Compare gene expression data with GTEx

Q&A
#1

DepMap recently received the following question:

Since DepMap does not have gene expression data for cell lines from normal (non-cancer) tissue, I planned to use data from GTEx. However, the normalization method is different (according to GTEx), “Expression values were normalized between samples using TMM as implemented in edgeR”.

For each gene, expression values were normalized across samples using an inverse normal transform.). I need to compare gene expression between cancer cell lines and normal tissues. Is there a way to make expression data from the two sources comparable? Thanks

#2

Our gene expression analysis pipeline is adapted from GTEX’s. So, you could start from the gene-level TPM data (available on the GTEX portal) and compare that pretty directly to the DepMap gene expression data. Note that our data is provided as log(TPM+1).

We too have thought it’d be valuable to add to the portal the capability to compare between the expression data from the DepMap project and the expression data from GTEx. However, we have yet to investigate what methodology would be best for comparing them.