Figure 3

Functional significance of methylated CpG islands in melanoma cells.

(A) The functional class distribution of CpG methylation in the five cell lines. Gene annotation was taken from Refseq at UCSC genome browser. Promoter region was defined as 3000 bp upstream of the transcription starting site (TSS) and the downstream region is defined as 3000 bp downstream of translation stop sequence. (B) Heatmap of methylation fold change in ± 1000 bp windows centered at TSS for cancer related genes in the five cell lines. The rows represent 3,688 cancer-related genes downloaded from the CancerGene database by Higgin et al.⁶⁶, which were filtered for significant methyl CpG levels in melanoma lines relative to HEM-1. Color scale on the right represents MBD2-enrichment, i.e., methyl CpG, fold change. (C) Functional enrichment analysis of diseases and disorders of the gene set in (B).