Fig. 4.

IGV screenshots showing methylation across several genomic locations and boxplots for all significant sites. a–f Tracks shown are as follows: I. Methylation sites present on the HumanMethylation450 K Chip, II. Color-coded methylation values from control samples, III. Color-coded methylation values from AF samples, IV. Differentially methylated 10-kbp tiling regions called by ADMIRE, V. Differentially methylated 5-kbp tiling regions called by ADMIRE. The color bar encodes the m value, with blue indicating low methylation values and red indicating high methylation values. The absolute scale is created indvidually for each bar. Track IV and V are only used if the search with the corresponding input (5- or 10-kB tiling size) resulted in a significant region. a A 5-kbp region from chr17 called to be differentially methylated by RnBeads with an adjusted p value of 0.00008. b–f Top 5 differentially methylated regions from Admire with q values between 0.0004 and 0.003. g Boxplots for 20 significantly changed protein coding genes (higher in AF sample) identified by ADMIRE. Each box illustrates the distribution of absolute differences of the methylation values in the respective significantly changed region (see also Additional file 4). The cutoff at median methylation value of 5 % is shown as red dashed line