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. 2012 Dec 27;2:197. doi: 10.3389/fonc.2012.00197

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Copyright © 2012 Tang, Varadan, Kamalakaran, Zhang, Dimitrova and Hicks.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.

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Significant DMRs tend to co-localize with breakpoints enriched regions. The copy number profile of all 108 breast tumors is shown on the top track (CNV). The middle track (DMR) shows the amplitude of the DNA methylation level change compared to normal across genome. Hypo-methylated regions are assigned a negative score, defined as log10(p) while hyper-methylated regions take a score equal to −log(p). Significant DMRs are marked by peaks with a score greater than ±2. The bottom track (BER) shows the locations of breakpoint enriched regions. Breakpoint enriched DMRs (BEDMR), i.e., DMRs occurring in the vicinity of a BER are marked by vertical yellow lines and black arrows.