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PRJNA207719: Tissue specific transcriptome profiling
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Results for rfx3_rfx2+rfx4
Z-value: 3.75
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Transcription factors associated with rfx3_rfx2+rfx4
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
| ENSDARG00000014550 | regulatory factor X, 3 (influences HLA class II expression) | |
| ENSDARG00000013575 | regulatory factor X, 2 (influences HLA class II expression) | |
| ENSDARG00000026395 | regulatory factor X, 4 | |
| ENSDARG00000116861 | regulatory factor X, 4 |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| rfx4 | dr11_v1_chr18_-_15373620_15373620 | 0.97 | 6.8e-03 | Click! |
| rfx3 | dr11_v1_chr10_-_625441_625441 | 0.97 | 6.8e-03 | Click! |
| rfx2 | dr11_v1_chr8_-_20138054_20138251 | 0.47 | 4.3e-01 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr24_-_205275 Show fit | 9.12 |
ENSDART00000108762
|
VOPP1, WBP1/VOPP1 family member |
|
| chr17_-_6759006 Show fit | 3.56 |
ENSDART00000184692
ENSDART00000180530 |
visinin-like 1b |
|
| chr21_+_26697536 Show fit | 3.07 |
ENSDART00000004109
|
guanine nucleotide binding protein (G protein), gamma 3 |
|
| chr19_-_103289 Show fit | 2.96 |
ENSDART00000143118
|
adhesion G protein-coupled receptor B1b |
|
| chr6_+_13933464 Show fit | 2.91 |
ENSDART00000109144
|
protein tyrosine phosphatase, receptor type, Nb |
|
| chr16_-_13662514 Show fit | 2.86 |
ENSDART00000146348
|
shisa family member 7a |
|
| chr19_-_9472893 Show fit | 2.79 |
ENSDART00000045565
ENSDART00000137505 |
vesicle-associated membrane protein 1 |
|
| chr5_-_23317477 Show fit | 2.71 |
ENSDART00000090171
|
neuroligin 3b |
|
| chr18_-_46763170 Show fit | 2.69 |
ENSDART00000171880
|
delta/notch-like EGF repeat containing |
|
| chr9_-_31747106 Show fit | 2.66 |
ENSDART00000048469
ENSDART00000145204 ENSDART00000186889 |
sodium leak channel, non-selective |
Network of associatons between targets according to the STRING database.
First level regulatory network of rfx3_rfx2+rfx4
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 6.6 | GO:0006470 | protein dephosphorylation(GO:0006470) |
| 0.0 | 5.7 | GO:0071804 | cellular potassium ion transport(GO:0071804) potassium ion transmembrane transport(GO:0071805) |
| 0.0 | 5.5 | GO:0007264 | small GTPase mediated signal transduction(GO:0007264) |
| 0.0 | 5.4 | GO:0000226 | microtubule cytoskeleton organization(GO:0000226) |
| 0.1 | 4.7 | GO:0007019 | microtubule depolymerization(GO:0007019) |
| 0.1 | 3.8 | GO:1903670 | regulation of sprouting angiogenesis(GO:1903670) |
| 0.3 | 3.2 | GO:0021631 | optic nerve morphogenesis(GO:0021631) |
| 0.5 | 3.1 | GO:0089700 | protein kinase D signaling(GO:0089700) regulation of lymphangiogenesis(GO:1901490) |
| 0.7 | 3.0 | GO:0090387 | phagosome maturation involved in apoptotic cell clearance(GO:0090386) phagolysosome assembly involved in apoptotic cell clearance(GO:0090387) |
| 0.3 | 2.9 | GO:0048172 | regulation of short-term neuronal synaptic plasticity(GO:0048172) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 9.6 | GO:0030659 | cytoplasmic vesicle membrane(GO:0030659) |
| 0.1 | 7.8 | GO:0043025 | neuronal cell body(GO:0043025) |
| 0.1 | 6.8 | GO:0030141 | secretory granule(GO:0030141) |
| 0.0 | 5.8 | GO:0045202 | synapse(GO:0045202) |
| 0.1 | 4.4 | GO:0099634 | postsynaptic density membrane(GO:0098839) postsynaptic specialization membrane(GO:0099634) |
| 0.0 | 4.3 | GO:0043235 | receptor complex(GO:0043235) |
| 0.0 | 4.2 | GO:0043005 | neuron projection(GO:0043005) |
| 0.1 | 3.6 | GO:0000159 | protein phosphatase type 2A complex(GO:0000159) |
| 0.2 | 3.1 | GO:0031680 | G-protein beta/gamma-subunit complex(GO:0031680) |
| 0.2 | 2.9 | GO:0032591 | dendritic spine membrane(GO:0032591) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 5.4 | GO:0003924 | GTPase activity(GO:0003924) |
| 0.0 | 5.1 | GO:0004725 | protein tyrosine phosphatase activity(GO:0004725) |
| 0.0 | 4.8 | GO:0030695 | GTPase regulator activity(GO:0030695) |
| 0.0 | 4.4 | GO:0015631 | tubulin binding(GO:0015631) |
| 0.1 | 3.8 | GO:0017075 | syntaxin-1 binding(GO:0017075) |
| 0.1 | 3.7 | GO:0005200 | structural constituent of cytoskeleton(GO:0005200) |
| 0.0 | 3.7 | GO:0019888 | protein phosphatase regulator activity(GO:0019888) |
| 0.1 | 3.2 | GO:0017124 | SH3 domain binding(GO:0017124) |
| 0.1 | 3.1 | GO:0031681 | G-protein beta-subunit binding(GO:0031681) |
| 0.1 | 3.1 | GO:0004697 | protein kinase C activity(GO:0004697) calcium-dependent protein kinase C activity(GO:0004698) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 3.1 | PID IGF1 PATHWAY | IGF1 pathway |
| 0.1 | 2.6 | PID IFNG PATHWAY | IFN-gamma pathway |
| 0.1 | 2.3 | PID ILK PATHWAY | Integrin-linked kinase signaling |
| 0.1 | 1.7 | ST DIFFERENTIATION PATHWAY IN PC12 CELLS | Differentiation Pathway in PC12 Cells; this is a specific case of PAC1 Receptor Pathway. |
| 0.0 | 1.4 | PID RHOA REG PATHWAY | Regulation of RhoA activity |
| 0.0 | 1.2 | PID IL12 2PATHWAY | IL12-mediated signaling events |
| 0.0 | 0.8 | PID FRA PATHWAY | Validated transcriptional targets of AP1 family members Fra1 and Fra2 |
| 0.0 | 0.6 | ST INTEGRIN SIGNALING PATHWAY | Integrin Signaling Pathway |
| 0.0 | 0.5 | PID LIS1 PATHWAY | Lissencephaly gene (LIS1) in neuronal migration and development |
| 0.0 | 0.5 | PID FGF PATHWAY | FGF signaling pathway |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 4.5 | REACTOME PROTEOLYTIC CLEAVAGE OF SNARE COMPLEX PROTEINS | Genes involved in Proteolytic cleavage of SNARE complex proteins |
| 0.2 | 3.1 | REACTOME THROMBOXANE SIGNALLING THROUGH TP RECEPTOR | Genes involved in Thromboxane signalling through TP receptor |
| 0.1 | 3.1 | REACTOME SPHINGOLIPID DE NOVO BIOSYNTHESIS | Genes involved in Sphingolipid de novo biosynthesis |
| 0.9 | 2.6 | REACTOME CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF CAMKII | Genes involved in CREB phosphorylation through the activation of CaMKII |
| 0.0 | 2.5 | REACTOME ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION | Genes involved in Antigen processing: Ubiquitination & Proteasome degradation |
| 0.1 | 2.0 | REACTOME VOLTAGE GATED POTASSIUM CHANNELS | Genes involved in Voltage gated Potassium channels |
| 0.0 | 2.0 | REACTOME FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION | Genes involved in Factors involved in megakaryocyte development and platelet production |
| 0.1 | 1.8 | REACTOME SYNTHESIS OF GLYCOSYLPHOSPHATIDYLINOSITOL GPI | Genes involved in Synthesis of glycosylphosphatidylinositol (GPI) |
| 0.1 | 1.7 | REACTOME POST CHAPERONIN TUBULIN FOLDING PATHWAY | Genes involved in Post-chaperonin tubulin folding pathway |
| 0.1 | 1.7 | REACTOME ACTIVATED NOTCH1 TRANSMITS SIGNAL TO THE NUCLEUS | Genes involved in Activated NOTCH1 Transmits Signal to the Nucleus |