Reproducibility and concordance of differential DNA methylation and gene expression in cancer.

ABSTRACT:

Background

Hundreds of genes with differential DNA methylation of promoters have been identified for various cancers. However, the reproducibility of differential DNA methylation discoveries for cancer and the relationship between DNA methylation and aberrant gene expression have not been systematically analysed.

Methodology/principal findings

Using array data for seven types of cancers, we first evaluated the effects of experimental batches on differential DNA methylation detection. Second, we compared the directions of DNA methylation changes detected from different datasets for the same cancer. Third, we evaluated the concordance between methylation and gene expression changes. Finally, we compared DNA methylation changes in different cancers. For a given cancer, the dire

SUBMITTER: Yao C 

PROVIDER: S-EPMC3250460 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature