Using these thresholds, we found that 26% of compounds, 8% of cDNAs, and 34% of shRNAs gave a single signature across multiple cell lines. The comparatively larger proportion of shRNAs that give a single signature may be attributed to the higher transcriptional activity of shRNAs. We observe that about 36% of genes with at least 3 high-TAS shRNAs have at least 50% of those shRNAs flagged as single-signature reagents. This is not notably different from the 34% rate at which shRNAs give single signatures in general, suggesting that whether or not an shRNA gives a single signature is more dependent on the shRNA itself (and possibly its off-target effects) than it is on the specific gene the shRNA is targeting. cDNAs least frequently give a common signature. This was somewhat unexpected, given that they have a similar transcriptional impact as compounds, and may be due to their relative lack of off-target effects. Having fewer off-target effects may result in a signature that predominantly contains the effect of over-expressing a single gene, which may be quite different depending on the gene and cell context.
