Table 1

DNA methylation levels of two classes of enhancers in ES cells
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.

Teng and Tan

Teng and Tan BMC Genomics 2012 13:301   doi:10.1186/1471-2164-13-301

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