Fig. 1

Exploring cancer pathway analysis through simulation. a Simulated somatic mutation dataset including two FMPs (genes 1–5) and an FMG (gene 16). Mutated genes are shown in red and non-mutated genes are shown in white. A reduced set of tumors and genes (10 × 20) is shown as an example; the full simulation is (1000 × 1000). b Network-based propagation of mutations over a simulated gene interaction network. Shades of red show propagated mutation values for tumor sample #3. c Mutation dataset from a following network propagation. d Tumor stratification performance with increasing frequency of background mutations, when no random interactions are presented. Performance is measured by calculating Adjusted Random Index (ARI) between the true subtypes and the tumor clusters derived by network stratification. e Tumor stratification performance with increasing density of interactions within FMPs, when no random interactions are presented. f Tumor stratification performance with increasing random gene interaction density