Figure 7

Observed tumor patterns. (A) Draft tumor evolution paths of putative driver aberrations based on recurrent patterns. Thicker arrows in the prostate path correspond to precedence relations that were confirmed in an independent cohort of 203 WES prostate samples. (B) Draft tumor evolution paths based on cancer pathways. Each node represents a set of genes (aka a pathway). For a pair of pathways P₁ and P₂, CLONET computes the number of dependencies from each gene in P₁ to each gene in P₂, d₁₂, and the inverse, d₂₁. If there is no dependency between P₁ and P₂, then it is expected that d₁₂ and d₂₁ are statistically comparable (that is, d₁₂ is generated from a symmetric binomial distribution with d₁₂ + d₂₁ trials). If d₁₂ > d₂₁ and the P-values of the binomial test with Benjamini-Hochberg FDR correction is <0.01, then the arc is reported.