Fig. 2

CBS- and PCF-segmented data (deletions). Significant copy number alterations (deletion, colored in blue) are shown in four different cohorts; breast, ovarian, endometrial, and cervical cancers, analyzed by the two different segmentations algorithms PCF and CBS. For both methods, the threshold for calling copy number gains and losses can be adjusted. For PCF-segmentation, γ = {14, 13, 16, and 25} was selected and for CBS-segmentation α = {0.05, 0.05, 0.02, and 0.005} was defined. The X-axis indicates the statistical significance of the aberrations (q-values). Chromosome positions are indicated alongside the y-axis with centromere positions designated by dotted lines. The significance threshold is allocated by a green line