Title: oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA.

Authors: Xu, Zongli; Taylor, Jack A; Leung, Yuet-Kin; Ho, Shuk-Mei; Niu, Liang

Published In Bioinformatics, (2016 Dec 01)

Abstract: 5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are important epigenetic regulators of gene expression. 5mC and 5hmC levels can be computationally inferred at single base resolution using sequencing or array data from paired DNA samples that have undergone bisulfite and oxidative bisulfite conversion. Current estimation methods have been shown to produce irregular estimates of 5hmC level or are extremely computation intensive.We developed an efficient method oxBS-MLE based on binomial modeling of paired bisulfite and oxidative bisulfite data from sequencing or array analysis. Evaluation in several datasets showed that it outperformed alternative methods in estimate accuracy and computation speed.oxBS-MLE is implemented in Bioconductor package ENmix.niulg@ucmail.uc.eduSupplementary information: Supplementary data are available at Bioinformatics online.

PubMed ID: 27522082

MeSH Terms: 5-Methylcytosine/analogs & derivatives*; 5-Methylcytosine/chemistry*; Computational Biology/methods*; CpG Islands; DNA Methylation*; DNA/chemistry*; Models, Theoretical; Sequence Analysis, DNA