Finding Specific Types of Data for Cancer Studies
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6 weeks ago
Vincent Laufer ★ 2.4k

Hi Biostars,

I have been working in autoimmune disease for quite some time. Lately, I have found myself doing a bit more cancer research. I don't have the same knowledge of databases and their relative strengths and weaknesses for cancer biology. To get a sense for this, I'd like to ask a few illustrative questions.

  1. Suppose I want to Learn what SBS are present in intrahepatic cholangiocarcioma --> I can go to COSMIC, or GDC, or other tools. But, suppose I want to get more specific, and narrow down iCCA into its various subtypes, then get the relevant SBS for each of those. Tools like __- have only a few pts. per tumor type - is there a more comprehensive dataset, or do you have to calculate it yourself?
    1. Suppose I wish to access cancer data with reasonably covariate information. For instance, not only do I want to study GBM, but I want to study GBM treated with TMZ. OK, now I want to separate this data into pre and post TMZ treatment files, OK now I want. ....
    • Which DBs, generally, have the best annotated cancer data?
    1. Suppose I want to know the location of every gatekeeper mutation on every RTK that we know of so far. What kind of DB would store this?
    2. Are there large repositories of IC50 data specifically for chemo drugs? What about repositories of panel testing of IC50 across many genes?
    3. What about Variant allele frequencies? For germlline, used to frequent things like VEP, but not as sure what to do when looking for VAF in a cancer subtype...

Thank you!!!!

TCGA GDC Cancer Entrez GEO • 118 views
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