FastDMA: An Infinium Humanmethylation450 Beadchip Analyzer

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FastDMA: An Infinium Humanmethylation450 Beadchip Analyzer

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Title: FastDMA: An Infinium Humanmethylation450 Beadchip Analyzer
Author(s):
Wu, D.;
Gu, J.;
Zhang, Michael Q. (UT Dallas)
Sponsors: Center for Systems Biology
Item Type: Article
Keywords: FastDMA
DNA--Methylation
Human genome
Cancer--Research
Abstract: DNA methylation is vital for many essential biological processes and human diseases. Illumina Infinium HumanMethylation450 Beadchip is a recently developed platform studying genome-wide DNA methylation state on more than 480,000 CpG sites and a few CHG sites with high data quality. To analyze the data of this promising platform, we developed FastDMA which can be used to identify significantly differentially methylated probes. Besides single probe analysis, FastDMA can also do region-based analysis for identifying the differentially methylated region (DMRs). A uniformed statistical model, analysis of covariance (ANCOVA), is used to achieve all the analyses in FastDMA. We apply FastDMA on three large-scale DNA methylation datasets from The Cancer Genome Atlas (TCGA) and find many differentially methylated genomic sites in different types of cancer. On the testing datasets, FastDMA shows much higher computational efficiency than current tools. FastDMA can benefit the data analyses of large-scale DNA methylation studies with an integrative pipeline and a high computational efficiency. The software is freely available via http://bioinfo.au.tsinghua.edu.cn/software/fastdma/.
ISSN: 1932-6203
Persistent Link: http://hdl.handle.net/10735.1/3936
https://doi.org/10.1371/journal.pone.0074275
Terms of Use: CC-BY 3.0 (Attribution)

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CC-BY 3.0 (Attribution) Except where otherwise noted, this item's license is described as CC-BY 3.0 (Attribution)