Bicluster ID | Enhancer class | # enhancers | Median DNA methylation | P-value |
|---|
M12 | I | 447 | 0.76 | 1 |
M13 | I | 33 | 0.71 | 0.08 |
M1A9 | I | 127 | 0.74 | 1 |
M1A27 | I | 664 | 0.76 | 1 |
M12A27 | I | 222 | 0.74 | 0.29 |
M1A927 | I | 47 | 0.60 | 0.03 |
M23 | II | 371 | 0.67 | 5.1e-40 |
M2A9 | II | 342 | 0.69 | 4.8e-18 |
M2A27 | II | 1136 | 0.74 | 2.6e-8 |
M3A9 | II | 153 | 0.63 | 5.7e-25 |
M3A27 | II | 193 | 0.66 | 4.8e-27 |
M23A9 | II | 109 | 0.64 | 3.3e-19 |
M23A27 | II | 144 | 0.66 | 9.5e-21 |
M2A927 | II | 140 | 0.68 | 7.0e-14 |
M3A927 | II | 69 | 0.65 | 5.3e-12 |
M23A927 | II | 56 | 0.65 | 2.2e-9 |
- Enhancer class is defined by the presence (class I) or absence (class II) of the histone mark H3K4me1 in their histone states. To compute the median DNA methylation level of a given bicluster, we first calculated a methylation level for each CpG cytosine with at least 10 sequencing reads as the ratio of the number of methylated reads versus the total number of reads, using the single-base-resolution methylome map by Lister et al. [32]. Next, for each enhancer region, an average DNA methylation level of all CpG cytosines was calculated. Finally, a median DNA methylation level of all enhancers in a bicluster was then calculated. The median DNA methylation level of all 2744 ES cell enhancers used in this study is 0.76. We compared the DNA methylation levels of each set of bicluster enhancers to that of all ES cell enhancers used in this study using the Komolgonov-Smirnov test. P-values are corrected for multiple testing using the Bonferroni method.
