Additional file 9.

Characterizing the clock CpGs using DNA sequence properties. Figure titles are preceded by ' + ’ or '-’ if they report properties of positively related or negatively related clock CpGs, respectively. Panels in the first row (A-E) relate the clock CpGs to chromatin state annotation provided in [29]. The y-axis reports the mean number of cell lines (out of 9 cell lines) for which the CpGs were in the chromatin state mentioned in the title. (A) The bar plots shows that the 193 positively related CpGs were significantly (P = 1.6E-6) less likely to be in chromatin state 1 (active promoters) than the other 21k CpGs, which is not the case for the 160 negatively related CpGs (C). (B) Positively related CpGs were more likely to be in chromatin state 3 regions (poised promoters). (D) Negatively related CpGs were more likely to be in chromatin states 2 (weak promoters). (E) Negatively related CpG are often located chromatin state 4 regions (strong enhancers). (F) No significant relationship with CpG island status can be observed for the positively related CpGs. (K) Negatively related CpGs are significantly over-represented in shores. (G) Positively related CpGs were outside of RNApol2 bound regions (annotation from [87]). This is not the case for negatively related CpGs (L). (H-J) Positively related CpGs are over-represented near Polycomb-group target genes, that is, in regions with high occupancy of Suz12 (P = 7.1E-6, H), EED (P = 0.0030, I), and H3K27m3 (P = 0.0048, J). This is not the case for the negatively related CpGs (M-O).

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Horvath Genome Biology 2013 14:R115   doi:10.1186/gb-2013-14-10-r115