Question: TCGA RNA Seq: compare expression in several malignancies
0
gravatar for mwball00
3.2 years ago by
mwball000
United States
mwball000 wrote:

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?

rna-seq tcga • 1.1k views
ADD COMMENTlink modified 3.2 years ago by roy.granit800 • written 3.2 years ago by mwball000
0
gravatar for mwball00
3.2 years ago by
mwball000
United States
mwball000 wrote:

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.

ADD COMMENTlink written 3.2 years ago by mwball000
0
gravatar for roy.granit
3.2 years ago by
roy.granit800
Israel/LabWorm
roy.granit800 wrote:

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

ADD COMMENTlink written 3.2 years ago by roy.granit800
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