Fig. 3: Integration of protein reproducibility ranks and gene-specific mRNA–protein correlations.

a Association between aggregated protein reproducibility ranks from Upadhya et al.²⁶ and mRNA–protein correlations in the ProCan-DepMapSanger dataset. Aggregated protein reproducibility ranks are binned (upper), with Spearman’s correlation from unbinned data shown (lower). b Scatter plot of mRNA–protein correlation against aggregated protein reproducibility rank, with cancer drivers indicated by triangle data points. Labels indicate genes highlighted in the text and shown in (c). c For each gene indicated in (b), plots show the distribution of mRNA-protein correlations across tissues in the ProCan-DepMapSanger (pink solid line), Clinical Proteomic Tumor Analysis Consortium (CPTAC; light dashed line) and Cancer Cell Line Encyclopedia (CCLE; dark dashed line) datasets. Background (grey solid line) indicates the median mRNA-protein correlation from all genes in the ProCan-DepMapSanger dataset. Only tissues with data from more than ten samples are included. d mRNA–protein correlation of CTNNB1 for each tissue type in the ProCan-DepMapSanger dataset. e Distribution of CTNNB1 mRNA expression across samples from the ProCan-DepMapSanger dataset, with outliers (>3 standard deviations above the mean) indicated. f Scatterplot showing mRNA expression and protein abundance for CTNNB1 (upper) and distribution of CTNNB1 protein abundance (lower) across samples in the ProCan-DepMapSanger dataset. Outliers indicated in f are those calculated from mRNA expression data in (e).