Fig. 3

Comparison of DNA methylation and mRNA expression between LMS groups. a Global methylation differences between LMS subgroups. For each LMS sample, the mean methylation was calculated by averaging all available CpG probes. Groups were compared pairwise with the Wilcoxon test. b mRNA expression of known smooth muscle marker genes [11]. Samples were hierarchically clustered within the LMS groups in columns and genes were clustered in rows using the Euclidean distance metric and complete linkage. c Estimated relative cellular composition of the LMS groups based on MethylCIBERSORT [12]. The results suggest the presence of immune cells and fibroblasts in several samples across all LMS subgroups. Tumor purity correlated with estimated immune cell content, but not with fibroblast content (Pearson correlation purity—immune cell fraction − 0.82, Pearson correlation purity—fibroblast fraction -0.06). No association of major blood vessel involvement with any LMS group was observed