Fig. 4

Performance of the second layer of iCAGES. a Performance of the iCAGES score compared to MutSigCV, evaluated on 14,169 TCGA patients. A higher AUC score indicates better performance. The 95% CI was computed with 2000 stratified bootstrap replicates (testing dataset I). b Performance of iCAGES compared to IntOgen, evaluated on data from 6748 patients used in the Rubio-Perez et al. study. Each bar represents the number of patients whose cancer driver gene can be identified by iCAGES or by IntOgen. Top One, Top Five, Top Ten and Top Twenty refer to using the top gene, top five genes, top ten genes, and top 20 genes from prediction, respectively. A significant advantage of iCAGES compared to other tools is indicated with ***P ≤ 0.0001 (Bonferroni correction; testing dataset II). c Performance of iCAGES compared to IntOgen, Phen-Gen, and MuSiC evaluated on data from 3178 patients used in the Kandoth et al. study (testing dataset III). d Performance of iCAGES compared to IntOgen, Phen-Gen, and MuSiC evaluated on data from 71 patients used in the Kandoth et al. study but not in the Rubio-Perez et al. study (testing dataset IV)