Can I use AME - Analysis of Motif Enrichment - for RNA-Seq data?

Question

[Chris Gene]

Hi all. I have a list of differentially expressed genes from a mouse RNA-Seq experiment, where I looked at the knock down from a putative transcription factor that is not in any of the databases (JASPAR, uniprobe).

I want to know whether they are enriched for transcription factor binding sites. Is AME - Analysis of Motif Enrichment - good for this? I have used it through the MEME suite online installation. Is there another algorithm that would be more suited for RNA-Seq data rather than ChIP?

Thanks!

Answer 1

[ivivek_ngs]

There are plenty , MEME takes a lot of time so others are well justified. You can use HOMER motif analysis or pScan. These tools usually takes input as user supplied gene list or rather say refseq ids with a user define promoter window and try to find consensus TF binding sites on the genes. Ideally it should be done direction based if RNA-Seq DEGs are used. This is enable you to understand what known motifs are there in your DEGs and what upstream TFs are in fact controlling your DEGs for a co-regulation or co-binding thus resulting in a some biological effect. HOMER also does de novo motif discovery but I have not tried that.