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ENCODE: ATAC-seq of different tissues during embryonic development
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CREMA is a free online tool that recognizes most
important transcription factors that change the chromatin
state across different samples.
Results for Foxf1
Z-value: 3.68
Motif logo
Correlations of motif activity and signal intensity at CREs associated with the motif's TFs:
This plot shows correlation between observed signal intensity of a CRE associated with the transcription factor across all samples and activity of the motif.
For each TF, only the top 5 correlated CREs are shown.
| CRE | Gene | Distance | Association probability | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|---|---|
| Foxf1 | chr8_121083687_121083870 | 608 | 0.358926 | 0.82 | 2.4e-14 | Click! |
| Foxf1 | chr8_121084168_121084657 | 26 | 0.791052 | 0.80 | 3.5e-13 | Click! |
| Foxf1 | chr8_121083930_121084161 | 341 | 0.598551 | 0.77 | 6.6e-12 | Click! |
Showing 1 to 3 of 3 entries
Top target CREs of the motif:
| Cis Regulatory Element (CRE) | Target Score | Top associated gene | Gene Info | Distance of CRE to TSS | CRE/Gene association probability |
|---|---|---|---|---|---|
| chr1_162037946_162038745 | 22.41 |
2810442N19Rik |
RIKEN cDNA 2810442N19 gene |
33173 |
0.12 |
| chr10_111696233_111696479 | 16.19 |
Gm30624 |
predicted gene, 30624 |
28828 |
0.14 |
| chr13_81089992_81090512 | 15.79 |
Gm18517 |
predicted gene, 18517 |
2688 |
0.21 |
| chr12_79674954_79675872 | 14.52 |
9430078K24Rik |
RIKEN cDNA 9430078K24 gene |
249320 |
0.02 |
| chr8_19707145_19707732 | 13.96 |
Gm7760 |
predicted gene 7760 |
4267 |
0.18 |
| chr9_48723467_48723688 | 13.56 |
Zbtb16 |
zinc finger and BTB domain containing 16 |
112368 |
0.06 |
| chr10_9549977_9550305 | 13.03 |
Gm48755 |
predicted gene, 48755 |
2620 |
0.19 |
| chr4_108092707_108093041 | 12.61 |
Podn |
podocan |
3571 |
0.17 |
| chr5_143992575_143993038 | 12.37 |
Ccz1 |
CCZ1 vacuolar protein trafficking and biogenesis associated |
222 |
0.89 |
| chr2_178454797_178455512 | 11.83 |
Cdh26 |
cadherin-like 26 |
5476 |
0.22 |
Histogram of CRE-TSS distances for CREs targeted by :
Rank distribution of CRE target scores:
Distribution of target CREs across different genomic regions:
Network of associatons between targets according to the STRING database.
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 4.2 | 12.7 | GO:0061470 | T follicular helper cell differentiation(GO:0061470) |
| 1.6 | 11.5 | GO:0021942 | radial glia guided migration of Purkinje cell(GO:0021942) |
| 1.0 | 11.4 | GO:0032060 | bleb assembly(GO:0032060) |
| 1.5 | 10.6 | GO:0045602 | negative regulation of endothelial cell differentiation(GO:0045602) |
| 1.5 | 10.2 | GO:0014745 | negative regulation of muscle adaptation(GO:0014745) |
| 0.3 | 10.0 | GO:0032233 | positive regulation of actin filament bundle assembly(GO:0032233) |
| 0.2 | 9.9 | GO:0031532 | actin cytoskeleton reorganization(GO:0031532) |
| 1.0 | 9.2 | GO:0060391 | positive regulation of SMAD protein import into nucleus(GO:0060391) |
| 3.0 | 9.1 | GO:0010908 | regulation of heparan sulfate proteoglycan biosynthetic process(GO:0010908) positive regulation of heparan sulfate proteoglycan biosynthetic process(GO:0010909) positive regulation of proteoglycan biosynthetic process(GO:1902730) |
| 1.8 | 9.1 | GO:1900227 | positive regulation of NLRP3 inflammasome complex assembly(GO:1900227) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 48.4 | GO:0005924 | cell-substrate adherens junction(GO:0005924) focal adhesion(GO:0005925) |
| 0.5 | 31.0 | GO:0097517 | stress fiber(GO:0001725) contractile actin filament bundle(GO:0097517) |
| 0.1 | 23.5 | GO:0005578 | proteinaceous extracellular matrix(GO:0005578) |
| 0.5 | 16.4 | GO:0016235 | aggresome(GO:0016235) |
| 0.1 | 16.1 | GO:0015629 | actin cytoskeleton(GO:0015629) |
| 0.3 | 15.8 | GO:0005581 | collagen trimer(GO:0005581) |
| 0.1 | 14.8 | GO:0005667 | transcription factor complex(GO:0005667) |
| 0.1 | 13.2 | GO:0005789 | endoplasmic reticulum membrane(GO:0005789) |
| 0.1 | 11.6 | GO:0045177 | apical part of cell(GO:0045177) |
| 0.0 | 11.6 | GO:0005829 | cytosol(GO:0005829) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 44.0 | GO:0003779 | actin binding(GO:0003779) |
| 0.2 | 23.0 | GO:0017124 | SH3 domain binding(GO:0017124) |
| 0.4 | 19.7 | GO:0005518 | collagen binding(GO:0005518) |
| 0.2 | 14.2 | GO:0003705 | transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding(GO:0003705) |
| 0.2 | 14.0 | GO:0005178 | integrin binding(GO:0005178) |
| 0.2 | 12.8 | GO:0004714 | transmembrane receptor protein tyrosine kinase activity(GO:0004714) |
| 0.2 | 12.1 | GO:0005089 | Rho guanyl-nucleotide exchange factor activity(GO:0005089) |
| 0.1 | 12.0 | GO:0004867 | serine-type endopeptidase inhibitor activity(GO:0004867) |
| 0.1 | 11.8 | GO:0005096 | GTPase activator activity(GO:0005096) |
| 0.3 | 10.2 | GO:0033613 | activating transcription factor binding(GO:0033613) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.5 | 22.9 | PID RHOA REG PATHWAY | Regulation of RhoA activity |
| 0.3 | 20.0 | PID AP1 PATHWAY | AP-1 transcription factor network |
| 0.7 | 16.5 | PID INTEGRIN A9B1 PATHWAY | Alpha9 beta1 integrin signaling events |
| 0.4 | 14.3 | PID SYNDECAN 1 PATHWAY | Syndecan-1-mediated signaling events |
| 0.1 | 14.1 | NABA ECM GLYCOPROTEINS | Genes encoding structural ECM glycoproteins |
| 0.1 | 12.1 | NABA ECM REGULATORS | Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix |
| 0.3 | 11.8 | PID AJDISS 2PATHWAY | Posttranslational regulation of adherens junction stability and dissassembly |
| 0.3 | 11.1 | PID TGFBR PATHWAY | TGF-beta receptor signaling |
| 0.4 | 9.6 | PID ALK1 PATHWAY | ALK1 signaling events |
| 0.5 | 9.1 | ST WNT CA2 CYCLIC GMP PATHWAY | Wnt/Ca2+/cyclic GMP signaling. |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 18.4 | REACTOME SIGNALING BY RHO GTPASES | Genes involved in Signaling by Rho GTPases |
| 0.5 | 15.9 | REACTOME AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE | Genes involved in Amino acid transport across the plasma membrane |
| 0.1 | 14.0 | REACTOME G ALPHA Q SIGNALLING EVENTS | Genes involved in G alpha (q) signalling events |
| 0.2 | 12.8 | REACTOME COLLAGEN FORMATION | Genes involved in Collagen formation |
| 0.9 | 12.3 | REACTOME DCC MEDIATED ATTRACTIVE SIGNALING | Genes involved in DCC mediated attractive signaling |
| 0.5 | 12.0 | REACTOME SMOOTH MUSCLE CONTRACTION | Genes involved in Smooth Muscle Contraction |
| 0.3 | 11.3 | REACTOME INTERFERON GAMMA SIGNALING | Genes involved in Interferon gamma signaling |
| 0.3 | 10.4 | REACTOME BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION | Genes involved in BMAL1:CLOCK/NPAS2 Activates Circadian Expression |
| 0.4 | 10.2 | REACTOME SEMA4D IN SEMAPHORIN SIGNALING | Genes involved in Sema4D in semaphorin signaling |
| 0.1 | 9.7 | REACTOME NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX | Genes involved in Nonsense Mediated Decay Enhanced by the Exon Junction Complex |