TCGA RNA Seq: compare expression in several malignancies

Question

[mwball00]

Hi,

I have searched the forum but cannot find an answer to this question. I want to compare expression of a single gene in 3 different malignancies using TCGA RNA-seq data. I have a beautiful graph from firebrowse that looks like there will be a signficant different in expression, but I need to do the stats to prove this. What is the best way to obtain the raw data, and how should it be normalized?

Answer 1

[mwball00]

Well, it looks like one very easy way to do it is to use the Firebrowse Web-API: http://firebrowse.org/api-docs/#!/Samples/mRNASeq

Select gene of interest and cohort.

Answer 2

[roy.granit]

It can also be done with cBioPrtal. select the cancer types you are interested in, type in the gene name and switch to the 'expression' tab and there download the data