Fig. 2: Fuels of epigenetic ITH in ESCC.

a Methylation level comparison between paired Tumor (n = 186) and adjacent normal (n = 36) samples. Two-sided paired t test is used for comparison. b, c Enrichment of hypermethylated DMRs (b) and hypomethylated DMRs (c) for annotated genomic elements between tumor (n = 186) and paired normal (n = 36) samples. *P < 0.05, **P < 0.01, ***P < 0.001; two-sided Fisher’s exact test. d The pairwise distance of tumor samples from the same patient is based on the DMRs and SCNA profiles. Each dot represents a pair of tumor samples from the same patient. Spearman’s correlation coefficient (rho) and corresponding P-value is shown (n = 452 tumor region pairs). Line of best fit shown in blue and gray area represents 95% confidence bands. e Phylogenetic and phyloepigenetic trees were constructed using ESCC14 and ESCC25. f Distribution of entropy, epipolymorphism, and discordantly methylated read (PDR) scores between neutralnd somatic copy-number alterations regions across 36 ESCC patients with 186 tumor regions. Box plot center line represents median value; lower and upper hinges represent 25th and 75th percentiles; the minimum and maximum are indicated by the extremes of the box plot; ***P < 0.001, NS, no significance, P > 0.05; two-sided Wilcoxon rank-sum test.