Question about interpreting Gene Effect

Q&A
,
1

Hi, I have a question about interpreting gene effect in terms of selection of genes that are ‘hits’.

Is using gene effect for a specific cell line sufficient to do this? In other words, can I select a threshold for a negative gene effect and call genes that score below that threshold as hits in my cell line of interest? If so, what would you recommend as the best approach to selecting the threshold?

I can see that the skewed-LRT data isn’t publicly available therefore I’m trying to figure out whether using gene effect to select gene hits is appropriate.

2

Skewed-LRT scores are computed across cell lines, so they describe whether a gene has a long tail. This is to say, that metric characterizes the distribution of gene effects, which sounds to me, different than identifying hits.

If you are interested in calling a “hit” in a cell line as which lines are dependent, it may make sense to look at the “dependency probability” dataset and call those lines where the probably is > 0.5 as hits.

(see also: What thresholds should I use to decide if a gene is really having a significant effect on a cell line? )