Fig. 2: CNA-mRNA-protein correlation.

Histograms of the distributions of the per-gene Spearman correlation coefficients (a) for CNA-mRNA and (b) mRNA-protein expression. sig.: significant. c Venn diagram of the number of enriched Reactome pathways for genes/proteins ranked by CNA-mRNA expression correlation (orange) and mRNA-protein expression correlation (blue). Enrichment and statistical significance were defined by gene set enrichment analysis. Multiple correction was performed using the Benjamini–Hochberg method. Barplot of selected Reactome pathways enriched among genes with high CNA-mRNA expression correlation (orange) and/or with high mRNA-protein expression correlation (blue). Statistically significant normalized enrichment scores (NES, p < 0.05) are shown in darker shades (dark orange/blue) while non-significant NESs are shown in lighter shades (light orange/blue). d Scatterplot of the per-gene Spearman correlation coefficients (y-axis) between mRNA and protein expression against (x-axis) between CNA and mRNA. Genes in five of the recurrently altered regions as defined by GISTIC2 are colored according to the color key. Inset shows the genes with >0.5 correlation coefficients in both comparisons. Dysregulated genes (compared to normal livers) on both the mRNA and protein levels are underlined. Source data are provided as a Source Data file.