Extended Data Fig. 4: Association of TE-chimeric transcripts with methylation, chromatin accessibility, and driver mutations.

a, Scatter plot of global methylation versus number of candidates across samples in 21 tumor types. The regression line is plotted, and the Spearman rho coefficient is displayed on each plot. b, Heat map of ATAC-seq peak expression z-score (left) and transcript RNA expression in z-score (right) for 149 TE-chimeric transcripts. c, Dot plot of difference in number of candidates between samples that have a particular driver mutation and those that do not in a specific cancer type. Dots are ordered by difference. Wilcoxon rank sum test (two-sided) was used with Benjamin-Hochberg correction. Supplementary Table 5 has exact p-values. d, Bar plot of the distribution of types of TP53 mutations across cancer types. e, Box and dot plots of global methylation levels of samples with (purple) and without (blue) TP53 mutations. *P < 0.05, **P < 0.01, ***P < 0.001. Wilcoxon rank sum test (two-sided) was used with Benjamin-Hochberg correction. The ‘N=’ lists the number of tumor samples in each boxplot. Expact p-values are the following: LGG: 9.11E-01, SARC: 1.30E-01, LUAD: 5.52E-03, HNSC: 8.03E-02, BRCA: 9.11E-01, COAD: 2.04E-02, STAD: 8.43E-12, LUSC: 1.40E-03, PRAD: 1.75E-03, UCEC: 1.75E-03, BLCA: 6.65E-01, LIHC: 1.75E-03, SKCM: 1.81E-01. f, Box plot of number of tumor samples in each cancer separated by TP53 mutation type. The ‘N=’ lists the number of tumor samples in each boxplot. All box plots follow the following format: center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; points, outliers.