Figure 2

Methylated genes are enriched for alternative splicing. Genome-wide DNA methylation data was overlaid with genes and the occurrence of alternative transcripts predicted from a de novo transcriptome assembly. The proportion of methylated genes that were alternatively spliced (triangles) was significantly greater than for unmethylated genes (circles) for several minimum expression thresholds (Fisher’s exact test, P < 1e-10 for each minimum FPKM); expression is measured as the expected number of fragments per kilobase of transcript per million reads (FPKM). We tested several minimum FPKM values to show that enrichment is robust despite the possibility that transcript abundance estimation may be inaccurate at low expression (FPKM). Raw data were the same as for Figure1.