Novartis Project Drive data questions

Q&A
1

Hi,

First of all, thanks to everyone who has contributed to making this great resource! I’m pretty new to working with all of this data, so sorry if my question is a bit naive.

I was wondering if the Novartis/Drive data contained in RNAi combined file D2_combined_gene_dep_scores.csv was the most recent version released by the Drive team, or if it was from a certain snapshot in time.

Also, I noticed different cell lines come up when ranking dependencies on a certain gene when I use the Novartis/Drive interface (DRIVE DATA PORTAL) vs the D2_combined data from the file above. I assume this is due to different ways of processing the data and accounting for off-target shRNA effects (Ataris vs Demeter2). Is this a correct assumption, or is there something else I should consider as well?

2

Thanks!

The published Novartis DRIVE dataset is available here. You can download the raw and processed versions of the data they generated there.

We reprocessed the DRIVE dataset, along with a couple other large-scale RNAi screens, using the DEMETER2 algorithm. The files labeled “D2_DRIVE” contain just the Novartis DRIVE data reprocessed with DEMETER2. The files labeled “D2_combined” are actually the result of running DEMETER2 on the combination of 3 datasets: Novartis DRIVE, Broad Achilles, and a Marcotte et al. breast cancer screen dataset. Thus, if you’re looking for the version most comparable to what the Novartis team published I’d use the “D2_DRIVE” dataset. It should be pretty similar in terms of the per-gene relative dependency profiles.

Hope that helps!