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

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
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written by Dan • Dan

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

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written by ATpoint ATpoint

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

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written by Dan • Dan

1 answer

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.

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written by Mensur Dlakic Mensur Dlakic

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