Dataset Information
OxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA.
Ontology highlight
ABSTRACT: Motivation
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.Results
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.Availability and implementation
oxBS-MLE is implemented in Bioconductor package ENmix.Contact
niulg@ucmail.uc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
SUBMITTER: Xu Z
PROVIDER: S-EPMC5181539 | biostudies-literature | 2016 Dec
REPOSITORIES: biostudies-literature
Publications
oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA.
Bioinformatics (Oxford, England) 20160813 23
<h4>Motivation</h4>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.<h4>Results</h4>We developed an efficient ...[more]