Question: Chipseq Motif In Set Of Genes
1
gravatar for Honey
5.8 years ago by
Honey200
Honey200 wrote:

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 • 1.5k views
ADD COMMENTlink modified 2.3 years ago by Biostar ♦♦ 20 • written 5.8 years ago by Honey200
1
gravatar for Ido Tamir
5.8 years ago by
Ido Tamir5.0k
Austria
Ido Tamir5.0k wrote:

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 COMMENTlink written 5.8 years ago by Ido Tamir5.0k
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