Obtaining transcription factors from DNA consensus motif

Question

[drautuna]

Hello all,

I had some variant sites which were allele specifically expressed, so I took those sites and got the surrounding sequences around them and ran them through MEME in MEME Suite to find a common motif at those sites. Now that I've found motif(s) through the MEME output, I'm trying to see what known transcription factors would bind at the motifs. What kind of program would I use for this? This is in the human genome, by the way.

Thanks

[komal.rathi]

You need to run FIMO (part of MEME suite) for this.

Answer 1

[ATpoint]

Refreshing this in 2019: fimo is not the choice here as it scans individual sequences for motif occurrence. You want to match motifs to a database, which is why tomtom from the MEME-suite is the choice here:

tomtom [options] <query motif file> <target motif file>+

The <query motif file> is a motif file in MEME format and the <target motif file>+ are known motif file to compare your motifs against. This can be obtained e.g. from the download sections of HOCOMOCO or JASPAR. Both provide them in MEME format already. In case of JASPAR you can download the individial motif files and simply concatenate them using cat into one big motif file. tomtom will then spill out all motifs that significantly resemble your <query motif file>. You might want to lower the default significance threshold from tomtom to be a bit more stringent than the default of 0.5. Output Uamong others) is a html file with the results that can be opened conveniently in any web browser.