Introduction

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.

Publications

  1. oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA.
    Cite this
    Xu Z, Taylor JA, Leung YK, Ho SM, Niu L, 2016-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Zongli Xu
    Developer

  2. Jack A Taylor
    Developer

    Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, United States of America

  3. Yuet-Kin Leung
    Developer

    Department of Environmental Health, College of Medicine, United States of America

  4. Shuk-Mei Ho
    Developer

    Department of Environmental Health, College of Medicine, United States of America

  5. Liang Niu
    Investigator

    Department of Environmental Health, College of Medicine, United States of America

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Summary
AccessionBT001055
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByLiang Niu