Chipseq Motif In Set Of Genes

Question

[Honey]

I have a Chip-seq data and have identified a motif de-novo in MEME (http://meme.nbcr.net/meme/doc/meme-chip.html), I also have a list of genes from Chipseq data which are (promoters) get enriched. Obviously this list of genes is derived from Coordinates where peaks are detected. Now what I would like to find out is- 1. take one de-novo motif and find out which gene/s have that motif from the set of cell death genes (50 or so). This subset of genes were identified by pathway analysis from enriched coordinates of Chip-seq experiment.

Answer 1

[Ido Tamir]

get the sequence of the genes including up and downstream sequences. Then enter these sequences + your motif into http://meme.nbcr.net/meme/cgi-bin/fimo.cgi But you should have some background model also.