Sung H, et al. Global Cancer statistics 2020: GLOBOCAN estimates of incidence and Mortality Worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49.

Article  PubMed  Google Scholar 

Schabath MB, Cote ML. Cancer Progress and priorities: Lung Cancer. Cancer Epidemiol Biomarkers Prev. 2019;28(10):1563–79.

Article  PubMed  PubMed Central  Google Scholar 

Hao D, et al. The single-cell Immunogenomic Landscape of B and plasma cells in early-stage lung adenocarcinoma. Cancer Discov. 2022;12(11):2626–45.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ciechomska M, Roszkowski L, Maslinski W. DNA methylation as a future therapeutic and diagnostic target in rheumatoid arthritis. Cells, 2019. 8(9).

Tian H, et al. PHF14 enhances DNA methylation of SMAD7 gene to promote TGF-β-driven lung adenocarcinoma metastasis. Cell Discov. 2023;9(1):41.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen D, et al. DNA methylation of Cannabinoid Receptor Interacting Protein 1 promotes pathogenesis of Intrahepatic Cholangiocarcinoma through suppressing parkin-dependent pyruvate kinase M2 ubiquitination. Hepatology. 2021;73(5):1816–35.

Article  CAS  PubMed  Google Scholar 

Shang Y, et al. TET2-BCLAF1 transcription repression complex epigenetically regulates the expression of colorectal cancer gene Ascl2 via methylation of its promoter. J Biol Chem. 2022;298(7):102095.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kulis M, Esteller M. DNA Methylation cancer Adv Genet. 2010;70:27–56.

PubMed  Google Scholar 

Baylin SB, Jones PA. Epigenetic determinants of Cancer. Cold Spring Harb Perspect Biol, 2016. 8(9).

Zane L, Sharma V, Misteli T. Common features of chromatin in aging and cancer: cause or coincidence? Trends Cell Biol. 2014;24(11):686–94.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu Y, et al. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nat Biotechnol. 2019;37(4):424–9.

Article  CAS  PubMed  Google Scholar 

Vaisvila R, et al. Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. Genome Res. 2021;31(7):1280–9.

Article  PubMed  PubMed Central  Google Scholar 

Zhou W, et al. SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions. Nucleic Acids Res. 2018;46(20):e123.

PubMed  PubMed Central  Google Scholar 

Jühling F, et al. Metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Res. 2016;26(2):256–62.

Article  PubMed  PubMed Central  Google Scholar 

Tian Y, et al. ChAMP: updated methylation analysis pipeline for Illumina BeadChips. Bioinformatics. 2017;33(24):3982–4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhou W, Laird PW, Shen H. Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes. Nucleic Acids Res. 2017;45(4):e22.

PubMed  Google Scholar 

Jaffe AE, et al. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol. 2012;41(1):200–9.

Article  PubMed  PubMed Central  Google Scholar 

Cavalcante RG, Sartor MA. Annotatr: genomic regions in context. Bioinformatics. 2017;33(15):2381–3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wu T, et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innov (Camb). 2021;2(3):100141.

CAS  Google Scholar 

Loyfer N, et al. A DNA methylation atlas of normal human cell types. Nature. 2023;613(7943):355–64.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized Linear models via Coordinate Descent. J Stat Softw. 2010;33(1):1–22.

Article  PubMed  PubMed Central  Google Scholar 

Simon N, et al. Regularization paths for Cox’s proportional hazards Model via Coordinate Descent. J Stat Softw. 2011;39(5):1–13.

Article  PubMed  PubMed Central  Google Scholar 

Sengupta RBD. Modeling Survival Data: extending the Cox Model by Terry M. Therneau; Patricia M. Grambsch. Sankhya Ser A. 2003;65(4):843–4.

Google Scholar 

Blanche P, Dartigues JF, Jacqmin-Gadda H. Estimating and comparing time-dependent areas under receiver operating characteristic curves for censored event times with competing risks. Stat Med. 2013;32(30):5381–97.

Article  PubMed  Google Scholar 

Yang JD, Roberts LR. Epidemiology and management of hepatocellular carcinoma Infect Dis Clin North Am, 2010. 24(4): pp. 899–919, viii.

Ye C, et al. Whole-genome DNA methylation and hydroxymethylation profiling for HBV-related hepatocellular carcinoma. Int J Oncol. 2016;49(2):589–602.

Article  CAS  PubMed  Google Scholar 

Ferlay J, et al. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int J Cancer. 2015;136(5):E359–86.

Article  CAS  PubMed  Google Scholar 

Han Y, et al. Comparison of EM-seq and PBAT methylome library methods for low-input DNA. Epigenetics. 2022;17(10):1195–204.

Article  PubMed  Google Scholar 

Morris TJ, Beck S. Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data. Methods. 2015;72:3–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dedeurwaerder S, et al. A comprehensive overview of Infinium HumanMethylation450 data processing. Brief Bioinform. 2014;15(6):929–41.

Article  CAS  PubMed  Google Scholar 

Suzuki H, et al. DNA methylation and microRNA dysregulation in cancer. Mol Oncol. 2012;6(6):567–78.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen BF, et al. microRNA-199a-3p, DNMT3A, and aberrant DNA methylation in testicular cancer. Epigenetics. 2014;9(1):119–28.

Article  CAS  PubMed  Google Scholar 

Heilmann K, et al. Genome-wide screen for differentially methylated long noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as regulated by enhancer DNA methylation with prognostic relevance for human breast cancer. Oncogene. 2017;36(46):6446–61.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Oyinlade O, et al. Analysis of KLF4 regulated genes in cancer cells reveals a role of DNA methylation in promoter- enhancer interactions. Epigenetics. 2018;13(7):751–68.

Article  PubMed  PubMed Central  Google Scholar 

Benetatos L, Vartholomatos G. Enhancer DNA methylation in acute myeloid leukemia and myelodysplastic syndromes. Cell Mol Life Sci. 2018;75(11):1999–2009.

Article  CAS  PubMed  Google Scholar 

Liang Y, et al. Reactivation of tumour suppressor in breast cancer by enhancer switching through NamiRNA network. Nucleic Acids Res. 2021;49(15):8556–72.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Qian C, et al. LncRNA PROX1-AS1 promotes proliferation, invasion, and migration in prostate cancer via targeting miR-647. Eur Rev Med Pharmacol Sci. 2020;24(17):8628.

CAS  PubMed  Google Scholar 

Jiang W, Zhao X, Yang W. MiR-647 promotes cisplatin-induced cell apoptosis via downregulating IGF2 in non-small cell lung cancer. Minerva Med. 2021;112(2):312–3.

Article  PubMed  Google Scholar 

Huang Z, et al. Deregulation of circ_003912 contributes to pathogenesis of erosive oral lichen planus by via sponging microRNA-123, -647 and – 31 and upregulating FOXP3. Mol Med. 2021;27(1):132.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu X, et al. LINC00472 suppresses oral squamous cell carcinoma growth by targeting miR-455-3p/ELF3 axis. Bioengineered. 2022;13(1):1162–73.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Weber M, et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet. 2007;39(4):457–66.

Article  CAS  PubMed