Figure 6

Hypersilencing of some of the H3K27me3 target genes may involve loss of the histone mark and DNA hypermethylation. In (A,B) the different gene groups presented in the bottom part of the figure correspond to all genes marked by H3K4me3 (A) or H3K27me3 (B) in both patients normal (p1p2n) or tumor samples (p1p2t) and in HT29 cell line. The Shared category included all those genes shared between normal, tumor and HT29 gene groups, either for H3K4me3 (A) or H3K27me3 (B). Similarly, the unique groups include those genes that are only found in normal (n_unique), tumor (t_unique) or HT29 (HT29_unique), when comparing the normal, tumor and HT29 gene groups. For each of these groups of genes, the expression values for normal colon (red), tumor samples (blue) and HT29 cell line (green) are indicated by boxplots and were obtained as described in Figure 4 D-E. In (C), only genes where both DNA methylation and ChIP-chip data were available were considered (Total genes = 7547), which was mainly limited by the coverage of the arrays used in the DNA methylation study. Then, for the same gene groups as in Figure 5B, we calculated the percentage of genes in each group represented with respect to the total of genes (grey) or those genes hypermethylated in CRC (red) as determined in Keshet el al [48]. Using a hypergeometric test we calculated if genes in the different gene groups were significantly over-represented (*, p.value < 0.01) among DNA hypermethylated genes compared to all genes.