Effect of over- and underexpression on itselves

[holgerman]

Hi Daniel,

thank you very much for sharing this work. As a computational biologist, this data seems very interesting for lookup of hypothesis won in another dataset in a wet lab data, great!

I had a look at the datasets you kindly provided in https://github.com/dhimmel/lincs/tree/gh-pages/data/consensi and checked the effect of overexpression/underexpression of a gene as perturbagen on itself:

About a third of the genes showed nominal significant (z score <= -1.96) underexpression when it was itself the repressing perturbagen. When looking on overexpression, about 10 percent of genes showed overexpression when they were the overexpressed perturbagen itself.

My first question is: While this is truly a clear enrichment in the right direction, is this rather low efficiency of a gene as perturbagen on itself expected?

My second question is: Do you suggest to filter for genes that have an effect as perturbagen on itself for quality control?

To illustrate this issue, here is a histogram of z-scores showing effect as perturbagen on itselves vs. effect on other genes:

Thanks and best, Holger