How to find enhancer for tss-promoter

[JennyHu]

Hi all,
Now I got the location of a TSS-promoter for one gene.
chr1 :198906525 - 198906959

And I want to use the Homer to find enhancers for this promoter.

Finding Super Enhancers using Homer:
$ findPeaks <tag directory> -i <input tag directory> -style super -o auto

I can using makeTagDirectory to get the <input tag directory> from alignment as follows:
makeTagDirectory Test/ 31513_TH0.rmdup.bam

But I don't know how to get the "tag directory", I try:
makeTagDirectory Promoter/ TSS.bed

In the TSS.bed, only one location of the TSS :
chr11 198906525 198906959

My question is how to get the TSS tag directory, please?

Best,
Jenny

[jerryschen]

Hi Jenny,
From my understanding, HOMER findPeaks identifies transcription factor binding sites given a ChIP-SEQ dataset as input. The "super enhancers" option simply identifies those regions that are dense with lots of TF binding sites. What you are trying to do - that is, find those enhancers that associate with a given TSS-promoter is not done using findPeaks. Usually promoter-associated enhancers are discovered with techniques such as Hi-C/3C (chromatin conformation capture).

As far as the tag directory, you just do the following:
$ makeTagDirectory [myDirectory] [my BAM file]
$ findPeaks [myDirectory/] -options > myOutputFile.bed

Hope that helps!
-Jerry
------------------------------------------------
Jerry Chen, Ph.D.
Bioinformatics Scientist
Encoded Genomics, Inc.

[JennyHu]

Enhancer prediction software tools

Hi Jerry,
Thanks for you reply.You know, I want to predict the enhancers of a given TSS-promoter, and then check them in the wet lab.
I think the promoter is a regions with lots of TF binding sites , and not the enhancer is. But the enhancer will help TSS-promoter to binding TFs.

BTW, if the HOMER can't get the enhancers' location, how to get them by bioinformatic method.
I found some enhancer prediction software tools form this link :
http://omictools.com/enhancer-prediction-c1691-p1.html . Which one do you think it's best one, please?

Thanks,
Jenny
Postdoc in the Stanford U.

[jerryschen]

Hi Jenny,
I work with promoter-enhancer interactions as well, but I actually haven't done any research on any good bioinformatics tools for finding enhancers associated with a given promoter. If any of the ones you listed or other ones are good, please let me know - thanks!

-Jerry
--------------------------------------------------------
Jerry Chen, Ph.D.
Bioinformatics Scientist, Encoded Genomics Inc.

[JennyHu]

Ok, thanks Jerry.