Differential methylation tests of regulatory regions

Duchwan Ryu, Hongyan Xu, Varghese George, Shaoyong Su, Xiaoling Wang, Huidong Shi, Robert H. Podolsky

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

Differential methylation of regulatory elements is critical in epigenetic researches and can be statistically tested. We developed a new statistical test, the generalized integrated functional test (GIFT), that tests for regional differences in methylation based on the methylation percent at each CpG site within a genomic region. The GIFT uses estimated subject-specific profiles with smoothing methods, specifically wavelet smoothing, and calculates an ANOVA-like test to compare the average profile of groups. In this way, possibly correlated CpG sites within the regulatory region are compared all together. Simulations and analyses of data obtained from patients with chronic lymphocytic leukemia indicate that GIFT has good statistical properties and is able to identify promising genomic regions. Further, GIFT is likely to work with multiple different types of experiments since different smoothing methods can be used to estimate the profiles of data without noise. Matlab code for GIFT and sample data are available at http://www.augusta.edu/mcg/biostatepi/people/software/gift.html.

Original languageEnglish (US)
Pages (from-to)237-251
Number of pages15
JournalStatistical Applications in Genetics and Molecular Biology
Volume15
Issue number3
DOIs
StatePublished - Jun 1 2016

Keywords

  • Bisulfite sequencing
  • differentially methylated regions
  • smoothing

ASJC Scopus subject areas

  • Statistics and Probability
  • Molecular Biology
  • Genetics
  • Computational Mathematics

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