GraphPad Prism 5 (GraphPad Software) was used for statistical analysis. The difference between two groups was calculated by independent Student’s t-test or Wilcoxon signed-rank test. The correlation among methylation and eRNA/mRNA expression was analyzed using Pearson correlation test. Chi-square test with Yates correction was used to determine whether distributions of H3K27ac levels differ between promoters and enhancers. Kaplan–Meier survival analysis was used to determine the overall and disease-free survival rates, which were calculated from the date of curative surgery to death, HCC recurrence or the last follow-up; the differences were compared by log-rank Mantel–Cox test.
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