulged adenosine as nucleophile(GO:0000377) mRNA splicing, via spliceosome(GO:0000398) |
| 0.1 | 7.0 | GO:0051028 | mRNA transport(GO:0051028) |
| 0.0 | 4.3 | GO:0090630 | activation of GTPase activity(GO:0090630) |
| 0.4 | 3.6 | GO:0031670 | cellular response to nutrient(GO:0031670) cellular response to vitamin(GO:0071295) |
| 1.2 | 3.5 | GO:0000212 | meiotic spindle organization(GO:0000212) |
| 1.1 | 3.4 | GO:0055109 | invagination involved in gastrulation with mouth forming second(GO:0055109) morphogenesis of an epithelial fold(GO:0060571) |
| 0.3 | 2.9 | GO:0043928 | exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay(GO:0043928) |
| 0.1 | 2.5 | GO:1901663 | ubiquinone metabolic process(GO:0006743) ubiquinone biosynthetic process(GO:0006744) quinone biosynthetic process(GO:1901663) |
| 0.1 | 2.5 | GO:0032011 | ARF protein signal transduction(GO:0032011) regulation of ARF protein signal transduction(GO:0032012) |
| 0.0 | 2.4 | GO:0034968 | histone lysine methylation(GO:0034968) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 4.5 | GO:0005685 | U1 snRNP(GO:0005685) |
| 0.1 | 4.0 | GO:0005876 | spindle microtubule(GO:0005876) |
| 0.0 | 3.9 | GO:0005802 | trans-Golgi network(GO:0005802) |
| 0.0 | 3.5 | GO:0000139 | Golgi membrane(GO:0000139) |
| 0.1 | 3.1 | GO:0030496 | midbody(GO:0030496) |
| 0.2 | 2.9 | GO:0030015 | CCR4-NOT core complex(GO:0030015) |
| 0.1 | 2.9 | GO:0010494 | cytoplasmic stress granule(GO:0010494) |
| 0.0 | 2.7 | GO:0016607 | nuclear speck(GO:0016607) |
| 0.0 | 2.2 | GO:0000118 | histone deacetylase complex(GO:0000118) |
| 0.0 | 2.2 | GO:0005925 | focal adhesion(GO:0005925) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 7.0 | GO:0044822 | mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822) |
| 0.6 | 4.5 | GO:0030619 | U1 snRNA binding(GO:0030619) |
| 0.1 | 4.4 | GO:0061631 | ubiquitin conjugating enzyme activity(GO:0061631) |
| 0.0 | 4.3 | GO:0005096 | GTPase activator activity(GO:0005096) |
| 0.0 | 3.8 | GO:0003730 | mRNA 3'-UTR binding(GO:0003730) |
| 0.3 | 3.5 | GO:0043027 | cysteine-type endopeptidase inhibitor activity involved in apoptotic process(GO:0043027) cysteine-type endopeptidase regulator activity involved in apoptotic process(GO:0043028) |
| 0.0 | 3.5 | GO:0004867 | serine-type endopeptidase inhibitor activity(GO:0004867) |
| 0.2 | 2.9 | GO:0008266 | poly(U) RNA binding(GO:0008266) |
| 0.2 | 2.9 | GO:0004535 | poly(A)-specific ribonuclease activity(GO:0004535) |
| 0.9 | 2.8 | GO:0045174 | glutathione dehydrogenase (ascorbate) activity(GO:0045174) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 3.8 | PID UPA UPAR PATHWAY | Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling |
| 0.1 | 2.8 | PID AURORA B PATHWAY | Aurora B signaling |
| 0.0 | 2.3 | PID ERA GENOMIC PATHWAY | Validated nuclear estrogen receptor alpha network |
| 0.0 | 2.2 | PID HDAC CLASSI PATHWAY | Signaling events mediated by HDAC Class I |
| 0.1 | 1.7 | PID AURORA A PATHWAY | Aurora A signaling |
| 0.0 | 1.7 | PID MYC ACTIV PATHWAY | Validated targets of C-MYC transcriptional activation |
| 0.0 | 1.4 | PID TELOMERASE PATHWAY | Regulation of Telomerase |
| 0.0 | 1.3 | NABA ECM AFFILIATED | Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins |
| 0.1 | 1.2 | PID ECADHERIN KERATINOCYTE PATHWAY | E-cadherin signaling in keratinocytes |
| 0.1 | 1.1 | PID HDAC CLASSIII PATHWAY | Signaling events mediated by HDAC Class III |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 3.6 | REACTOME CYTOCHROME P450 ARRANGED BY SUBSTRATE TYPE | Genes involved in Cytochrome P450 - arranged by substrate type |
| 0.0 | 3.3 | REACTOME MRNA SPLICING | Genes involved in mRNA Splicing |
| 0.2 | 2.9 | REACTOME DEADENYLATION OF MRNA | Genes involved in Deadenylation of mRNA |
| 0.2 | 2.8 | REACTOME GLUTATHIONE CONJUGATION | Genes involved in Glutathione conjugation |
| 0.0 | 2.5 | REACTOME ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION | Genes involved in Antigen processing: Ubiquitination & Proteasome degradation |
| 0.0 | 2.4 | REACTOME ION TRANSPORT BY P TYPE ATPASES | Genes involved in Ion transport by P-type ATPases |
| 0.1 | 2.2 | REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION | Genes involved in NOTCH1 Intracellular Domain Regulates Transcription |
| 0.0 | 2.2 | REACTOME DIABETES PATHWAYS | Genes involved in Diabetes pathways |
| 0.1 | 2.0 | REACTOME SIGNAL TRANSDUCTION BY L1 | Genes involved in Signal transduction by L1 |
| 0.0 | 1.9 | REACTOME HOST INTERACTIONS OF HIV FACTORS | Genes involved in Host Interactions of HIV factors |