Extended Data Figure 9. Gene expression correlates of drug response identified in Haibe-Kains et al.⁷ have better agreement when using more stringent FDR Cutoffs.

a, Scatter plots of the IC₅₀ based gene-drug association statistic (column “stat” in Haibe-Kains et al.⁷ suppl. Data sets 2 and 3 and Figure S6) with FDR between 0 and 0.01 (purple), 0.01 and 0.05 (cyan), 0.05 and 0.2 (green). In each panel the two black lines intersect at the origin and define the agreement quadrants (top right and bottom left quadrants). b, Proportion of genes in the agreement quadrants (same sign between the two studies). c, Additional measures of agreement between the two studies: Agreement measures increase with more stringent FDR cutoff, suggesting that false discovery drives agreement down. Uncentered measures (cosine correlation, uncentered covariance, agreement quadrant proportion) yield better agreement between the studies (see Supplementary Text for details).