How to validate meme's suite results

[Gonzalo Sepulveda]

Hi to everyone, i was wondering if there is any standard way to validate the results obtained by meme's suite. 

In particular, first i used MEME to define some TFBS  (properly validated with TOMTOM against JASPAR) and then search them against a custom database of promoter regions with FIMO.

So my question, there is a common way to validate those results? rather than discriminating by q-value?

i was thinking a sort of cross-validation by performing a similar search against another organism (maybe like A. thaliana) where the TFBS where already described, but i'm not quite sure if this is correct.

Any help would be very appreciated

Best regards!

[CharlesEGrant]

What is it you are trying to validate? If you are just trying to validate that the tools are generating reasonably calibrated p-values, you could shuffle your sequence and re-scan it, or re-scan it with motifs where the frequencies in each position have been shuffled. Presumably the motif matches from the shuffled sequence or motif won't score nearly as high as your original matches.

Unfortunately the underlying problem is that even a perfect match to a motif doesn't guarantee that a motif occurrence is biologically active. The posting FIMO returns no results when scanning large genomes may be of interest to you.

If you want to verify that motif occurrences found by MEME Suite are biologically active you may want to look at DNase I hypersensitivity data or ChIP-Seq experiments.