Question: RPKM values in normal cells
gravatar for akantusz
4.2 years ago by
akantusz0 wrote:


I would like to compare gene expression level data from COSMIC to expression level data of normal cells.

I've found the TCGA level 3 data (RPKM and normalized count values in case of RNASeq and RNASeqV2 platforms), from which COSMIC data derive, but where could I find RPKM scores for normal cells?


rna-seq tcga cosmic • 1.8k views
ADD COMMENTlink modified 4.2 years ago by ashah9030 • written 4.2 years ago by akantusz0
gravatar for Giovanni M Dall'Olio
4.2 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

There are many resources. The most recent are the Protein Atlas ( ), providing data from 122 samples and 32 tissues (plus data for cell lines), and the GTEx portal (, with data from ~3,000 samples in 30 tissues.

ADD COMMENTlink written 4.2 years ago by Giovanni M Dall'Olio26k
gravatar for ashah90
4.2 years ago by
ashah9030 wrote:

The TCGA data portal has matched normal cell data as well. If you look at the data matrix ( on the very right there is an option for "Normal-matched". Furthermore, if you don't like the data matrix you can always download the data in bulk using Broad's GDAC Firehose ( and using the TCGA patient barcodes to determine whether the cell is a normal cell. You can determine that using this wiki ( and looking at the "Sample" field. If I remember correctly, a "01" or "11" in the sample fields means it is a normal cell.

ADD COMMENTlink written 4.2 years ago by ashah9030
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2169 users visited in the last hour