Fig. 4

Distinct methylation patterns of HCV-HCC REs across groups. Heatmaps were generated using the methylation levels of 136 CpGs located in the 12 LINE-1 and 9 CpGs in the 3 Alu. a Heatmap with samples manually ordered by five groups. b Heatmap with samples and genes clustered by hierarchical cluster analysis using Manhattan distance and Ward’s linkage algorithm. HCC clusters were independent of cirrhosis/normal clusters. Furthermore, HCV-HCC samples (purple stripe) and EtOH-HCC samples (brown stripe) were largely clustered with each other with no misclassification as shown in the dendrogram (pointed by purple and brown arrows, respectively). Cirrhotic liver samples and normal were less distinguishable