Best tool for Motif enrichment of TFs

Question

[lucatucciarone]

Hello, I'm currently using Homer "AnnotatePeaks.pl" to have this data. Would you suggest other tools?

Answer 1

[ATpoint]

Assuming you have a genomic regions from an NGS experiment, aiming to find overrepresented motifs in them, the standard tools are either Homer findMotifsGenome.pl/findMotifs.pl or MEME-CHIP from the MEME suite. Both have extensive documentation and threads covering these can be found on Biostars using the search fucntion.

Answer 2

[ResearchR]

Maybe this helps:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702883/

Answer 3

[simon.vanheeringen]

Try GimmeMotifs! You can scan for known motifs, or identify de novo motifs. Amongst many other tools, both MEME and homer are included as de novo motif finding tools.

Answer 4

[Charles Warden]

I don't think there is exactly one "best" motif prediction tool, but checking the results for a few programs may be useful.

I've sometimes found i-cisTarget and HOMER to be a good combination, but you could also try some of the tools from the MEME Suite (such as meme-chip, web-based or command line).

Answer 5

[ahmad mousavi]

Hi

enrichR has a good tool for showing relation among genes and TFs, it worth to try it. It has variety of tools, but you could find relative information on ChEA.

Also, some years ago I have tried MatInsepctor in Genomatix online software. It was not free but it works for some days trial. It ranks the TF candidate targets.

Answer 6

[lucatucciarone]

Thanks everyone guys! I'll surely try out your tools but my question was little bit different. I am interested in the understanding if a particular TF motif is enriched in a subset of Gene's promoters. I've tried to run homer "for an unbiased approach" but I'd like a tool that actually tells me: YES, this particular motif is statistically in your promoters. Any ideas?

[simon.vanheeringen]

Yes. The subtool gimme roc from GimmeMotifs can do this (as can Homer and many other tools). For GimmeMotifs, you can install it via bioconda and run the following command:

$ gimme roc subset.fa all_promoter.fa -r roc.report

Here subset.fa are your promoters of interest and all_promoters.fa are (a random selection of) all other promoters as background. The output directory roc.report will contain an html file with a report.

[lucatucciarone]

So good! Gonna try this and come back to you : )