Imprinted genes are differentially methylated in HCC. (A) Volcano plot for the comparison of HCC tumors vs. adjacent tissues (surrounding/tumor). The horizontal line defines the P value threshold of 0.001. Two representative hypermethylated (APC and RASSF1) and hypomethylated (GABRA5 and MEST) genes are shown respectively in red and blue fonts. (B) Distribution of differentially methylated CpG sites (n = 244) according to chromosomal location (blue bars). Reference proportion for all probes is shown as red bars. (C) Heatmap of differentially methylated imprinted CpG sites (n = 43), with high methylation represented in red and low methylation in blue. Annotations in the lower bars correspond to tumor vs. surrounding tissues, associated risk factors, and tumor stage. No data is shown for surrounding tissues (NA). (D) Estimated proportion of imprinted genes in the total dataset (upper pie chart) and the differentially methylated CpG sites (lower pie chart). Preferential maternal and paternal expressions are shown separately. (E) Validation of selected imprinted genes was assessed by pyrosequencing using 5 tumor/surrounding pairs. *P value <0.05.