Table 1.
Clinical and Pathological Characteristics of 27 HCC cases.
Figure 1.
Genome-wide Methylation450 BeadChip DNA methylation portrait.
A. Left: Significant differential methylation (DM) among the 485,577 CpG loci with a cut-off as Bonferroni adjusted p-value <0.05 (red) for statistical significance (blue; p-value >0.05). A. Right: The percentage of hypomethylated (hypo, blue) and hypermethylated (hyper, red) loci among the 62,692 DM CpG loci. B. Functional location of 1,634 hypermethylated loci and their sublocation in promoter regions including TSS1500, TSS200 or 1st Exon and 5′UTR. C. Functional location of the 61,058 hypomethylated loci and their sublocation in promoter regions.
Figure 2.
Methylation profiles of 10,775 promoter region DM loci by DMRs and in relation to CpG islands.
A. Distribution of DM loci in CpG islands and the surrounding shore (0–2 kb from promoter CpG islands), shelf (2–4 kb from promoter CpG islands) and Open sea (other regions in promoter) DM areas. B. DM locus distribution by known differentially methylated regions (DMRs), reprogramming specific DMRs (rDMRs), cancer specific DMRs (cDMRs) and potential novel DMRs in HCC. C. Unsupervised hierarchical clustering of beta values for 702 Shelves, 1,952 Shores, 982 CpG island, and 7,139 Open seas loci (rows) in 47 samples (columns). Blue and red blocks on top of the maps represent 20 adjacent normal and 27 HCC tissues, respectively, while red for the loci represents hypermethylation and blue hypomethylation.
Figure 3.
Distribution of promoter methylation levels.
Genomic surroundings of the 10,775 promoter DM loci excluding the Open seas are shown A. in normals and B. in HCC tumors. The illustrative box plots present the median by a line in the box with the 25th percentile, 75th percentile and the range of the Beta values. Outlier values are shown with yellow color dots extending above or below the range markers. Density of functional loci on each genomic region is indicated on the top part of the figure. Averages of the Beta values are shown on each box plot. *previously known DMRs, cDMRs, rDMRs, Enhancers.
Figure 4.
Dot plots of Beta values for 5 hypo- and hypermethylated loci among the 20 top based on the Delta-beta values from the tumor (n = 27, red) versus adjacent normal comparison (n = 20, blue).
Each point represents the Beta value for an individual. The median Beta value for each locus and tissue type is indicated by a line inside each box-and-whisker within the graph. Paired samples are connected by a line.
Table 2.
Top 20 hypomethylated and hypermethylated loci in HCC based on Delta-beta values.
Table 3.
Biological functions of 10 IPA networks of the genes harboring 982 differentially methylated (DM) loci in the promoter CpG islands.
Figure 5.
Validation results of 8 DM loci by Pyrosequencing.
Gene name, Target ID (locus) by Illumina, and the correlation coefficients (r) are presented. Beta values for each individual HCC (red) and normal (blue) samples are presented by dots. The x-axis and y-axis indicate the Beta value from the Methylation450 BeadChip analysis and the methylation level by Pyrosequencing, respectively.