How to find RNASeq V2 RSEM normalized expression values for various cancer studies in order to compare to tumor data from cBioportal?

Question

[tsangj15]

Hi,

I am using the cBioportal to get mRNA expression data for various cancer studies (e.g. lung, liver, thyroid etc). However, I need expression levels from normal/control samples in order to make comparisons to these tumor samples from cBioportal.

Does anyone know or have used control/normal samples from TCGA and can point me to it?
Do you know of a good resource (preferably RNASeq V2 RSEM normalized expression values or z-scores) for control/normal samples?

How would I match these tumor and normal samples in order to make better comparisons? In addition, what are some tips to make comparisons between normal data and tumor data?

Any help is appreciated. I am a little lost.

Thanks

Answer 1

[Samuel Brady]

Often normal samples are mixed into TCGA data. Look at each of your sample barcodes, which will have the format TCGA-02-0001-01. If the bold italicized digits are between 10 and 19 it's a normal sample. If it's 01 it's a solid tumor. (See the TCGA barcodes website.)

I'm not sure if cBioPortal includes the TCGA normal samples. The GDC Data Portal, however, should have the TCGA normal samples included. If you download all breast cancer RNA-Seq data, for example, there will be perhaps 1000 cancer samples and a few normal samples if I recall correctly.

This paper and its associated github enable you to download RNA-Seq data from 24 cancer types from TCGA, including 9264 tumor and 741 normal samples aggregated together. That would be even easier than using cBioPortal or GDC Portal.