Answers.Body: <p>One such database/tool is <code>“[PharmacoGx][1]: an R package for analysis of large pharmacogenomic datasets.” Bioinformatics (Oxford, England)</code>.</p>
  
  <p>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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-27T00:57:02.943Z
Answers.Text: Do you mind to include a simple example?
Answers.UserDisplayName: 0x90
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-27T09:38:56.810Z
Answers.Text: 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: http://bioconductor.org/packages/release/bioc/vignettes/PharmacoGx/inst/doc/PharmacoGx.pdf
Answers.UserDisplayName: haci
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Answers.CreationDate: 2019-09-27T13:08:34.753Z
Answers.Text: I see. What about the databases COSMICS, TCGA, and immport. Aren’t they supposed to have such things?
Answers.UserDisplayName: 0x90
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-27T13:25:30.640Z
Answers.Text: 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.
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-26T11:46:41.417Z
Answers.LastActivityDate: 2019-09-26T11:46:41.417Z
Answers.UserDisplayName: haci
Body: <p>Are there databases that contain information about gene or protein expression before and after targeted therapy or chemotherapy? </p>
  
  <p>I am curious about different cancer cell lines or cancer types. </p>
  
  <p>Any suggestion on a set of resources I should look into?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-26T06:52:15.383Z
Comments.Text: "Are there databases..." As a general rule, no, there are almost never specialized databases for anything.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-26T07:19:58.090Z
Comments.Text: @DevonRyan, any idea how to extract expression ratio before and after cancer treatment from https://portal.gdc.cancer.gov/, https://bioinformatics.mdanderson.org/public-datasets/, https://www.immport.org/shared/home, https://cancer.sanger.ac.uk/cosmic, or http://www.cbioportal.org/
Comments.UserDisplayName: 0x90
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-26T07:22:50.073Z
Comments.Text: Find appropriate samples, match them up, find expression metrics, write a program to do that. Never expect tools for random things like this.
Comments.UserDisplayName: Devon Ryan
Tags: <public-databases><cancer><data-retrieval><public-dataset>
Title: Are there databases or resources that contain expression of proteins or genes before and after cancer treatment?
ThreadText: # Are there databases or resources that contain expression of proteins or genes before and after cancer treatment?
  
  (Asked by: username_0 on 2019-09-26)
  
  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?
  
  **Tags:** public-databases, cancer, data-retrieval, public-dataset
  
  > **Comments:**
  > **username_1**: "Are there databases..." As a general rule, no, there are almost never specialized databases for anything.  
  > **username_0**: @username_1, any idea how to extract expression ratio before and after cancer treatment from https://portal.gdc.cancer.gov/, https://bioinformatics.mdanderson.org/public-datasets/, https://www.immport.org/shared/home, https://cancer.sanger.ac.uk/cosmic, or http://www.cbioportal.org/  
  > **username_1**: Find appropriate samples, match them up, find expression metrics, write a program to do that. Never expect tools for random things like this.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-09-26. Score: 2 | Accepted answer
  
  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.
  
  > **Comments:**
  > **username_0**: Do you mind to include a simple example?  
  > **username_2**: 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: http://bioconductor.org/packages/release/bioc/vignettes/PharmacoGx/inst/doc/PharmacoGx.pdf  
  > **username_0**: I see. What about the databases COSMICS, TCGA, and immport. Aren’t they supposed to have such things?  
  > **username_2**: 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.  
  
  ---
  
  