Is there a web-based interactive way in DepMap or elsewhere online to identify differentially expressed genes between two sets of cell lines? More generally, one might be interested in any differently measured quantity between two groups of cell lines.
Using DepMap it’s straightforward to select a set of cell lines that meet a criteria, but once a set is created in Cell Line Selector I’d like to generate a list or a volcano plot of changes in gene expression or other features.
I can download the data and perform a rank test between expression levels of two groups, but can we do this sort of analysis interactively?
Yes, this is what “Custom analysis” in data explorer is for. If you click “Custom analysis” in the Data Explorer app, you’ll be given the option to perform a “two-class comparison”
Here, you can give the group of cell lines that you defined and compare to a different group of lines. The comparison will be performed by computing a t-test for each gene independently and a volcano plot will be shown on the left summarizing the results.
Thanks,
Phil
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