Although MYC was amplified in CCA-Like, Blast-Like, and HCC, only in the Blast-Like and HCC classes was gene expression and copy number correlated (Blast-Like and HCC p-value < 1.0e−4), whereas gene expression and copy number were not correlated in any class for FOXC1 (Supplementary Fig. 7d, e). Here, FOXC1 is linked to cholangiocarcinoma.