Figure 4

Correlation between shRNA knockdown efficacy and scoring for six published algorithms for siRNA. Algorithm scores for each shRNA target site from Table 2 are plotted against observed knockdown efficiency for the Hsieh et al. (A), 5' ΔΔG (free energy differential) (B), Reynolds et al. (C), Amarzguioui et al. (D), Ui-Tei et al. (E) and Takasaki et al. (F) algorithms. The 5' ΔΔG score is plotted on a reverse horizontal axis since knockdown efficacy is predicted to correlate with negative 5' ΔΔG value. A trend line is shown along with the R² value for each plot. Knockdown of less than 10% is plotted as zero.