Hi all.
I want to use oncoscan for my research and Oncoscan is specially aimed at targeting hot spots regions for Cancer
I heard that there are several cancer related genes in oncoscan sites.
However, I cannot find the cancer genelist in oncoscan.
Does anybody know where they are?
You can obtain a BED file of coordinates targeted by the Oncoscan assay here: http://www.affymetrix.com/estore/support/file_download.affx?onloadforward=/analysis/downloads/na33/genotyping/OncoScan.na33.r1.bed.zip
I believe you will be required to log in before you can download this file. You can intersect these coordinates with known gene/transcript annotations (e.g. using bedtools) to determine the identity of genes covered by the assay.
Or you could download the annotation file provided by Affy here: http://www.affymetrix.com/Auth/analysis/downloads/na33/genotyping/OncoScan.na33.r1.annot.csv.zip
More generally, here is a thread that covers others sources of cancer related genes: Database Of Tumor Suppressors And/Or Oncogenes
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written
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Malachi Griffith
Thanks for your reply.
Here is one more question.
After clicking the site above (second address you mentioned)
http://www.affymetrix.com/Auth/analysis/downloads/na33/genotyping/OncoScan.na33.r1.annot.csv.zip
the only I can see is the affymetrix main pages and I didn't know where I should go to find annotation file. (of course , I am logged in)
Could you check one more time for me please?
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