Extended Data Fig. 5: Comparison of PRISM viability data to reference datasets.

a, Pairwise Pearson correlations between drug response AUCs of publicly available datasets. AUC values were recomputed for 84 compounds and 318 cell lines (median 236 cell lines per compound) over the same dose-range for each compound-cell line pair in all 3 datasets (GDSC, CTD2, REP), and capped at 1. The Pearson correlation across shared compound-cell line pairs of the datasets is above 0.6. 44.8% of cell line-compound pairs show inactivity (AUC > 0.8) in all three datasets (n = 16650 compound-cell line pairs). b, Pairwise Pearson correlations between drug response AUCs after removing inactive cell line-compound pairs. Pearson correlations were re-calculated after filtering out the inactive data points (AUC > 0.8 in at all three datasets) (n = 9188 compound-cell line pairs). c, Compound-wise correlation between publicly available datasets. Correlation between PRISM data and other datasets is similar to correlation between other datasets. Points represent Pearson correlations and error bars represent 95% confidence intervals computed using Fisher’s z-transform. GDSC vs. CTD2 is in blue and REP vs. GDSC/CTD2 is in red. The number of cell lines shared by all three datasets is shown after each drug name. Paired t-tests on compound-wise correlations show statistically significant (two-sided p-value: 0.012 and 0.014 for top and bottom, respectively) but small mean of differences (0.049 and 0.039 for top and bottom, respectively). The number of data points used to compute each correlation is given in the figure for each compound.