Dear, Dr. Ethan Cerami

46 views

Skip to first unread message

Solip Park

unread,

Jul 30, 2012, 9:11:20 AM7/30/12

to cbiop...@googlegroups.com, cancerg...@cbio.mskcc.org

Dear, Dr. Ethan Cerami.

I'm Solip Park working in the Genetic Systems Laboratory, CRG, Spain.

Your published paper in the Cancer Discov, "The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data", is very impressed to me.
It's well designed and give a great insight to the cancer genome and I trust that your paper provides one of the best resource for cancer research.

I'm also working with cancer genome, and want to analyze the homozygous/ hemizygous deletion in cancer genome. So, your program is very useful to me.
But I have one problem. I want to genome-wide analyze the homozygous/ hemizygous deletion in cancer genome, but your web site only allows to 100 genes.
So, could you suggest how to obtain whole-genome data from your web site?
I know it's possible from TCGA website, but I want to download from your web site because you already calculated the Putative copy-number alterations from GISTIC.

I'm really sorry to bother you.
If you give some advise to my work, I'll very appreciate you.

Thank you for your reading and have cool summer :)

Best wishes,

Solip Park

Nikolaus Schultz

unread,

Jul 30, 2012, 5:16:18 PM7/30/12

to Solip Park, cbiop...@googlegroups.com

Dear Solip,

Thank you for the nice feedback. We do not currently provide bulk downloads of all data, but you can get the discretized copy-number data of all TCGA projects via the Broad's TCGA Firehose. Their website is available at gdac.broadinstitute.org. We use the all_thresholded_by_gene.txt file from their GISTIC analysis (see analyses runs).

Your best download option may be the Firehose Get utility (https://confluence.broadinstitute.org/display/GDAC/Download).