Batch effects in differential DNA methylation research
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 have not been systematically analysed. Here,using array data for nine types of cancers, we evaluated the effects of experimental batches on differential DNA methylation detection. The results showed batch effects could greatly affect the discovery of DNA methylation biomarkers. Then, we compared the directions of DNA methylation changes detected from different datasets for the same cancer. We found for a given cancer, the directions of methylation and expression changes detected from different datasets, excluding potential batch effects, were highly consistent.
Batch effects TCGA DNA methylation Reproducibility
Chen Yao Hongdong Li Xiaopei Shen Zheng He Zheng Guo
Bioinformatics Centre and Key Laboratory for NeuroInfomation of the Education Ministry of China,Scho Bioinformatics Centre and Key Laboratory for NeuroInfomation of the Education Ministry of China,Scho
国际会议
The 5th International Congress on Mathematical Biology(第五届国际生物数学大会 ICMB 2011)
南京
英文
1617-1621
2011-06-01（万方平台首次上网日期，不代表论文的发表时间）