Comparison of methods for DNA methylation data analyses

EPIC array data

• We first use public data set (GSE126672) to compare different methods since these data are from WI-38 fibroblast cell line, and the difference of DNA methlylation of the two sample groups, contorl and NNMT overexpressed groups, were already known in the published paper:Proteomics reveals NNMT as a master metabolic regulator of cancer-associated fibroblasts (https://www.ncbi.nlm.nih.gov/pubmed/31043742).

• Then the placenta data set from our lab were used to comfirm the differeces of results obtained from different methods.

• After comparing bumphunter, Probe Lasso and DMRcate, DMRcate is recommended for detecting DMRs using placenta samples.