Fig. 3: Validation of differential methylation of “HCC-spec” and “HCC-detect” CpG sites in the GSE63775 dataset.
From: A high-throughput test enables specific detection of hepatocellular carcinoma
The top panel shows the count of methylated reads in genomic regions containing each of the 5 CpGs of the markers for tumor tissue samplesfrom HCC (n = 27), NAT (n = 27), while the bottom panel shows the same for plasma samples from HCC (n = 27), cirrhosis (n = 16), and NAT (n = 29). The CpGs analyzed were from A. CHFR, B. VASH2, C. GRID2IP, D. CCNJ, and E. F12. To evaluate significance in tumor tissues, we used a nonparametric two-tailed t-test. For plasma samples, we used Kruskal-Wallis nonparametric ANOVA with Dunn’s multiple comparisons test (****p < 0.0001, ***p < 0.001, **p < 0.01, *p < 0.05, n.s. nonsignificant). The data points were plotted on a log2 scale on the y-axis, and each zero value on the y-axis was replaced with 0.001 to avoid undefined logarithm. The line at the median with 95% confidence interval is shown in all plots. Source data are provided as a Source Data file.
