Fig. 2.

DNA methylation alterations in HCC are detectable in CLD. (A) PC analysis of 12 healthy liver samples, and 10 paired CLD and HCC samples, showing PC1 and PC3. (B, C) Differential methylation analysis [−log₁₀(q) against log₂ fold change (M value)] comparing CLD (B) and HCC (C) with healthy livers. Significant CpG sites (|log₂ fold change| > 1.5, q < 0.05) are coloured according to the legend. (D) T statistics (absolute values) of 339 differentially methylated CpG sites in both CLD and HCC compared with normal livers. DM: |log2FC| > 1.5, q < 0.05. P computed from paired Wilcoxon test. (E) Distribution of differentially methylated CpG sites (DMPs) according to their genomic features, detected in 10 CLD and 10 HCC compared with 12 normal livers. (F) Venn diagram showing intersection of DMRs called in CLD and HCC samples compared with normal livers. PC: Principal component; CLD: chronic liver disease; HCC: Hepatocellular carcinoma; DM: differentially methylated; DMP: differentially methylated probes; DMR: differentially methylated region.