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?