Figure 5

MOABS reveals differential methylation underlying TFBSs. (a) UCSC genome browser illustration of one TF binding site. The tracks from top to bottom are genomic positions, RefSeq Gene, HSC Methylation, ESC Methylation, and TFBS. For each CpG, an upward bar denotes the methylation ratio. (b) Distribution of the number of DMCs underlying TFBSs. The inserted boxplot indicates the length distribution of TFBSs with 1–3 DMCs. (c) Number of differentially methylated TFBSs predicted by different methods at 5% FDR. (d) Running enrichment scores for TFBSs. All the CpGs are ranked by each method. The score increases if the CpG is in a TFBS or decreases if not. Only 10000 CpGs are sampled to make this plot, as indicated by the x-axis. The 10000 times of random shuffle of TFBSs determined p-values of the maximum enrichment score to be 1.4E-3, 1.6E-3, and 4E-3 for MOABS, FETP and BSMOOTH respectively. (e) and (f) Same as (c) and (d) with 4X sequencing depth by random sampling. The 10000 times of random shuffle of TFBSs determined p-values of the max enrichment score to be 2.9E-2, 5.1E-2, and 9.2E-2 for MOABS, FETP and BSMOOTH respectively.