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. 2007 Jun 8;3(6):e110. doi: 10.1371/journal.pcbi.0030110

Figure 2. Co-Localization between the Five Components of the Open Chromatin Score and the Three CpG Island Maps.

Figure 2

(A) shows the relative frequency of overlap between epigenetically modified sites and CpG islands (percentage values).

(B) shows the degree of over-representation relative to a simulated case where sites are uniformly distributed over the chromosomes (base-2 log scores). Yellow boxes correspond to frequent overlap, blue boxes to rare overlap. H3D, histone H3K4 dimethylation; H3T, histone H3K4 trimethylation; H3A, histone H3K9/14 acetylation; DHS, DNase I hypersensitive sites; TFS, SP1 transcription factor binding, plus the CpG island abbreviations used throughout this study (TJU, GGF, and GGM). (B) is symmetrical as the result of averaging, therefore only the upper right triangular matrix is reported. (A) is not symmetrical, as is obvious from an example: 51.4% of all 578 known DNase I hypersensitive sites on Chromosomes 21 and 22 overlap with a GGM CpG island, while only 5.0% of all 5,913 GGM CpG islands overlap with an experimentally determined DNase I hypersensitive site.