Quantitative methylation-specific PCR (qMSP) and gene expression test of MethylCap-seq library data using tissue DNA and RNA templates. The screening analysis generated a set of 33 genes that are informative of hepatocellular carcinoma (HCC). This set of genes was further analyzed by qMSP and gene expression using real-time PCR in DNA and RNA samples from 10 health control (HC), 29 liver cirrhosis (LC) and 30 HCC tissues. Three representative gene results are shown here. A) The UCSC scheme of the gene locus and examined promoter region are shown as well as the methylation information in HC, chronic hepatitis B infection (CHB), LC and HCC groups. B) Quantification of the methylation status in HC, LC and HCC. C) Relative gene expression assay by RT-PCR in HC, LC and HCC. For statistical significance, *P <0.05; **P <0.01; ***P <0.001; NS, not significant.