Additional file 2.
Supplementary Figures. Supplementary Figure 1: Sensitivity of the MIRA technique. Supplementary Figure 2: The distribution of MESs from MIRA-seq, input and randomized methylome of normal. Supplementary Figure 3: Goodness of fit was tested for two basic normalized MESs (MESt and MESl), two background normalized MESs (MESt-MESbg and MESl-MESbg), and raw readcounts against the Poisson and Gaussian model. Supplementary Figure 4: Average MES pattern of human promoters which were subgrouped into high, intermediate, and low CpG density promoters (HCP, ICP, and LCP, respectively). Supplementary Figure 5: Chromosome-wide average MESs for normal (black circle) and cancerous (red circle) tissue. Supplementary Figure 6: Chromosomal distribution of the average MES (black (normal) and red (cancer) curve corresponding to the left axis) and the average CpG observed/expected ratio (gray shade corresponding to the left axis) in 1 Mb sliding windows. Supplementary Figure 7: Average MES pattern of subgrouped CGIs (5'CGIs, intergenic CGIs and intergenic CGIs). Supplementary Figure 8: Plots of several genes with 5'CGIs hypermethylation. Supplementary Figure 9: MDM2 methylation level of normal and cancerous tissue in three individual samples by pyrosequencing. Supplementary Figure 10: Amplification ratio of several genes (DYRK2, IFNG, IL26, MDM1, and MDM2) within chromosome 12q14 LRES region by real-time qPCR. Supplementary Figure 11: Amplification ratio of specific locus in an upstream region of MDM2 by real-time qPCR.
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Park et al. BMC Medical Genomics 2011 4:82 doi:10.1186/1755-8794-4-82