Finding motifs in 5' of genes

[tamari]

Hi,

I have a list of differentially expressed genes that I would like to search for a 5' utr motif in them.
What tool would you suggest to use or is there some kind of pipeline?

Thanks in advance,
Tamari

[simonandrews]

I guess our workflow for this would be to use BioMart to pull out the UTR sequences and then use xxmotif to do the motif detection.

You'll need to be careful about what you use as a control set of sequences for this analysis. We'd probably use a set of 5'UTRs from genes which were reasonably well expressed in your experimental system but which didn't change. Just doing a blind motif detection will likely find many spurious matches.

[sphil]

Extract 5' UTR of your genes and there are several tools you can use:
I usually use MEME but there are plenty more, see this Biostar discussion: Motif Finding / Biostar