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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for lhx2b+lhx9
Z-value: 1.03
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Transcription factors associated with lhx2b+lhx9
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| lhx9 | dr11_v1_chr22_-_23253252_23253252 | -0.77 | 1.8e-04 | Click! |
| lhx2b | dr11_v1_chr8_+_3085120_3085219 | -0.73 | 5.5e-04 | Click! |
Network of associatons between targets according to the STRING database.
First level regulatory network of lhx2b+lhx9
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 7.3 | GO:0018230 | peptidyl-L-cysteine S-palmitoylation(GO:0018230) peptidyl-S-diacylglycerol-L-cysteine biosynthetic process from peptidyl-cysteine(GO:0018231) |
| 0.0 | 5.7 | GO:0043413 | protein glycosylation(GO:0006486) macromolecule glycosylation(GO:0043413) |
| 1.6 | 4.7 | GO:0034154 | toll-like receptor 7 signaling pathway(GO:0034154) |
| 0.8 | 3.8 | GO:0006700 | C21-steroid hormone biosynthetic process(GO:0006700) |
| 0.6 | 3.1 | GO:0016338 | calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules(GO:0016338) |
| 0.0 | 3.1 | GO:0030917 | midbrain-hindbrain boundary development(GO:0030917) |
| 0.3 | 2.9 | GO:0006622 | protein targeting to lysosome(GO:0006622) |
| 0.1 | 2.9 | GO:0016233 | telomere capping(GO:0016233) |
| 0.1 | 2.7 | GO:0000079 | regulation of cyclin-dependent protein serine/threonine kinase activity(GO:0000079) regulation of cyclin-dependent protein kinase activity(GO:1904029) |
| 0.3 | 2.6 | GO:0072383 | plus-end-directed vesicle transport along microtubule(GO:0072383) plus-end-directed organelle transport along microtubule(GO:0072386) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 10.8 | GO:0005794 | Golgi apparatus(GO:0005794) |
| 0.0 | 4.7 | GO:0070160 | bicellular tight junction(GO:0005923) occluding junction(GO:0070160) |
| 0.0 | 4.0 | GO:0005871 | kinesin complex(GO:0005871) |
| 0.0 | 3.2 | GO:0005834 | heterotrimeric G-protein complex(GO:0005834) |
| 0.1 | 3.0 | GO:0010494 | cytoplasmic stress granule(GO:0010494) |
| 1.0 | 2.9 | GO:0031310 | integral component of vacuolar membrane(GO:0031166) intrinsic component of vacuolar membrane(GO:0031310) |
| 0.9 | 2.7 | GO:0097124 | cyclin A2-CDK2 complex(GO:0097124) |
| 0.0 | 2.2 | GO:0005681 | spliceosomal complex(GO:0005681) |
| 0.1 | 2.0 | GO:0032588 | trans-Golgi network membrane(GO:0032588) |
| 0.0 | 1.9 | GO:0005942 | phosphatidylinositol 3-kinase complex(GO:0005942) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 7.3 | GO:0019707 | protein-cysteine S-palmitoyltransferase activity(GO:0019706) protein-cysteine S-acyltransferase activity(GO:0019707) |
| 0.1 | 6.3 | GO:0003727 | single-stranded RNA binding(GO:0003727) |
| 0.0 | 3.9 | GO:0003729 | mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822) |
| 1.3 | 3.8 | GO:0016713 | cholesterol monooxygenase (side-chain-cleaving) activity(GO:0008386) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen(GO:0016713) |
| 0.0 | 3.7 | GO:0004879 | RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding(GO:0004879) |
| 0.5 | 3.6 | GO:0008118 | N-acetyllactosaminide alpha-2,3-sialyltransferase activity(GO:0008118) |
| 0.1 | 3.4 | GO:0005044 | scavenger receptor activity(GO:0005044) |
| 0.2 | 3.0 | GO:0008266 | poly(U) RNA binding(GO:0008266) |
| 0.0 | 3.0 | GO:0042802 | identical protein binding(GO:0042802) |
| 0.0 | 2.8 | GO:0008083 | growth factor activity(GO:0008083) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 4.1 | PID HDAC CLASSI PATHWAY | Signaling events mediated by HDAC Class I |
| 0.1 | 3.4 | PID AURORA B PATHWAY | Aurora B signaling |
| 0.0 | 2.8 | NABA SECRETED FACTORS | Genes encoding secreted soluble factors |
| 0.2 | 2.7 | SA REG CASCADE OF CYCLIN EXPR | Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases. |
| 0.1 | 2.0 | PID FOXM1 PATHWAY | FOXM1 transcription factor network |
| 0.0 | 1.8 | PID ECADHERIN STABILIZATION PATHWAY | Stabilization and expansion of the E-cadherin adherens junction |
| 0.0 | 1.5 | NABA ECM AFFILIATED | Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins |
| 0.0 | 1.4 | PID TELOMERASE PATHWAY | Regulation of Telomerase |
| 0.0 | 1.3 | PID BARD1 PATHWAY | BARD1 signaling events |
| 0.0 | 1.1 | PID IL3 PATHWAY | IL3-mediated signaling events |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 4.7 | REACTOME TRAFFICKING AND PROCESSING OF ENDOSOMAL TLR | Genes involved in Trafficking and processing of endosomal TLR |
| 0.4 | 3.8 | REACTOME ENDOGENOUS STEROLS | Genes involved in Endogenous sterols |
| 0.2 | 2.7 | REACTOME CYCLIN A B1 ASSOCIATED EVENTS DURING G2 M TRANSITION | Genes involved in Cyclin A/B1 associated events during G2/M transition |
| 0.0 | 2.5 | REACTOME FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION | Genes involved in Factors involved in megakaryocyte development and platelet production |
| 0.0 | 2.4 | REACTOME RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2 | Genes involved in Response to elevated platelet cytosolic Ca2+ |
| 0.1 | 2.1 | REACTOME SYNTHESIS OF GLYCOSYLPHOSPHATIDYLINOSITOL GPI | Genes involved in Synthesis of glycosylphosphatidylinositol (GPI) |
| 0.1 | 2.0 | REACTOME RESOLUTION OF AP SITES VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY | Genes involved in Resolution of AP sites via the single-nucleotide replacement pathway |
| 0.1 | 1.9 | REACTOME SYNTHESIS OF PIPS AT THE PLASMA MEMBRANE | Genes involved in Synthesis of PIPs at the plasma membrane |
| 0.0 | 1.8 | REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION | Genes involved in NOTCH1 Intracellular Domain Regulates Transcription |
| 0.1 | 1.5 | REACTOME SEMA4D INDUCED CELL MIGRATION AND GROWTH CONE COLLAPSE | Genes involved in Sema4D induced cell migration and growth-cone collapse |