Figure 2: Proteogenomic correlation analysis in PDX samples.

(a) Correlation between mRNA and iTRAQ protein expression levels identified pathways with significantly concordant or discordant mRNA-protein expressions. Genes were aligned along the x axis by the rank of their Spearman correlation coefficient between mRNA and protein expression levels. Each colour represents one significantly associated pathway, and each bar represents one gene in the pathway. (b) Proteogenomic summary of xenograft shows relationships among mutation, CNV (normalized log-R ratio), mRNA (log-transformed and normalized RSEM values), proteomic (normalized log2 ratio to reference), and phosphoproteomic expression (normalized log2 ratio to reference) levels of breast cancer-related genes in 24 PDX samples across 4 intrinsic subtypes. Expression values from each dataset were calculated as described (Methods) and truncated to a maximum of 10 and a minimum of −10 for visualization.