Question: RNA-Seq database of cancer patients other than TCGA and ICGC?
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gravatar for thejustpark
9 weeks ago by
thejustpark60
United States
thejustpark60 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 • 202 views
ADD COMMENTlink modified 8 weeks ago by Pappu1.9k • written 9 weeks ago by thejustpark60

Which entity/entities?

ADD REPLYlink written 9 weeks ago by ATpoint14k

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 9 weeks ago by thejustpark60

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 9 weeks ago by ATpoint14k

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

ADD REPLYlink written 9 weeks ago by thejustpark60

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 9 weeks ago by Kevin Blighe39k
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gravatar for Pappu
8 weeks ago by
Pappu1.9k
Pappu1.9k wrote:

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

ADD COMMENTlink written 8 weeks ago by Pappu1.9k
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