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. 2011 Dec 8;6(12):e28503. doi: 10.1371/journal.pone.0028503

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Wrzeszczynski et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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We isolated genes (all points) with extreme copy number variation from the TCGA (A and C) and MSKCC (B and D) data sets. Methylation and tumor to normal expression ratio was then compared for genes at low CNV (A and B) and high CNV (C and D). Genes with oncogenic features (blue ovals; high expression and low methylation) and tumor suppressor features (red ovals; low expression and high methylation) were identified (Table 3).