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Question: retrieve genes near enhancers
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gravatar for doublehelixlf
3.1 years ago by
United States
doublehelixlf10 wrote:

We have done a number of ChIP-seq experiments and now have coordinates for a list of enhancers. The next question is what genes are potentially regulated by these enhancers. To get a quick idea, we wish to retrieve 5 genes flanking each of these enhancers, and then perform some GO and GSEA analyses. Can anyone recommend some package(s) that would be a good start to retrieve the genes? Thanks!

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by doublehelixlf10
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gravatar for Guangchuang Yu
3.1 years ago by
Guangchuang Yu1.0k
Hong Kong
Guangchuang Yu1.0k wrote:

You can use ChIPseeker, which can annotate genomic coordinates with all genes within specific flanking distance, see http://ygc.name/2014/10/01/multiple-annotation-in-chipseeker/. All corresponding distances of the flanking genes listed will also reported. You can use the distance to select 5 genes that are mostly closest.

 

For more detail, please refer to the online vignette, http://www.bioconductor.org/packages/3.2/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html

 

ADD COMMENTlink written 3.1 years ago by Guangchuang Yu1.0k
0
gravatar for doublehelixlf
3.1 years ago by
United States
doublehelixlf10 wrote:

Thanks Guangchuang! Will try it out.

ADD COMMENTlink written 3.1 years ago by doublehelixlf10
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