Fig. 3

Genomic alterations and stemness scores associated with consensus subtypes. A Violin and box plots of the number of nonsynonymous mutations in the consensus subtypes (n = 338). CGS5 showed a significantly higher mutation burden than other subtypes (P < 0.001 in all comparisons by Student t-test). Within each violin, the horizontal distance between the left and right curved boundaries represents the distribution of mutations in each subtype. In the box plots, the boundaries of each box indicate the 25th to 75th percentile, and the black line within the box marks the mean. Whiskers above and below the box indicate the 10th and 90th percentiles. B Fraction of the genome altered by copy number gain and loss, estimated by gistic2 analysis for each tumor (n = 382). CGS3 and CGS4 had significantly higher proportions of copy number alterations than the other subtypes (P < 0.001 in all comparisons by Student t-test). C Heat map of copy number alterations of the 22 autosomes (n = 382). Red and blue indicate gain and loss of chromosome copy number, respectively. D, E Distribution of stemness (STEM) scores in the consensus subtypes in the training (d) and validation (e) cohorts. The boundaries of each box indicate the 25th to 75th percentile, and the black line within the box marks the mean. Whiskers above and below the box indicate the 10th and 90th percentiles. F Subtype probabilities from GPICS120 in the validation cohort plotted against their stemness scores. The significance is estimated by Pearson correlation coefficient