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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for hoxa9a+hoxa9b
Z-value: 0.94
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Transcription factors associated with hoxa9a+hoxa9b
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| hoxa9b | dr11_v1_chr16_+_20915319_20915319 | -0.91 | 1.5e-07 | Click! |
| hoxa9a | dr11_v1_chr19_+_19747430_19747430 | -0.90 | 4.6e-07 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr1_-_33647138 Show fit | 3.86 |
ENSDART00000142111
ENSDART00000015547 |
claudin g |
|
| chr17_-_4245902 Show fit | 3.00 |
ENSDART00000151851
|
growth differentiation factor 3 |
|
| chr16_+_29509133 Show fit | 2.38 |
ENSDART00000112116
|
cathepsin S, ortholog2, tandem duplicate 1 |
|
| chr19_-_27550768 Show fit | 2.30 |
ENSDART00000142313
|
si:dkeyp-46h3.8 |
|
| chr21_-_13690712 Show fit | 2.22 |
ENSDART00000065817
|
POU domain, class 5, transcription factor 3 |
|
| chr17_-_4245311 Show fit | 2.11 |
ENSDART00000055379
|
growth differentiation factor 3 |
|
| chr17_-_2595736 Show fit | 2.10 |
ENSDART00000128797
|
zona pellucida glycoprotein 3, tandem duplicate 2 |
|
| chr7_+_30626378 Show fit | 2.04 |
ENSDART00000173533
ENSDART00000052541 |
cyclin B2 |
|
| chr10_-_8053753 Show fit | 2.04 |
ENSDART00000162289
|
si:ch211-251f6.7 |
|
| chr19_-_31042570 Show fit | 1.96 |
ENSDART00000144337
ENSDART00000136213 ENSDART00000133101 ENSDART00000190949 |
basic leucine zipper and W2 domains 2 |
Network of associatons between targets according to the STRING database.
First level regulatory network of hoxa9a+hoxa9b
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.0 | 5.1 | GO:0038107 | nodal signaling pathway involved in determination of left/right asymmetry(GO:0038107) regulation of nodal signaling pathway involved in determination of left/right asymmetry(GO:1900145) |
| 0.8 | 3.9 | GO:0016338 | calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules(GO:0016338) |
| 0.1 | 3.2 | GO:0000079 | regulation of cyclin-dependent protein serine/threonine kinase activity(GO:0000079) regulation of cyclin-dependent protein kinase activity(GO:1904029) |
| 0.9 | 2.8 | GO:0043654 | recognition of apoptotic cell(GO:0043654) |
| 0.1 | 2.6 | GO:0035459 | cargo loading into vesicle(GO:0035459) |
| 0.0 | 2.6 | GO:0090090 | negative regulation of canonical Wnt signaling pathway(GO:0090090) |
| 0.0 | 2.5 | GO:0043484 | regulation of RNA splicing(GO:0043484) |
| 0.0 | 2.3 | GO:0051028 | mRNA transport(GO:0051028) |
| 0.3 | 2.2 | GO:0035284 | central nervous system segmentation(GO:0035283) brain segmentation(GO:0035284) |
| 0.1 | 2.1 | GO:0035803 | binding of sperm to zona pellucida(GO:0007339) egg coat formation(GO:0035803) regulation of acrosome reaction(GO:0060046) positive regulation of acrosome reaction(GO:2000344) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 5.0 | GO:0000421 | autophagosome membrane(GO:0000421) |
| 0.0 | 5.0 | GO:0070160 | bicellular tight junction(GO:0005923) occluding junction(GO:0070160) |
| 0.0 | 4.9 | GO:0031234 | extrinsic component of cytoplasmic side of plasma membrane(GO:0031234) |
| 0.0 | 3.4 | GO:0005764 | lysosome(GO:0005764) |
| 0.1 | 3.2 | GO:0005685 | U1 snRNP(GO:0005685) |
| 0.1 | 3.2 | GO:0000307 | cyclin-dependent protein kinase holoenzyme complex(GO:0000307) |
| 0.1 | 2.6 | GO:0070971 | endoplasmic reticulum exit site(GO:0070971) |
| 0.1 | 2.6 | GO:0005680 | anaphase-promoting complex(GO:0005680) |
| 0.1 | 2.5 | GO:0044853 | caveola(GO:0005901) plasma membrane raft(GO:0044853) |
| 0.3 | 1.9 | GO:0005784 | Sec61 translocon complex(GO:0005784) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 5.7 | GO:0042802 | identical protein binding(GO:0042802) |
| 0.2 | 5.0 | GO:0032266 | phosphatidylinositol-3-phosphate binding(GO:0032266) |
| 0.0 | 4.8 | GO:0008083 | growth factor activity(GO:0008083) |
| 0.0 | 3.5 | GO:0004197 | cysteine-type endopeptidase activity(GO:0004197) |
| 0.0 | 3.5 | GO:0044822 | mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822) |
| 0.1 | 3.3 | GO:0016538 | cyclin-dependent protein serine/threonine kinase regulator activity(GO:0016538) |
| 0.4 | 3.2 | GO:0030619 | U1 snRNA binding(GO:0030619) |
| 0.0 | 3.1 | GO:0004715 | non-membrane spanning protein tyrosine kinase activity(GO:0004715) |
| 0.2 | 2.9 | GO:0030552 | cAMP binding(GO:0030552) |
| 0.6 | 2.8 | GO:0030169 | low-density lipoprotein particle binding(GO:0030169) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 5.1 | NABA SECRETED FACTORS | Genes encoding secreted soluble factors |
| 0.0 | 2.2 | PID FOXM1 PATHWAY | FOXM1 transcription factor network |
| 0.0 | 1.9 | PID P53 REGULATION PATHWAY | p53 pathway |
| 0.1 | 1.7 | PID IL12 STAT4 PATHWAY | IL12 signaling mediated by STAT4 |
| 0.1 | 1.7 | PID GLYPICAN 1PATHWAY | Glypican 1 network |
| 0.0 | 1.7 | PID AURORA B PATHWAY | Aurora B signaling |
| 0.0 | 1.5 | PID LKB1 PATHWAY | LKB1 signaling events |
| 0.1 | 1.4 | PID DNA PK PATHWAY | DNA-PK pathway in nonhomologous end joining |
| 0.0 | 1.2 | PID HDAC CLASSIII PATHWAY | Signaling events mediated by HDAC Class III |
| 0.0 | 1.0 | PID CDC42 REG PATHWAY | Regulation of CDC42 activity |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 3.2 | REACTOME MRNA SPLICING | Genes involved in mRNA Splicing |
| 0.2 | 2.8 | REACTOME HDL MEDIATED LIPID TRANSPORT | Genes involved in HDL-mediated lipid transport |
| 0.1 | 2.6 | REACTOME CONVERSION FROM APC C CDC20 TO APC C CDH1 IN LATE ANAPHASE | Genes involved in Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase |
| 0.1 | 2.3 | REACTOME SMOOTH MUSCLE CONTRACTION | Genes involved in Smooth Muscle Contraction |
| 0.1 | 2.0 | REACTOME CYCLIN A B1 ASSOCIATED EVENTS DURING G2 M TRANSITION | Genes involved in Cyclin A/B1 associated events during G2/M transition |
| 0.4 | 1.9 | REACTOME ACYL CHAIN REMODELLING OF PS | Genes involved in Acyl chain remodelling of PS |
| 0.2 | 1.7 | REACTOME SIGNALING BY NODAL | Genes involved in Signaling by NODAL |
| 0.0 | 1.4 | REACTOME REGULATION OF APOPTOSIS | Genes involved in Regulation of Apoptosis |
| 0.2 | 1.2 | REACTOME ETHANOL OXIDATION | Genes involved in Ethanol oxidation |
| 0.1 | 1.2 | REACTOME MITOCHONDRIAL FATTY ACID BETA OXIDATION | Genes involved in Mitochondrial Fatty Acid Beta-Oxidation |