RNA-Seq database of cancer patients other than TCGA and ICGC?

Question

[thejustpark]

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!

[ATpoint]

Which entity/entities?

[thejustpark]

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.

[ATpoint]

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?

[thejustpark]

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

[Kevin Blighe]

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:

• EGA
• SRA
• GEO

Answer 1

[Pappu]

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