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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for clocka+clockb+npas2
Z-value: 2.72
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Transcription factors associated with clocka+clockb+npas2
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| clocka | dr11_v1_chr20_+_22130284_22130284 | -0.47 | 5.1e-02 | Click! |
| npas2 | dr11_v1_chr5_+_22791686_22791686 | 0.38 | 1.2e-01 | Click! |
| clockb | dr11_v1_chr1_+_19433004_19433004 | 0.15 | 5.5e-01 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr18_+_184746 Show fit | 8.87 |
ENSDART00000140897
|
La ribonucleoprotein domain family, member 6a |
|
| chr16_-_34195002 Show fit | 8.70 |
ENSDART00000054026
|
regulator of chromosome condensation 1 |
|
| chr12_+_13091842 Show fit | 6.93 |
ENSDART00000185477
ENSDART00000181435 ENSDART00000124799 |
si:ch211-103b1.2 |
|
| chr12_-_33359654 Show fit | 5.75 |
ENSDART00000001907
|
solute carrier family 16 (monocarboxylate transporter), member 3 |
|
| chr3_-_3398383 Show fit | 5.71 |
ENSDART00000047865
|
si:dkey-46g23.2 |
|
| chr15_-_17099560 Show fit | 5.32 |
ENSDART00000101724
|
v-mos Moloney murine sarcoma viral oncogene homolog |
|
| chr14_+_22076596 Show fit | 4.94 |
ENSDART00000106147
ENSDART00000100278 ENSDART00000131489 |
solute carrier family 43 (amino acid system L transporter), member 1a |
|
| chr24_+_36317544 Show fit | 4.86 |
ENSDART00000048640
ENSDART00000156096 |
pseudouridylate synthase 3 |
|
| chr14_-_49992709 Show fit | 4.60 |
ENSDART00000159988
|
family with sequence similarity 193, member B |
|
| chr19_+_20201254 Show fit | 4.56 |
ENSDART00000010140
|
insulin-like growth factor 2 mRNA binding protein 3 |
Network of associatons between targets according to the STRING database.
First level regulatory network of clocka+clockb+npas2
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 10.8 | GO:0030490 | maturation of SSU-rRNA(GO:0030490) |
| 1.5 | 10.3 | GO:0045905 | positive regulation of translational elongation(GO:0045901) positive regulation of translational termination(GO:0045905) |
| 0.3 | 10.2 | GO:0030488 | tRNA methylation(GO:0030488) |
| 0.1 | 9.2 | GO:0001756 | somitogenesis(GO:0001756) |
| 1.2 | 8.7 | GO:1901673 | regulation of mitotic spindle assembly(GO:1901673) |
| 0.2 | 8.4 | GO:0006270 | DNA replication initiation(GO:0006270) |
| 0.5 | 7.1 | GO:0009303 | rRNA transcription(GO:0009303) |
| 0.7 | 6.9 | GO:0006189 | 'de novo' IMP biosynthetic process(GO:0006189) |
| 1.4 | 6.8 | GO:1990481 | mRNA pseudouridine synthesis(GO:1990481) |
| 0.1 | 6.5 | GO:0051028 | mRNA transport(GO:0051028) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 24.3 | GO:0005730 | nucleolus(GO:0005730) |
| 0.9 | 11.1 | GO:0000808 | origin recognition complex(GO:0000808) nuclear origin of replication recognition complex(GO:0005664) |
| 0.2 | 9.8 | GO:0005643 | nuclear pore(GO:0005643) |
| 0.2 | 8.4 | GO:0005788 | endoplasmic reticulum lumen(GO:0005788) |
| 0.0 | 8.1 | GO:0005789 | endoplasmic reticulum membrane(GO:0005789) |
| 0.1 | 8.0 | GO:0030176 | integral component of endoplasmic reticulum membrane(GO:0030176) |
| 0.0 | 6.8 | GO:0005667 | transcription factor complex(GO:0005667) |
| 0.0 | 5.8 | GO:0000139 | Golgi membrane(GO:0000139) |
| 0.0 | 5.1 | GO:0000786 | nucleosome(GO:0000786) |
| 0.4 | 4.7 | GO:0005736 | DNA-directed RNA polymerase I complex(GO:0005736) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 11.8 | GO:0008175 | tRNA methyltransferase activity(GO:0008175) |
| 0.1 | 11.5 | GO:0003730 | mRNA 3'-UTR binding(GO:0003730) |
| 0.2 | 10.6 | GO:0043022 | ribosome binding(GO:0043022) |
| 0.3 | 8.3 | GO:0034062 | DNA-directed RNA polymerase activity(GO:0003899) RNA polymerase activity(GO:0034062) |
| 0.7 | 8.0 | GO:0015129 | lactate transmembrane transporter activity(GO:0015129) |
| 0.1 | 7.7 | GO:0015171 | amino acid transmembrane transporter activity(GO:0015171) |
| 0.0 | 7.6 | GO:0005085 | guanyl-nucleotide exchange factor activity(GO:0005085) |
| 0.4 | 7.3 | GO:0009982 | pseudouridine synthase activity(GO:0009982) |
| 0.1 | 7.2 | GO:0019905 | syntaxin binding(GO:0019905) |
| 0.0 | 6.7 | GO:0042393 | histone binding(GO:0042393) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 15.3 | PID MYC ACTIV PATHWAY | Validated targets of C-MYC transcriptional activation |
| 0.3 | 7.4 | ST ERK1 ERK2 MAPK PATHWAY | ERK1/ERK2 MAPK Pathway |
| 0.2 | 6.5 | PID FRA PATHWAY | Validated transcriptional targets of AP1 family members Fra1 and Fra2 |
| 0.3 | 5.3 | PID SMAD2 3PATHWAY | Regulation of cytoplasmic and nuclear SMAD2/3 signaling |
| 0.1 | 4.1 | PID CMYB PATHWAY | C-MYB transcription factor network |
| 0.1 | 3.5 | PID FOXO PATHWAY | FoxO family signaling |
| 0.2 | 2.6 | PID CIRCADIAN PATHWAY | Circadian rhythm pathway |
| 0.1 | 2.6 | PID AJDISS 2PATHWAY | Posttranslational regulation of adherens junction stability and dissassembly |
| 0.0 | 2.0 | PID TELOMERASE PATHWAY | Regulation of Telomerase |
| 0.1 | 1.8 | PID PRL SIGNALING EVENTS PATHWAY | Signaling events mediated by PRL |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 12.0 | REACTOME PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION | Genes involved in PTM: gamma carboxylation, hypusine formation and arylsulfatase activation |
| 0.7 | 11.1 | REACTOME E2F ENABLED INHIBITION OF PRE REPLICATION COMPLEX FORMATION | Genes involved in E2F-enabled inhibition of pre-replication complex formation |
| 0.8 | 10.8 | REACTOME PURINE RIBONUCLEOSIDE MONOPHOSPHATE BIOSYNTHESIS | Genes involved in Purine ribonucleoside monophosphate biosynthesis |
| 0.5 | 8.3 | REACTOME BILE SALT AND ORGANIC ANION SLC TRANSPORTERS | Genes involved in Bile salt and organic anion SLC transporters |
| 0.1 | 8.2 | REACTOME LATE PHASE OF HIV LIFE CYCLE | Genes involved in Late Phase of HIV Life Cycle |
| 0.2 | 8.1 | REACTOME ACTIVATION OF CHAPERONE GENES BY XBP1S | Genes involved in Activation of Chaperone Genes by XBP1(S) |
| 0.4 | 7.6 | REACTOME RNA POL III TRANSCRIPTION TERMINATION | Genes involved in RNA Polymerase III Transcription Termination |
| 0.1 | 7.1 | REACTOME DIABETES PATHWAYS | Genes involved in Diabetes pathways |
| 0.5 | 6.0 | REACTOME MRNA DECAY BY 3 TO 5 EXORIBONUCLEASE | Genes involved in mRNA Decay by 3' to 5' Exoribonuclease |
| 0.4 | 5.2 | REACTOME MITOCHONDRIAL FATTY ACID BETA OXIDATION | Genes involved in Mitochondrial Fatty Acid Beta-Oxidation |