Figure 2. Comparative analysis of grade 3 PNST CISs to human MPNSTs.

CNA, methylome, and microarray expression data from human MPNST data (Supplementary Fig. 6–8, Supplementary Tables 3,5) were combined into a “bubble plot”. The y-axis displays the methylation state (negative number indicating hypomethylation and positive number indicating hypermethylation) of each gene’s CpG-IS nearest to the transcriptional start site (TSS) in MPNSTs versus NHSCs (methylation analysis described in detail in online methods and Supp Table 5). The x-axis depicts the CNA observed in MPNSTs versus NHSCs (determination of CNA is described in online methods and Supp Table 3). Numbers reflect the percentage of the 51 patient samples that have a CNA. Negative numbers indicated CNA loss while positive numbers indicate CNA gains. The yellow shaded area indicates the 95^th percentile for significant recurrent CNAs. Microarray expression was represented by size from 1X-10X (determination of expression changes are described in online methods and Supp Fig 8) and color to depict genes that are upregulated in red (a), downregulated in blue (b), or have no change or have no probes on the microarray in gray (c) in gene expression comparing MPNSTs to NHSCs. For recurrent CNAs, we considered a gene that shows the gain (or loss) pattern if the ratio of gain (or loss) out of all 51 patients is more than 1.5X that of the ratio of loss (or gain). Significant recurrent CNAs must be observed in 23/51 patient samples (95^th percentile).