Question

Is there a method to group and summarize the `homer` `findMotifsGenome.pl` output?

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22 months ago

Dan ▴ 180

Hello:

Is there a method to group and summarize the homer findMotifsGenome.pl output (http://homer.ucsd.edu/homer/ngs/peakMotifs.html )? enter image description here

There are a lot of duplicates in the AP1 family TFs. I want to group all the TFs belonging to a family. Thanks.

Motif-analysis • 905 views

ADD COMMENT • link 21 months ago by Dan ▴ 180

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Can you give an example of how the output should look like?

ADD REPLY • link 22 months ago by ATpoint 85k

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I would like to group all the Motifs with a TGAC(G)TCA core pattern together and name it AP-1 family. Is there a tool for this purpose? Thanks

ADD REPLY • link 21 months ago by Dan ▴ 180

score 2 · Accepted Answer · 2023-01-31

Don't know if there is a specific tool for this, but using your eyes should be sufficient to match similar sequence logos.

For example, Bach has a unique sequence from all others. Fra1 and Fra2 have similar sequence to Fos. Atf3 is similar to JunB, FosL2 and Jun-AP1. Not shown in your screenshot (but possibly present in the total output) are Maf proteins, as they also bind to an extended AP-1 site, either as homo-dimers, or hetero-dimers with various partners (often Bach). AP-1 is a subset of all of the other sites listed, so my general conclusion would be that you have an AP-1 site.

Chances are that all the listed proteins bind to this site either as homo- or hetero-dimers, but experiments would be needed to figure out which combination is physiologically relevant.