Table 1.
Baseline characteristics of the study subjects.
Fig 1.
Flow chart describing experiment and analysis.
Fig 2.
The mean chronological age and DNA methylation age (DNAm) of vascular tissues: right coronary artery in the area of advanced atherosclerotic plaques (CAP), internal mammary arteries (IMA), and great saphenous veins (GSV).
Fig 3.
Multi-dimensional scaling for genome-wide methylation of right coronary artery in the area of advanced atherosclerotic plaques (CAP), internal mammary arteries (IMA), and great saphenous veins (GSV).
Arabic numbers are sample IDs.
Table 2.
Comparison of β-values (average ± s.d.) in paired vascular tissues from six patients with atherosclerosis.
Fig 4.
Volcano plot of - log10 (P-value) against delta beta value, representing the methylation difference between right coronary arteries in the area of advanced atherosclerotic plaques (CAP) and internal mammary arteries (IMA).
A total of 194 CpG-sites hypermethylated in CAP with a delta beta ≥ 0.2 and FDR-adjusted p<0.05 are shown in red. A total of 164 CpG-sites hypomethylated in CAP with a delta beta ≤ -0.2 and FDR-adjusted p<0.05 are shown in blue. CpG-sites that exhibited a methylation level difference less 20% are shown in grey. Light red and light blue colors indicate highly differentially methylated CpG-sites (delta beta ≥ 0.40 or delta beta ≤ -0.40 with FDR-adjusted p<0.05). Dashed lines indicate cut-offs for significance.
Fig 5.
Heatmap analysis of 22 highly differentially methylated CpG-sites (delta beta ≥ 0.40 or delta beta ≤ -0.40 with FDR-adjusted p<0.05) between right coronary arteries in the area of advanced atherosclerotic plaques (CAP) and internal mammary arteries (IMA).
Regions shaded blue in the heat map represent hypomethylated regions, regions shaded red represent hypermethylated regions. The top black rectangles shows columns representing CpG-sites located inside CpG-island. Gene symbols and CpG-site IDs are shown on the bottom. Sample IDs are on the right.
Fig 6.
Volcano plot of - log10 (P-value) against delta beta value, representing the methylation difference between great saphenous veins (GSV) and internal mammary arteries (IMA).
A total of 200 CpG-sites hypermethylated in GSV with a delta beta ≥ 0.2 and FDR-adjusted p<0.05 are shown in red. A total of 135 CpG-sites hypomethylated in GSV with a delta beta ≤ -0.2 and FDR-adjusted p<0.05 are shown in blue. CpG-sites that exhibited a methylation level difference less 20% are shown in grey. Light red and light blue colors indicate highly differentially methylated CpG-sites (delta beta ≥ 0.40 or delta beta ≤ -0.40 with FDR-adjusted p<0.05). Dashed lines indicate cut-offs for significance.
Fig 7.
Heatmap analysis of 27 highly differentially methylated CpG-sites (delta beta ≥ 0.40 or delta beta ≤ -0.40 with FDR-adjusted p<0.05) between great saphenous veins (GSV) and internal mammary arteries (IMA).
Regions shaded blue in the heat map represent hypomethylated regions, regions shaded red represent hypermethylated regions. The top black rectangles shows columns representing CpG-sites located inside CpG-island. Gene symbols and CpG-site IDs are shown on the bottom. Sample IDs are on the right.
Table 3.
Methylation level (mean ±SD) at the promoter of HOXD4 gene in paired vascular tissues from twenty one patients with atherosclerosis.