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PostPosted: Sun Oct 07, 2012 8:49 am 
Dear GREAT developers!
I would like to use your zv9 annotation for calculating the enrichment within gene lists. I have found the answer at similar topic elsewhere in the forum. My specific question is - which gene table from UCSC should I use for my zebrafish genes? It it RefSeq or Ensemble?
Thank you very much for help,
Daria
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 Post subject: use custom gene table
PostPosted: Thu Oct 11, 2012 10:08 am 
Site Admin
Hi Daria,

GREAT uses a custom gene set that is a combination of RefSeq, Ensembl and Uniprot as described in our documentation (http://bejerano.stanford.edu/help/display/GREAT/Genes#Genes-Zebrafish). You can download this gene set on the same page (http://bejerano.stanford.edu/help/display/GREAT/Genes#Genes-SetofGenesforGREAT2.0).

If you want these genes in the UCSC genome browser, you can download the gene set and re-upload it or run a GREAT job, select "View all region-gene associations" from the Global Controls drop down and then in the "All genomic region-gene association tables" click one of the gene names to view it in the UCSC genome browser. At this point, GREAT creates custom tracks of your regions and genes for viewing in the UCSC genome browser.

Thanks,
Bejerano Team
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