Chipseq Motif In Set Of Genes
1
1
Entering edit mode
9.2 years ago
Honey ▴ 200

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.

chipseq motif • 2.2k views
ADD COMMENT
1
Entering edit mode
9.2 years ago
Ido Tamir 5.2k

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1223 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6