Fig. 3

qMSP analysis on DNA from 175 liver tissues. A DNA methylation score for the 11 selected DMMs in cirrhotic HCC livers compared to cirrhotic livers. B qMSP-based methylation levels relative to the ACTB reference gene were shown for the selected DMMs in 27 patients with cirrhotic HCC compared to 44 with cirrhosis (Mann–Whitney U test; ***, p < 0.001; ****, p < 0.0001). C Methylation levels for the 11 DMMs were presented in red or white. The red color indicated methylation values that exceed the 95 th percentile of the control group (cirrhosis) for each DMM (rows) across the tissue samples (columns). White boxes represented values that fall below the 95 th percentile threshold established in the control group. D DNA methylation scores of 11 tissue-derived DMMs in samples from non-cirrhotic HCC compared to those from patients with non-cirrhotic liver disease (NCLD) and benign hepatic lesions (BHL). E DNA methylation levels of the 11 DMMs, normalized by ACTB, were measured using qMSP in 54 non-cirrhotic HCC, 36 NCLD, and 14 BHL tissues (Mann–Whitney U test; ns, not significant; *, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001). F qMSP-based DNA methylation levels were represented using different colors, with red indicating values above the 95 th percentile of the control group (NCLD and BHL) and white representing values below this threshold