Dear Efstathios-Iason,
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More than the exact cut-offs used, I would be concerned about the number of cell lines used to define the filter. These screens usually suffer from considerable noise which necessitates using a much larger sample size. For example, one could look for compounds that preferentially kill a set of 10 cell liens more than another set of 10. You can run this type of Two class comparison using the Custom Analyses tool of the portal’s Data Explorer
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One thing you could look at is the top preferentially essential genes for each cell line that are listed on the cell line page (e.g., MCF7’s). To compute pathway enrichment for the top preferential dependencies you’d want to look at more than the top 10 that are currently displayed on the portal though. You can compute the full list yourself by downloading the data and following the methodology described on the page (hover over the question mark symbol).
You can also use the Custom Analyses tool to look for genetic dependencies correlated with drug sensitivity profiles. E.g.:
Hope this is helpful!
Best,
Aviad
