Extended Data Fig. 5: Expression profiles of Trim28+/D9-light hypo-methylated genes in ear biopsies, healthy and tumor tissues.
In all boxplots, the lower and upper hinges represent the first and third quartiles. The whiskers extend to the smallest and largest values within 1.5*the interquartile range (IQR). The solid black dot indicates the mean. a-d) Genomic snapshots of genes enriched for differentially methylated probes between Trim28+/D9-light and heavy male mice. Black dotted boxes highlight differentially methylated regions, and significant probes are marked with asterisks. Boxplots show DNA methylation levels (beta values) for each gene. P-values are assessed by two-sided Wilcoxon test. N=24 male mice (15 -heavy, 9 -light). Genes shown: Mycn (a), Jak3 (b), Hmga2 (c), and the Pcdha cluster (d). e) Boxplot of mean expression for Trim28+/D9-light hypo-methylated genes in WT vs Trim28+/D9 animals from day 10 ear biopsies. P-value = 4.1e-7, two-sided Wilcoxon test. N=15 male mice (5 WT, Trim28+/D9). f) Boxplot of mean DNA methylation levels of Trim28+/D9-light hypo-methylated probes in WT vs Trim28+/D9 from day 10 ear clips. P-value < 2.2e-16, two-sided Wilcoxon test. N=22 male mice (8 WT, 14 Trim28+/D9). g) Paired dot plots showing mean expression of Trim28+/D9-light hypo-methylated genes in normal vs matched tumor samples across tissues. P-values: prostate (<2.2e-16), seminal vesicles (1.3e-6), intestine (3.2e-9), lungs (4.7e-4), two-sided Wilcoxon test. h) Heatmap of Trim28+/D9-light hypo-methylated genes in normal and matched tumor tissues, with Z-score transformation. In g-h, N=36 tissues (5 healthy and 5 matched tumor biological replicates for prostate, seminal vesicle, and intestine tumors, and 3 healthy and 3 matched lung tumor biological replicates, all from Trim28+/D9animals). i) Representative boxplots showing expression of Trim28+/D9-light hypo-methylated genes in tumor samples from Trim28+/D9-light and -heavy tissues. N=18 tissues (prostate: 3 -light, 2 -heavy animals; seminal vesicle: 3 -light, 2 -heavy; intestine: 2 -light, 3 -heavy; lungs: 1 -light, 2 -heavy). j) Heatmap showing number of mutations for indicated genes in tissues from Trim28+/D9-light and -heavy animals. Relative percentages of samples with mutations, and predicted effects, are reported alongside. Under the heatmap, bar plots show the percentage of mutated reads per sample. N=16 tissues (5 intestines, 2 lungs, 5 prostate, 4 seminal vesicles).
