Enroth et al. BMC Cancer 2011, 11:450 http://www.biomedcentral.com/1471-2407/11/450 Page 9 of 13 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. was compared with those previously reported as fre- quently hypermethylated in CRC [48]. As shown in Fig- ure 6C, both H3K27me3 genes in normal and tumor colon samples were significantly over-represented among DNA hypermethylated genes. This was not the case for the HT29 genes. Over-representation was only significant for normal colon, when considering H3K27me3 unique groups, and in fact even a trend towards under-representation was observed for H3K27me3 genes unique to HT29 (Figure 6C). Discussion By comparing normal and tumor colon samples, it was observed that some regions, either shared or unique to