Question: How can I use TCGA Copy Number Portal?
0
gravatar for nijironohata
3.0 years ago by
nijironohata0 wrote:

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.

cnv tcga • 1.1k views
ADD COMMENTlink modified 3.0 years ago by raunakms1.1k • written 3.0 years ago by nijironohata0
1
gravatar for raunakms
3.0 years ago by
raunakms1.1k
Vancouver, BC, Canada
raunakms1.1k wrote:

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

ADD COMMENTlink written 3.0 years ago by raunakms1.1k

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.

ADD REPLYlink written 3.0 years ago by nijironohata0
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