How can I use TCGA Copy Number Portal?

Question

[nijironohata]

I have a list of 500 genes of my interest in a certain cancer type.

I would like to know if these genes are significantly amplified/loss or not respectively.

Is there any way to collect the CNV analysis result (such as q-value) for the 500 genes from TCGA CN portal (http://www.broadinstitute.org/tcga/home) ?

I read FAQ and help in TCGA CN portal, but I still don't know the way.

Also, I sent this question to the support e-mail address (tcga-help[at]broadinstitute.org), but it was rejected by the server.

I also knows there is GDAC Firehose pipeline though, I would like to use the TCGA CN portal pipeline.

Answer 1

[raunakms]

Use CBioPortal: http://www.cbioportal.org/ is you just want a quick check for your genes of interest,

[nijironohata]

I think cBio don't respond if each gene of my interest is significantly amplified/loss or not with p-value (or q-value). I want the result with statistic value. Thank you for your comment.