Are there databases that contain information about gene or protein expression before and after targeted therapy or chemotherapy?

I am curious about different cancer cell lines or cancer types.

Any suggestion on a set of resources I should look into?


1 Answer 1


One such database/tool is “[PharmacoGx][1]: an R package for analysis of large pharmacogenomic datasets.” Bioinformatics (Oxford, England).

They brought together a large compendium of experimental data (cell lines and the like if I remember correctly from a talk), standardized these and made available within a special object class. I think there is genomic and transcriptomic data, not sure if there is proteomic data though.

  • $\begingroup$ Do you mind to include a simple example? $\endgroup$
    – 0x90
    Sep 27, 2019 at 0:57
  • 1
    $\begingroup$ What you are trying is not a simple task overall, therefore I cannot provide a "simple" example. I can only point you to their vignette, they have worked-out cases there: bioconductor.org/packages/release/bioc/vignettes/PharmacoGx/… $\endgroup$
    – haci
    Sep 27, 2019 at 9:38
  • $\begingroup$ I see. What about the databases COSMICS, TCGA, and immport. Aren’t they supposed to have such things? $\endgroup$
    – 0x90
    Sep 27, 2019 at 13:08
  • $\begingroup$ Can't talk about others but TCGA is (mostly) treatment naive, you will need to check clinical information tables (of your cancer of interest) if patients got treatment or not though. If you decide go down that road, TCGABiolinks (and especially its vignettes) would be very helpful. $\endgroup$
    – haci
    Sep 27, 2019 at 13:25

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.