enhancer annotation for mouse mm9

Question

[tonja.r]

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?

Answer 1

[Ryan Dale]

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.

Answer 2

[predeus]

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NB: I would not use mm9 - it is very outdated by now.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

[Ryan Dale]

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.