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Table 3 Characteristics of the selected CpG sites

From: Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas

Short name CpG number Gene symbol 1/FC 1/FC Correlation CpG region Hypomethylated Hypermethylated Absolute d Kruskal–Wallis
(Gene expression) (Methylation) (β value) (β value) (β value) Pvalue
Negative correlation     
4–09 cg19510698 ALDH1A3 6.3 6.9 -0.49 GB 0.339 0.748 0.41 3.5 × 10–5
3–13 cg27652350 ALDH1A3 6.0 31.4 -0.44a GB 0.181 0.830 0.65 1.5 × 10–5
1–26 cg21359747 ALDH1A3 5.7 28.8 -0.38 P 0.121 0.751 0.63 2.5 × 10–5
2–37 cg23352695 EVI2A 1.8 8.4 -0.47a P 0.235 0.694 0.46 6.5 × 10–5
3–30 cg00250430 DMRT2 2.7 14.5 -0.41b P 0.138 0.652 0.51 1.2 × 10–4
2–18 cg20955688 TMEM71 1.6 11.6 -0.41 P 0.090 0.490 0.40 5.1 × 10–5
1–39 cg08687163 MST1R 1.6 19.0 -0.39b P 0.566 0.951 0.39 1.2 × 10–4
2–43 cg09874127 UBA7 4.5 6.8 -0.37 P 0.094 0.406 0.31 1.6 × 10–3
1–34 cg23418591 APCDD1L 5.9 36.6 -0.33 P 0.097 0.739 0.64 5.8 × 10–5
1–31 cg14546153 APCDD1L 5.2 22.2 -0.33 P 0.057 0.549 0.49 1.1 × 10–5
5–01 cg00201234 FBLN2 3.4 31.9 -0.32 P 0.075 0.662 0.59 1.1 × 10–4
4–21 cg22736323 PDGFRA 6.3 11.7 -0.31 P 0.182 0.679 0.50 4.8 × 10–2
1–24 cg01035422 PLIN 4.9 5.0 -0.31 P 0.167 0.544 0.38 1.4 × 10–3
1–01 cg22298088 NNAT 24.7 9.3 -0.30b P 0.492 0.876 0.38 1.1 × 10–5
1–13 cg12862537 NNAT 41.4 16.6 -0.27 P 0.548 0.940 0.39 2.0 × 10–4
2–16 cg22502502 TRIM38 1.7 7.2 -0.30 P 0.120 0.468 0.35 1.1 × 10–2
5–36 cg22836229 EFCAB1 1.6 16.1 -0.30 P 0.167 0.708 0.54 3.0 × 10–3
4–15 cg11391732 HSPB3 2.4 9.4 -0.30 P 0.361 0.795 0.43 6.7 × 10–3
1–03 cg18508525 CD36 13.5 17.4 -0.30 P 0.246 0.811 0.56 9.7 × 10–5
3–38 cg20786074 EFEMP1 1.9 11.0 -0.28a P 0.167 0.658 0.49 6.0 × 10–5
2–02 cg10150813 SEL1L3 1.5 14.1 -0.27 P 0.232 0.771 0.54 9.6 × 10–5
1–27 cg08278554 C15orf48 1.7 10.1 -0.27 P 0.183 0.640 0.46 1.3 × 10–5
2–01 cg08397758 PYROXD2 1.6 17.4 -0.26 P 0.159 0.709 0.55 3.2 × 10–4
4–06 cg00476577 ZNF217 1.6 9.7 -0.26 P 0.094 0.486 0.39 1.9 × 10–4
1–02 cg16907566 COL14A1 1.7 13.8 -0.26 P 0.120 0.606 0.49 9.6 × 10–5
1–20 cg01473816 ELF5 2.3 4.2 -0.25 P 0.461 0.758 0.30 6.3 × 10–4
1–11 cg25181284 GPD1 3.6 9.9 -0.25 P 0.524 0.910 0.39 1.5 × 10–4
4–07 cg26205432 PLN 3.4 3.8 -0.24 P 0.302 0.581 0.28 3.1 × 10–3
3–42 cg12567315 TSPAN13 1.5 19.8 -0.23 P 0.053 0.494 0.44 1.6 × 10–2
4–02 cg10062065 SPEG 2.4 15.2 -0.20 P 0.364 0.870 0.51 7.3 × 10–4
Positive correlation     
3–07 cg10895543 CDKN2A 0.3 17.9 0.58 GB 0.188 0.758 0.57 2.8 × 10–6
1–35 cg24690731 SOX7 0.6 12.1 0.30 P 0.217 0.735 0.52 4.3 × 10–4
1–14 cg04396791 SHANK2 0.4 52.7 0.25 P 0.079 0.759 0.68 8.9 × 10–4
1–18 cg10362475 SHANK2 0.5 18.1 0.25 GB 0.221 0.792 0.57 8.0 × 10–4
5–33 cg01820777 MICALL2 0.6 5.3 0.20 P 0.089 0.345 0.26 7.8 × 10–3
  1. aSignificant correlation of gene expression within the range of DNA hypermethylation.
  2. bSignificant correlation of gene expression within the range of DNA hypomethylation.
  3. GB, gene body; P, promoter.
  4. 1/FC is defined as the inverse value of the fold change.