Fig. 2

Molecular perturbation scores for point mutations, CNAs, transcriptome, and proteome data. a Distributions of the first type of molecular perturbation scores (DE_count’s) for the four grade groups (visualized as violin plots) at the mutation layer (upper left), CNA layer (upper right), mRNA layer (lower left), and protein layer (lower right). Points represent the actual values. The horizontal lines correspond to the median value in each of the four grade groups. b Distributions of the second type of molecular perturbation scores (DE_sum’s) for the four grade groups (visualized as violin plots) at the CNA layer (upper left), mRNA layer (upper right), and protein layer (lower left). Points represent the actual values. The horizontal lines correspond to the median value in each of the four grade groups. P values (in each of the titles) show the significance of the one-sided Wilcoxon rank sum test where the values of G3 and G4/5 are gathered together and compared to the values of G1 and G2 (also gathered together)