Hi everyone, I am a newman to research work. I wonder how to use this web to check the correlation between one gene loss and another? I read the paper “MTAP deletion confers enhanced dependency on the arginine methyltransferase PRMT5 in human cancer cells” these days and I’m interested in how they find PRMT5 and WDR77 by using shRNA data set. I wonder to know the details about this shRNA screening data and how to find it and use it. Thank you very much.
I can’t speak to what exactly the steps they took to find this relationship were, but I can illustrate how you can see this relationship in the DepMap portal.
They say “MTAP deletion” is associated with enhanced dependency in PRMT5. To “rediscover” this I could go to the “Custom analysis” tool in Data Explorer and say I want to find associations between MTAP copy-number and dependency profiles. I fill out the dialog as follow:
That will then show me the associations on as volcano plot on the left, and we can see the strongest association is PRMT5:
With PRMT5 selected, on the right we can see the relationship where points represent cell lines. Here, we see that those points on the left (representing a loss of MTAP) show lower dependency scores. By eye, the the mean is probably around -0.8 or so. Given that a gene effect of -1 is the median of a set of known essential genes, that’s suggests that loss of PRMT5 is lethal for those lines.