Motif finding using MEME

[sphil]

Hey guys,

i made an RNA-seq experiment under three conditions with 4 replicates each. After quantifying my counts I isolated several cluster of genes which seem to be regulated the same way condition wise. Now, to get a first hint, I used MEME to find common motifs in the upstream promotor regions of those genes. Unfortunately, it does not give the desired results . But it indicates that there is something in common. Do you know any other tool finding motifs while measuring statistical significance? Also is it possible to detect multiple occurences of those motifs inside the upstream region since this is a possibility too.

Thanks in advance!


Best

Phil

[GenoMax]

http://genie.dartmouth.edu/scope/

http://www.motifsearch.com/

[sphil]

thank you!