CpG Islands Methylation and Selective Pressure Figure 1. Methylation of HIR CGIs compared to methylation of CGIs in other genomic regions. For each cell line, the mean methylation value of CGIs inside HIR regions (open bars) and of the CGIs in the remaining part of the genome (closed bars) are reported. Inset shows the same data summarized by cell group (Cancer Transformed = CT, EBV transformed = EBV, Normal Untransformed = NU). Values are means +/2 Standard Error (SE). doi:10.1371/journal.pone.0023156.g001 obtained by comparing the methylation of CGIs inside 5LSRs with the methylation of CGIs localized in the other regions of the genome. Also for this different measure of selective pressure, in all cell lines analyzed, CGIs inside regions under selective pressure were less methylated than the remaining CGIs. The differences were highly statistical significant (Bootstrap p-value,1023) in 17 cell lines analyzed, but did not reach this significance in 8 cell lines (p,0.05). Nevertheless, combining the results of all 25 cell lines by means of the test statistic - 2 log (p1,p2 … p25), where p1, p2 … p25 are the p-values of the individual tests, we reached a combined statistical significance much less than 1023. Table S6 reports in detail the results of the analysis To check if the results could be due to the same CGIs identified by both methods, we searched for CGIs that are both within HIRs and within 5LSRs. We found only 70 CGIs in common between Figure 2. Methylation of 5LSRs CGIs compared to methylation of CGIs in other genomic regions. For each cell line, the mean methylation value of CGIs inside 5LSRs regions (open bars) and of the CGIs in the remaining part of the genome (closed bars) are reported. Inset shows the same data summarized by cell group (Cancer Transformed = CT, EBV transformed = EBV, Normal Untransformed = NU). Values are means +/2 SE. doi:10.1371/journal.pone.0023156.g002 PLoS ONE | www.plosone.org 3 August 2011 | Volume 6 | Issue 8 | e23156