SMAD3 and hepatocellular carcinoma: For each TGF-β context-specific gene group (MDA unique and HCC unique), we derived three sets of signatures: SMAD3-high gene set (genes that display higher levels of SMAD3 in the corresponding BTIC type), open chromatin-high gene set (genes with higher levels of either H3K4me3, H3K27ac or Pol II in the corresponding BTIC type), and DNA hypo-methylation gene set (genes with lower levels of TSS DNA methylation in the corresponding BTIC type) (Table S2).