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dc.contributor.authorWu, D.en_US
dc.contributor.authorGu, J.en_US
dc.contributor.authorZhang, Michael Q.en_US
dc.date.accessioned2014-08-27T20:40:56Z
dc.date.available2014-08-27T20:40:56Z
dc.date.created2013-09-05en_US
dc.date.issued2013-09-05en_US
dc.identifier.issn1932-6203en_US
dc.identifier.urihttp://hdl.handle.net/10735.1/3936
dc.description.abstractDNA 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/.en_US
dc.language.isoenen_US
dc.relation.urihttp://dx.doi.org/10.1371/journal.pone.0074275
dc.rightsCC BY 3.0 (Attribution)en_US
dc.rights©2013 The Authorsen_US
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/en_US
dc.sourcePLOS One
dc.subjectFastDMAen_US
dc.subjectDNA--Methylationen_US
dc.subjectHuman genomeen_US
dc.subjectCancer--Researchen_US
dc.titleFastDMA: An Infinium Humanmethylation450 Beadchip Analyzeren_US
dc.type.genreArticleen_US
dc.identifier.bibliographicCitationWu, D., J. Gu, and M. Q. Zhang. 2013. "FastDMA: An Infinium HumanMethylation450 Beadchip analyzer." PLOS One 8(9): e74275-1 to 7.en_US
dc.identifier.volume8en_US
dc.identifier.issue9en_US
dc.contributor.utdAuthorZhang, Michael Q.en_US
dc.contributor.ISNI0000 0001 1707 1372 (Zhang, MQ)
dc.contributor.LCNA99086074‏ ‎(Zhang, MQ)


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