A novel method for identification and quantification of consistently differentially methylated regions

Ching Lin Hsiao, Ai Ru Hsieh, Ie Bin Lian, Ying Chao Lin, Hui Min Wang, Cathy S.J. Fann

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Advances in biotechnology have resulted in large-scale studies of DNA methylation. A differentially methylated region (DMR) is a genomic region with multiple adjacent CpG sites that exhibit different methylation statuses among multiple samples. Many so-called "supervised" methods have been established to identify DMRs between two or more comparison groups. Methods for the identification of DMRs without reference to phenotypic information are, however, less well studied. An alternative "unsupervised" approach was proposed, in which DMRs in studied samples were identified with consideration of nature dependence structure of methylation measurements between neighboring probes from tiling arrays. Through simulation study, we investigated effects of dependencies between neighboring probes on determining DMRs where a lot of spurious signals would be produced if the methylation data were analyzed independently of the probe. In contrast, our newly proposed method could successfully correct for this effect with a well-controlled false positive rate and a comparable sensitivity. By applying to two real datasets, we demonstrated that our method could provide a global picture of methylation variation in studied samples. R source codes to implement the proposed method were freely available at http://www.csjfann.ibms.sinica.edu.tw/eag/programlist/ICDMR/ICDMR. html.

Original languageEnglish
Article numbere97513
JournalPLoS ONE
Volume9
Issue number5
DOIs
Publication statusPublished - 2014 May 12

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Methylation
methylation
Biotechnology
methodology
DNA methylation
DNA Methylation
sampling
biotechnology
genomics

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Hsiao, Ching Lin ; Hsieh, Ai Ru ; Lian, Ie Bin ; Lin, Ying Chao ; Wang, Hui Min ; Fann, Cathy S.J. / A novel method for identification and quantification of consistently differentially methylated regions. In: PLoS ONE. 2014 ; Vol. 9, No. 5.
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A novel method for identification and quantification of consistently differentially methylated regions. / Hsiao, Ching Lin; Hsieh, Ai Ru; Lian, Ie Bin; Lin, Ying Chao; Wang, Hui Min; Fann, Cathy S.J.

In: PLoS ONE, Vol. 9, No. 5, e97513, 12.05.2014.

Research output: Contribution to journalArticle

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