Hidden among the crowd: differential DNA methylation-expression correlations in cancer occur at important oncogenic pathways.

Once again, we observed a mildly significant enrichment among DCGs ( P -value = 0.017).

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Fifty-five DCGs contain Homeobox domains , which implies a highly significant enrichment ( Q -value = 7.85 × 10 −8 ); and 44 genes contain Pleckstrin homology domains ( Q -value = 0.048, hyper; Supplementary Table 3 ).

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However, among all the DCGs no significant difference in expression could be observed at a 5% FDR using SAM; and only 50 genes ranked significant at a 10% FDR, with a clear trend of these to be more expressed in normal breast (Supplementary Figure 10C ).

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Similarly, average methylation at non promoter-associated regions showed a trend toward hypermethylation in 112 DCGs (5% FDR), but no significant differences were associated with the remaining 93% of the DCGs (Supplementary Figure 10B ).

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