Question: RNA-Seq database of cancer patients other than TCGA and ICGC?
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gravatar for thejustpark
7 months ago by
thejustpark70
United States
thejustpark70 wrote:

For my computational cancer model using RNA-Seq data, I am going to use TCGA as a discovery cohort. Since ICGC or GDC have great overlap with TCGA data, I want to find independent databases as validation cohort. I can find several RNA-Seq data on cancer cell lines, such as CTRP, TARGET, CCLE, but can't find cancer patient data. If you have an idea about where go to for this, can you please let me know?

Thank you guys for your time and effort!

cancer rna-seq patient • 484 views
ADD COMMENTlink modified 7 months ago by Pappu1.9k • written 7 months ago by thejustpark70

Which entity/entities?

ADD REPLYlink written 7 months ago by ATpoint21k

I am sorry that I can't understand what you mean by entity. Assuming that you ask about response variable or covariate, I want to have their survival status with RNA-Seq data. If it's not what you asked, please let me know again.

Thank you very much.

ADD REPLYlink written 7 months ago by thejustpark70

It means what kind of cancer. You seem to require RNA-seq data but of what kind of cancer. Different genes contribute differently to cancer development and progression depending on the kind of cancer. What kind of data do you need?

ADD REPLYlink written 7 months ago by ATpoint21k

I am actually interested in pan cancer study, so does not matter (the more, the better).

ADD REPLYlink written 7 months ago by thejustpark70

Why not divide the TCGA samples into training and validation datasets? If not that, then check the ICGC Data Repository (ICGC does not overlap with TCGA as extensively as you imply).

Other than those, simply search:

ADD REPLYlink written 7 months ago by Kevin Blighe46k
0
gravatar for Pappu
7 months ago by
Pappu1.9k
Pappu1.9k wrote:

Check out http://www.cbioportal.org/

ADD COMMENTlink written 7 months ago by Pappu1.9k
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