A common question with respect to perturbational signatures is the extent to which they are consistent across different cellular contexts. To investigate this, we first restricted our analysis to the cell lines in which each perturbagen gave a signature whose transcriptional activity score (TAS) was greater than 95% of that of negative controls and considered only perturbagens that had high-TAS signatures in at least three cell lines. Using these thresholds, we analyzed 1,399 of 2,429 compounds, 1,088 of 2,160 cDNAs, and 3,926 of 13,187 shRNAs.
