First of all, I’d like to thank everyone involved in this project for the incredibly useful resource you have provided to the community.
I am interested in carrying out some bespoke analyses of Common Essential genes (e.g. by organelle, by cell lineage etc.) I am however finding it difficult to filter Common Essential genes, as I can’t seem to identify lists of genes that match up. For example, a subset of genes from the Common Essential list (from any of the studies) don’t appear on the Gene Effect list (“CRISPR (DepMap 21Q3 Public+Score, Chronos)”).
I appreciate that much of the numerical data is derived, and the effect scores are dependent on many factors, including post-hoc corrections for various parameters. However, as a general rule to simplify my analysis of whichever gene list I download, would it be sensible to:
- Calculate a mean effect score across all cell lines
- Use -0.5 as a cut off for common essential/non common essential
Apologies if the above isn’t very clear, and many thanks in advance!