Fig. 5

Within-patient similarity at the different layers. a Distributions of the within-group similarities for the four grade groups (visualized as violin plots) based on the Pearson correlation at the CNA layer (upper), mRNA layer (middle), and protein layer (lower). A “violin” with the correlations between TA1 and paired TA2 for the different patients has been added to all three plots and colored in purple. Points represent the actual values. The horizontal lines correspond to the median value in each of the groups. P values from the one-sided Wilcoxon rank sum test comparing the within-patient to the within-group similarities (where all values from the four groups are gathered together): 8.97e−09 for the CNA, 4.42e−08 for the mRNA, and 6.27e−04 for the protein layer. b The correlations between TA1 and paired TA2 for the different patients at one layer are plotted against the corresponding correlations at another layer for each pair of layers: mRNA versus CNA (upper), protein versus CNA (middle), and protein versus mRNA (lower). The points are labeled and colored based on the overall grade in all plots; r, Pearson correlation