issue with VISTA enhancer database

Question

[noushin.farnoud]

Dear BioStars,

I want to download the list of candidate enhancer for mouse from VISTA database. As you can see in the link below, the presented list also includes the flanking gene information: http://enhancer.lbl.gov/cgi-bin/imagedb3.pl?show=1;page=1;form=search;search.form=no;page_size=100;search.result=yes;order=mm;action=search

However, when I click on the "download data" link, somehow the gene information is lost! http://enhancer.lbl.gov/cgi-bin/imagedb3.pl?show=1;page=1;form=search;search.form=no;page_size=100;search.result=yes;order=mm;action=search;search.sequence=1

Although, one can find the flanking genes using the coordinates and another step, but I find it strange that gene info is missing when the data is downloaded. I was wondering if one has faced this and whether there's a quick fix for it?

Thanks,
Noushin

Answer 1

[Ryan Dale]

It doesn't look like there's any way to configure the download -- so no obvious quick fix. You'll probably have to extract the coords from each fasta record and use something like bedtools closest.

You might find parts of this script useful, which I had written to 1) only consider positively identified enhancers, 2) extract the coordinate info from the fasta header, and 3) liftover human enhancers to mouse coordinates.

The output file contains all positive enhancers in human and mouse in mm9 coordinates. So if you're working in mm9 then you could use that file directly with bedtools closest (plus an appropriate annotation file).