CRISPRGeneEffect vs CRISPRGenedependency

[rosario]

Hi, we want to identify genes that could be interesting as target for treatments. the idea is to observe a particular kind of cancer (lung) and filter for the genes that are fitness only in this category compared to other kind of cancers. We don’t know if we should use the CRISPRGeneEffect or the CRISPRGenedependency files. We observed differences in the rankings for the different genes in the 2 files. Thus they are not the same thing in the end. Could you please explain me what is the difference between them and which one is better for our objective.
Another question , just to understand: are the fitness genes of one cell line computed also considering the other cell lines data or each cell line’s gene fitness list is computed independently?
thanks
RB

[pmontgom]

Hello,

For your first question, please see this post, and let us know if you still have questions:

How is the probability of dependency different from the gene effect score?

The “gene effect” file contains the corrected CERES scores, which measure the effect size of knocking out a gene, normalized against the distributions of non-essential and pan-essential genes. The probabilities assess, given a gene score, how likely to be a member of the non-essential distribution or the common essential distribution in that cell line. The key difference between using a fixed threshold on CERES score and a threshold on the probabilities is that the probabilities take into accoun…

As for your second question:

are the fitness genes of one cell line computed also considering the other cell lines data or each cell line’s gene fitness list is computed independently?

The gene effect scores of each cell line is computed using information from all other cell lines. The computation of gene effect scores uses Chronos which fits a single model with a large number of parameters using the log-fold change data of all cell lines.

Thanks,
Phil