Fig. 3

Identification of coherent association. a Definition of four areas A–D in the interaction profile similarity map for association indices between two mRNAs measured by shared lncRNAs versus the indices measured by shared mRNAs. This map of mRNAs is defined similar to the density histograms of lncRNAs in Fig. 2. b Percentages of gene pairs with protein–protein interactions (PPI) among the associated mRNAs selected in the area A, B, C, or D. Each plot shows the analysis results of each breast cancer subtype obtained using five different association indices, respectively. c GO functional similarity between associated mRNA pairs selected in each area using five different association indices for the four breast cancer subtypes