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?
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1$\begingroup$ "Are there databases..." As a general rule, no, there are almost never specialized databases for anything. $\endgroup$– Devon RyanSep 26, 2019 at 6:52
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$\begingroup$ @DevonRyan, any idea how to extract expression ratio before and after cancer treatment from portal.gdc.cancer.gov, bioinformatics.mdanderson.org/public-datasets, immport.org/shared/home, cancer.sanger.ac.uk/cosmic, or cbioportal.org $\endgroup$– 0x90Sep 26, 2019 at 7:19
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1$\begingroup$ Find appropriate samples, match them up, find expression metrics, write a program to do that. Never expect tools for random things like this. $\endgroup$– Devon RyanSep 26, 2019 at 7:22
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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.
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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/… $\endgroup$– haciSep 27, 2019 at 9:38
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$\begingroup$ I see. What about the databases COSMICS, TCGA, and immport. Aren’t they supposed to have such things? $\endgroup$– 0x90Sep 27, 2019 at 13:08
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$\begingroup$ 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. $\endgroup$– haciSep 27, 2019 at 13:25