Enroth et al. BMC Cancer 2011, 11:450 http://www.biomedcentral.com/1471-2407/11/450 Page 5 of 13 Figure 3 Overlaps between genes marked with H3K4me3 in different samples. (A) Overlaps between genes associated with K4 enriched regions detected in patient 1 normal and tumor tissue. (B) Overlaps between genes associated with K4 enriched regions detected in tumor tissue from patient 1, tumor patient 2 and HT29. (C) Same as (B) but for normal tissue from patient 1 and 2. (CDC36+) where around 3% (693) of the genes were found to have bivalently marked promoters. Cui et al [25] performed their study using next generation sequencing and called more regions enriched through- out the genome suggesting that the main cause of differ- ence lies in stringency of the downstream analysis. Detection of genes and pathways with chromatin state differences between tumor and normal samples To identify the genomic regions differing in their chro- matin state between normal and tumor tissues (Meth- ods), the results were split in fifteen so called transitions each representing a combined state of one or more marks in normal and tumor. Three major groups were created; i) gaining or loosing a single mark, ii) keeping a mark and iii) changes involving both marks (Figure 4A and Additional file 2, Figure S4A). The majority fall into category ii), that is no change, and category i) which is in agreement with the large overlaps reported in the previous section (Additional file 2,Table S2). Category iii) implies chromatin transitions between normal and tumor that can result in a switch from tran- scriptionally active (e.g. H3K4me3) to inactive states (e. g. H3K27me3) or vice verse. Therefore, it is the most interesting category in terms of potentially functional consequences from an oncogenic point of view. How- ever, only 4 genes were common to both patients in category iii) (Additional file 2, Table S2). KLF7 (N K27 to T K4), a transcription factor belonging to the KLF family that plays critical roles in differentiation, develop- ment, and maintenance of tissue homeostasis [26], but, to the best of our knowledge, without a specific role in colon cancer. The remaining three common genes (EBF3, DKFZp667I0324 and RBMS1) were all bivalent in normal tissue but lost all their histone methylation in tumor. Among these genes, 2 have previously been functionally characterized. EBF3 is a transcription factor reported to be a tumor suppressor gene [27] with observed silencing in CRC cell line HCT116, was biva- lent in normal and lost both marks in tumor. RBMS1 is Table 2 Comparisons between H3K27me3 target genes in colon tissue samples and CRC cell lines. Patient 1 Patient 2 Cell Lines Patient 1 Patient 2 Cell Lines Normal Tumor Normal Tumor HT29 SW480 K27 K27 K27 K27 K27 SUZ12 Normal K27 600 Tumor K27 310 660 Normal K27 399 349 636 Tumor K27 237 242 282 512 HT29 K27 138 164 154 151 512 SW480 SUZ12 74 88 84 82 67 447 The different gene categories considered (in bold) consisted of the genes marked by H3K27me3 in normal or tumor samples from patient 1 or patient 2, genes bound by H3K27me3 in HT29 CRC cell line and genes bound by SUZ12 in SW480 CRC cell line. Only genes were both H3K27me3 data in tissues samples and HT29 cell line and SUZ12 data in SW480 cell line were available were considered (total = 7393), which was limited by the coverage of the arrays used. The numbers in the diagonal of the table (in bold) indicate all genes included in each category, while the remaining numbers indicate the overlaps between each pair of categories considered in each case.