a, Distribution of Pearson’s correlation coefficient between total protein levels as measured by RPPA and mRNA expression levels measured by RNA-seq (n = 890 cell lines, 154 genes). The empirical null distribution for correlation of mRNA and protein for two random genes is shown for comparison (P < 2.2 × 10−16, two-sided Wilcoxon rank-sum test). b, Effect of RPPA dynamic range on mRNA and protein correlation (n = 96). mRNA and protein correlation is plotted against dynamic range for each validated total protein antibody. Most antibodies with low mRNA and protein correlation tend to have low dynamic range with the exception of the gene VEGFR2, which despite high dynamic range, exhibits very low mRNA and protein correlation. P values determined by two-sided Pearson’s correlation test. c, Effect of RPPA antibody quality and target type on mRNA/protein correlation. On the left, mRNA/protein Pearson correlation is plotted for ‘validated’ (n = 96) and ‘with caution’ (n = 58) antibodies for antibodies against total proteins. On the right, mRNA and protein Pearson’s correlation is plotted for antibodies against total protein (n = 154) and antibodies against phospho-protein (n = 50). Median correlations are 0.62 (validated), 0.48 (caution), 0.54 (total protein), 0.21 (phospho-protein). P values determined by two-sided Wilcoxon rank-sum test. Box plots are as defined in Fig. 4d. d, Comparison of mRNA and protein correlations in CCLE and TCGA (n = 152). The Pearson’s correlation between mRNA and protein levels is calculated for each RPPA antibody in CCLE and TCGA separately. Each dot represents an antibody. Generally, the antibodies with low mRNA and protein correlation in CCLE also have low mRNA and protein correlation in TCGA data. P values determined by two-sided Pearson’s correlation test. e, Distribution of gene dependency (Achilles RNAi) correlations with RPPA pSHP2 level (left, n = 161–411, Supplementary Table 14) and PTPN11 mRNA expression (right, n = 192–478, Supplementary Table 14). PTPN11 dependency is strongly correlated with pSHP2 level, whereas there is no significant correlation with PTPN11 mRNA level. f, Comparison of pSHP2 levels in SHP099-sensitive and -resistant cell lines (n = 60). P value determined by two-sided Wilcoxon rank-sum test. SHP099 sensitivity data were obtained from a previous study26. Box plots are as defined in Fig. 4d. g, Pearson’s correlation of pSHP2 and Sanger GDSC drug sensitivity AUC dataset (n = 265 drugs and 198–588 overlapping cell lines). h, Model error for elastic net model of sensitivity to ponatinib with and without using RPPA data as predictive features. The y axis shows the cross-validation error (fivefold cross-validation) against parameter λ of elastic net (parameter α is fixed at 0.2). Data are mean ± s.d. for the five cross-validation sets. The minimum cross-validation error for models with and without using RPPA data are shown by arrows. i, Elastic net results for sensitivity to ponatinib. pSHP2 is the top feature selected by elastic net. On the left, elastic net weights (averaged over 200 bootstrapping trials) and colour-coded by the frequency each feature was selected by elastic net. The numbers in parentheses are the frequency each feature was selected. Each column is a cell line and each row is a feature. The cell lines are sorted by their sensitivity to ponatinib (shown at the bottom). j, Western blot analysis of pSHP2 and total SHP2 levels across AML and select CML cell lines. Western blots were performed twice independently with similar results. k, Validation of RPPA data for pSHP2. pSHP2 levels measured by western blot are plotted against pSHP2 levels measured by RPPA for the tested AML and control CML cell lines (n = 19). The cell lines are colour-coded by their sensitivity to ponatinib. P values determined by two-sided Pearson’s correlation test. l, In vivo mouse xenograft experiment survival curves of ponatinib-treated and control mice for the low pSHP2 primagraft DFAM-68555 (n = 7 mice in each treatment group). P values determined by log-rank (Mantle–Cox) test. m, Immunohistochemistry of spleen specimens from mice treated with control or ponatinib for 5 days using anti-CD45. Similar results were found using the other two independent sets of mice.