Fig. 1: Methylation and CNV based classification of the PNSTs. | Nature Communications

Fig. 1: Methylation and CNV based classification of the PNSTs.

From: Multiplatform molecular profiling uncovers two subgroups of malignant peripheral nerve sheath tumors with distinct therapeutic vulnerabilities

Fig. 1

a Unsupervised consensus hierarchical clustering of the 20,000 CpGs that show the highest median absolute deviation across the β values of 108 PNSTs. b Kaplan–Meier plot of progression-free survival as function of methylation subgroups. Log-Rank test (p < 0.0001). c Cumulative distribution function plot of the average β values of all CpG sites in the methylation subgroups. d Box plot of the mean β values of the CpG islands versus all other probes in the methylation subgroups (n = 108 samples). Show the median, first and third quartiles (boxes), and the whiskers encompass the 1.5X the interquartile range. One-way ANOVA (p < 2.2e−16 and p = 1.8e−13, respectively). e Volcano plot comparing the number of significant methylated probes of CpG islands in the promoter region between MPNST-G1 and MPNST-G2 (FDR corrected p value < 0.05 and mean β value difference > 0.1). f Differences in the number of methylated and silenced genes in MPNST-G1 versus MPNST-G2. Chi-Square Test (p < 0.0001). g Top 10 pathways affected by CpG island hypermethylation in MPNST-G1. -log (FDR corrected P-value) shown. h CNV heatmap generated from raw CONUMEE calls on methylation data for each subtype across all chromosomes. Inset shows a magnification of chromosome 9. Source data provided as source data file.

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