Fig. 4: Features of BAP1 mutations by 15-GEP Class status.

a Raincloud plot depicting tumor diameter in relation to 15-GEP Class and BAP1 mutation status (n = 1140 tumors). b Raincloud plot depicting tumor thickness in relation to 15-GEP Class and BAP1 mutation status (n = 1140 tumors). c Box plot comparing raw discriminant scores by 15-GEP Class and BAP1 allelic dosage reflected in BAP1 mutation and LOH3p status (n = 905 tumors). Box center line, lower boundary, and upper boundary for box plots in (a–c) represent the median, first quartile, and third quartile, respectively, while box range reflect the interquartile range (IQR). Lower whiskers extend to the minima, or the lowest value up to 1.5 times the IQR from the first quartile. Upper whiskers extend to the maxima, or the highest value up to 1.5 times the IQR from the third quartile. Survival analysis plots displaying the d metastasis-free survival and e overall survival probabilities for Class 1 (n = 715 tumors) and Class 2 (n = 418 tumors) UM according to absolute discriminant score at specified time points including 12 (red curves), 24 (light blue curves), 36 (green curves), 48 (dark blue curves), and 60 (orange curves) months. Significance for continuous variables was determined by two-tailed Wilcoxon rank-sum test. Significance for survival analysis was calculated by Cox proportional hazard analysis by Wald test. All data are available in the Source data file. Exact p values for thickness and diameter in Class 2/BAP1^mut versus Class 1/BAP1^wt were 4.8 × 10⁻²⁹ and 1.8 × 10⁻¹⁶, respectively, and in Class 2/BAP1^mut versus Class 1/BAP1^mut were 2.6 × 10⁻¹⁰ and 3.8 × 10⁻⁷, respectively. 15-GEP 15-gene expression profile, MFS metastasis-free survival, OS overall survival, BAP1^wt BAP1 wildtype, BAP1^mut BAP1 mutant.