Figure 2. Discovery of DNA methylation markers to distinguish BCa and normal tissue.

(A) Unsupervised hierarchical clustering of 26 methylation markers differentially methylated between NAT (n = 21) and BCa tumor tissue (n = 412) in the TCGA cohort. (B) Box plot presenting the β-value distribution of cg21472056 among BCa tumor tissue samples (n = 412), NAT (n = 21), and normal blood WBCs (n = 656). A β-value of zero represents no methylation, whereas 1 represents full methylation. The data are shown as median with the interquartile range. Statistical significance was assessed using 1-way ANOVA followed by Dunnett’s tests. (C) Unsupervised hierarchical clustering of 26 methylation markers differentially methylated among NAT (n = 21), BCa tumor tissue (n = 21), and matched urine (n = 18) in the SYSMH cohort. The unavailable value is shown in gray. (D) Box plot presenting the β-value distribution of cg21472056 among BCa tumor tissue (n = 21), matched urine (n = 18), and NAT (n = 21), which was detected by TOF-MS. The data are shown as median with the interquartile range. Statistical significance was assessed using 1-way ANOVA followed by Dunnett’s tests. (E) The Spearman correlation analysis of cg21472056 methylation level between the tumor tissue and matched urine in 18 patients. Pearson’s χ² test was used to analyze statistical significance. **P < 0.01 and ***P < 0.001.