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.
- 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?
- 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?
- 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?
- Are there large repositories of IC50 data specifically for chemo drugs? What about repositories of panel testing of IC50 across many genes?
- 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...