The gene expression was compared to the GISTIC copy number values for BAP1, FOXC1, and MYC. Decreased BAP1 gene expression was correlated to a decreased to the copy number status for all classes (across all samples, p-value = 2.2e−16, CCA, CCA-Like, Blast-Like, and HCC p < 0.001) (Supplementary Fig. 7c). This evidence concerns the gene BAP1 and cholangiocarcinoma.