1 2 N1 3 4 5 N2 6 7 8 0.0 Hox gene location A4 A3 A5 A6 A7 6.9 A9 A10 A11 A13 chr6:52190631 Liang et al. BMC Genomics 2011, 12:231 http://www.biomedcentral.com/1471-2164/12/231 Page 8 of 16 Peak# 1 2 1 2 1 2 1 2 5 5 1 2 1 2 5 5 1 2 1 2 5 5 1 2 1 2 5 5 1 2 1 2 1 1 B B D D 1 1 B B D D 1 1 B B D D 1 1 B B D Dchr6:52087777 E E N N A A E E N N A A E E N N A A E E N N A A A1 A2 Brain Heart P score color scheme 2.0 Liver Testis Figure 3 DS-DMRs: Heat Map of methyation signal in the Hoxa gene region during development in different tissues. A heat map was constructed based on the NimbleGen P scores of probes, in the Hoxa gene cluster region. Probes included in the heat map either have a P score ≥2 for both of the duplicated samples or at least one tissue/developmental stage or fall into the promoter region of a Hoxa gene. Each row of the color tiles in the heat map represents a NimbleGen probe, while each column represents a sample. The tissue name is labeled at the bottom, while the developmental stage is indicated at the top. The labeled arrows at the right side indicate the position of the TSS and direction of the Hoxa gene transcription. The T-DMRs and DS-DMRs methylation peaks corresponding to those in Additional file 14b are indicated by the numbers on the left side. gene expression either way in any tissue examined. The trend for DS-DMRs, based on analysis of a liver develop- ment expression data set (GSE13149 [44]), seems to be less clear except for adult unique DS-DMR, which are mostly T-DMRs as described earlier and show a similar pattern as T-DMRs (data now shown), suggesting that there might be some differences between T-DMRs and DS-DMRs in the ways they impact gene expression. Discussion Total number of T-DMRs and DS-DMRs MeDIP methylation analysis in conjunction with Nim- bleGen promoter + CpGi microarrays were used to identify adult tissue specific differentially methylated regions (T-DMRs) and developmental stage specific DMRs (DS-DMRs). We used relatively conservative cri- teria to identify methylation peaks requiring both