Hi! I am interested in seing the effect determined genes could have on the sensitivity to a compound, so I think it is necessary to compare the effect of the compound before and after knocking down/out every one of my genes of interest, so how could I get that information from depmap?
I also think that is necessary to point out that I am interested only in breast cancer cell lines.
Thanks in advance and sorry if it is a very naive question, but is my first time using depmap and the lack of a guide has me a little bit overwhelmed and lost.
In the DepMap project, we are knocking down individual genes and measuring the effect on viability, but we don’t have a treatment arm which includes any additional compounds.
The DepMap portal does have results from compound screens, but those are entirely separate experiments.
I believe we don’t have the data that’d be necessary for the question that you’re trying to ask.
One can ask questions like, “Does p53 inactivation sensitize cell lines to compound X?” because we have a fair number of models which have p53 already deactivated and so you can compare those models to models where it is not. That’s certainly a different question then the one you posed, but I think questions along those lines are as close as you can get with the data we have.