Question: Genome-Wide Motif Genomic Regions For Tfs
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gravatar for J.F.Jiang
7.3 years ago by
J.F.Jiang850
China
J.F.Jiang850 wrote:

Hi all, I am interested in the motif region for TFs in genome-wide. The ChiP-Seq data can directly told us the peak region for TF. However, I still want to know whether the binding region is within the TF motif region. Traditionally, we use TRANSFAC, JASPAR to calculate the motif enrichment, but these two database only offer the prediction matrix for calculation, but without the genomic region for all motifs.

So I am looking for public motif files in bed format, e.g., chr, start, end, TFsymbol. If anyone knows how to get the data, please kindly tell me.

Thanks.

motif • 2.0k views
ADD COMMENTlink modified 7.3 years ago by vj450 • written 7.3 years ago by J.F.Jiang850
0
gravatar for Alex Reynolds
7.3 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

You could use your matrices with FIMO to locate the genomic regions where motif hits are found.

ADD COMMENTlink written 7.3 years ago by Alex Reynolds31k
0
gravatar for vj
7.3 years ago by
vj450
UK
vj450 wrote:

You can look at HOMER where they have given genome-wide predictions of motif positions. It is present in the link I have provided, near the end of the web page.

ADD COMMENTlink modified 7.3 years ago • written 7.3 years ago by vj450
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