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. 2022 Feb 15;8:13. doi: 10.1038/s41421-021-00366-y

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a Spearman correlations between DNA methylation levels across gene bodies (including 15 kb flanking regions) and corresponding RNA expression levels in each cell type in representative patients. The boxplots at the bottom show the statistical test results between cancer cells and Norm_epi cells using the Wilcoxon rank-sum test. The promoter regions are from –1 to +0.5 kb around the transcription start site (TSS), and the gene body regions are +2 kb from the TSS to the transcription end site (TES). *P < 0.05; **P < 0.01; ****P < 0.0001. b Cancer cells have more genes with increased promoter DNA methylation. Representative genes across multiple patients are labeled. c Overlap of higher methylated promoters across all patients. The purple lines indicate shared genes, and the blue lines represent the same Gene Ontology terms. d Heatmap showing the top enriched biological terms of the cancer cell hypermethylated promoters in each patient. e Example genes show a reversed pattern between the promoter DNA methylation level and RNA expression level. The statistical test was carried out using the Wilcoxon rank-sum test. ****P < 0.0001.