What is the unit of RNASeq v2 mRNA expression profile in cross-cancer query?

Question

[huangyong]

H there,

I am trying to get a sense of mRNA expression levels of certain genes in different types of cancers. I queried TCGA studies and was able to gene expression plots based on RNASeq v2 data (here is an example of cross-cancer gene expression plot), but it is not clear to me what is the unit of the expression value. As this is cross-cancer query, I assume it shouldn't be z-score, am I right?

Thanks, Yong

Answer 1

[Samuel Brady]

This does not look like z-scores, which are usually between -2 and 2. It also does not look like TPM, FPKM, or CPM since there are negative values. It may be some normalized arbitrary units (which is often the result of batch-normalization approaches).

You can download TCGA RNA-Seq data for 24 cancer types in TPM format through this paper and github. It makes pan-cancer analysis much easier.