Fig. 2: Human and murine SMARCB1-deficient PTCLs share common methylation profiles.
From: Lack of SMARCB1 expression characterizes a subset of human and murine peripheral T-cell lymphomas
A Median global DNA methylation in human PTCLs (n = 4) and CD3 T cells (n = 5). UMAP analysis based on the 10,000 most variable CpGs and 5 neighbors. Heatmap showing 10,000 most variable CpGs. Boxplot settings: middle, median; lower hinge, 25% quantile; upper hinge, 75% quantile; upper/lower whisker, largest/smallest observation less/greater than or equal to upper/lower hinge ±1.5 × IQR. B Median global DNA methylation in murine PTCLs (n = 5), splenic cells (n = 5) and Cd3 T cells (n = 5). UMAP analysis based on the 10,000 most variable CpGs and 5 neighbors. Heatmap showing 10,000 most variable CpGs. Boxplot settings: middle, median; lower hinge, 25% quantile; upper hinge, 75% quantile; upper/lower whisker, largest/smallest observation less/greater than or equal to upper/lower hinge ±1.5 × IQR. C Overlap of genes hyper- or hypomethylated in murine in human PTCLs compared to Cd3 T cells. Hypomethylated cutoff: σ/σmax > 0.4, q < 0.01, Hypermethylated cutoff: σ/σmax > 0.4, q < 1e-5. D Biological process-associated GO terms assigned to concordantly hyper- and hypomethylated genes in PTCLs compared to Cd3 T cells. Over-representation analysis was performed using WebGestalt (https://2024.webgestalt.org/) with adjustment for multiple testing (Benjamini–Hochberg) (Table S9). Only gene sets with more than 10 genes were considered. (x axis, Enrichment ratio). Source data of A–D are provided as a Source Data file. A–C Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license.
