Fig. 5

Global protein-mRNA correlations across breast tissues and their association with tumor characteristics. a Density plot for global Spearman correlation between protein and mRNA pairs across tumors (n = 59; 5677 protein-mRNA pairs) and adjacent non-cancerous tissue (n = 38; 3316 pairs). Mean global correlation coefficients are significantly different between tumor and adjacent non-cancerous tissue (P < 2.2 × 10⁻¹⁶, Wilcoxon rank sum test). b Concordance between protein and mRNA pairs is associated with discrete pathways in KEGG, e.g., protein processing and metabolism-related pathways. Protein-mRNA pairs for these pathways tend to show significantly increased concordances. Shown are the 10 highest ranked KEGG pathways that are enriched for high concordance protein-mRNA pairs. Multiple test-adjusted P values from the Kolmogorov-Smirnov test. c Protein-mRNA correlation for all proteins in tumors (“proteins,” 5677 protein-mRNA pairs), for tumor proteins with significant differences in abundance between tumor and adjacent non-cancerous tissue (“tumor signature,” n = 2258 pairs), and for basal-like tumor proteins with significant differences in abundance between tumor and adjacent non-cancerous tissue (“basal-like signature,” 159 pairs). Basal-like signature protein-mRNA pairs have the highest concordance. Definition of the signatures is described in the “Methods” section. d Concordance between protein and mRNA levels in breast tumors is associated with the predicted stability of proteins and mRNAs. Protein-mRNA pairs consisting of a protein and mRNA that are both stable have the highest mean concordance