Genome-Wide Motif Genomic Regions For Tfs

Question

[J.F.Jiang]

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.

Answer 1

[Alex Reynolds]

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

Answer 2

[vj]

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.