As shown in Figure 2B, a comparison of the MeD-seq sequencing data demonstrated that the methylation levels of HOXA1, CLEC11A, and TSPYL5 in non-cirrhotic HCC were higher than in the control groups: the hypermethylation scores of HOXA1, CLEC11A, and TSPYL5 were able to discriminate non-cirrhotic HCC from cirrhosis, hepatitis, and benign lesions (p < 0.05), as is consistent with the qMSP data. Here, HOXA1 is linked to hepatocellular carcinoma.