Question: enhancer annotation for mouse mm9
gravatar for tonja.r
5.1 years ago by
tonja.r470 wrote:

I found a promoter, gene body, transcript, exons annotation via TxDb.Mmusculus.UCSC.mm9.knownGene with Bioconductor but they do not have enhancer regions. Where can I find enhancer region annotation for mm9? 

genome • 4.0k views
ADD COMMENTlink modified 5.1 years ago by Ryan Dale4.9k • written 5.1 years ago by tonja.r470
gravatar for Ryan Dale
5.1 years ago by
Ryan Dale4.9k
Bethesda, MD
Ryan Dale4.9k wrote:

The Ren lab has called enhancer data which you can download as zip files.

See this related answer for info on downloading ChromHMM tracks from UCSC and experimentally validated enhancers from the VISTA enhancer browser.

Depending on the cell/tissue type you're interested in, you may have to call your own enhancers. Here's an example of how to do that for MEL cells.

ADD COMMENTlink written 5.1 years ago by Ryan Dale4.9k
gravatar for predeus
5.1 years ago by
predeus1.4k wrote:

Enhancer annotation is not really that universal because they differ so much between cell types. 

What people usually mean by "enhancer annotation" is the union of all H3K4me1 peaks for many different cell lines and/or tissues. 

I would look for mouseENCODE papers and see if they published such track. If not, you can make it yourself quite easily using bedtools. 

NB: I would not use mm9 - it is very outdated by now. I recommend Gencode vM6 annotation and the appropriate genome assembly. 

Good luck

ADD COMMENTlink written 5.1 years ago by predeus1.4k

I would love to use mm9 . . . but most mouse ENCODE data is not available for mm10 as far as I know. Rather than re-map and/or liftOver everything, I tend to use mm9 for projects that need to compare with those data. 

ADD REPLYlink written 5.1 years ago by Ryan Dale4.9k
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