Question: Best tool for Motif enrichment of TFs
0
gravatar for lucatucciarone
21 months ago by
lucatucciarone50 wrote:

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

bash rna-seq chip-seq R • 1.2k views
ADD COMMENTlink modified 21 months ago • written 21 months ago by lucatucciarone50
1
gravatar for ATpoint
21 months ago by
ATpoint36k
Germany
ATpoint36k wrote:

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.

ADD COMMENTlink written 21 months ago by ATpoint36k
0
gravatar for ResearchR
21 months ago by
ResearchR70
ResearchR70 wrote:

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

ADD COMMENTlink written 21 months ago by ResearchR70
0
gravatar for simon.vanheeringen
21 months ago by
simon.vanheeringen200 wrote:

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.

ADD COMMENTlink written 21 months ago by simon.vanheeringen200
0
gravatar for Charles Warden
21 months ago by
Charles Warden7.8k
Duarte, CA
Charles Warden7.8k wrote:

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).

ADD COMMENTlink modified 21 months ago • written 21 months ago by Charles Warden7.8k
0
gravatar for ahmad mousavi
21 months ago by
ahmad mousavi480
Royan Institute, Tehran, Iran
ahmad mousavi480 wrote:

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.

ADD COMMENTlink written 21 months ago by ahmad mousavi480
0
gravatar for lucatucciarone
21 months ago by
lucatucciarone50 wrote:

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?

ADD COMMENTlink written 21 months ago by lucatucciarone50

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.

ADD REPLYlink written 20 months ago by simon.vanheeringen200

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

ADD REPLYlink written 20 months ago by lucatucciarone50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1553 users visited in the last hour