Thank you very much for the database you developed. For a given gene such as TP53, how do we calculate the Top Co-dependencies? Is it by comparing the correlation of differential genes after two genes are knocked out? I want to download gene expression profile data after CRISPR and RNAi. Do we have transcription profile data available?
No, we don’t have any post-perturbation expression data. Co-Dependencies are correlations between dependency profiles.
In other words, if we look at the co-dependencies tile for TP53, MDM2 is at the top:
This is saying that the pattern of killing across models that we observe when we knock out TP53 looks similar to the pattern of killing that we see when we knock out MDM2.
Although, the pearson correlation is negative, so the pattern is actually inverted. This is saying that on average, those models which are sensitive to TP53 knockout are insensitive to MDM2 knockout and vice versa.