使用DSS对亚硫酸氢盐测序进行差异甲基化分析。
Differential methylation analysis for bisulfite sequencing using DSS.
作者信息
Feng Hao, Wu Hao
机构信息
Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA.
Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.
出版信息
Quant Biol. 2019 Dec 31;7(4):327-334. doi: 10.1007/s40484-019-0183-8. Epub 2019 Dec 15.
Abstract
Bisulfite sequencing (BS-seq) technology measures DNA methylation at single nucleotide resolution. A key task in BS-seq data analysis is to identify differentially methylation (DM) under different conditions. Here we provide a tutorial for BS-seq DM analysis using Bioconductor package DSS. DSS uses a beta-binomial model to characterize the sequence counts from BS-seq, and implements rigorous statistical method for hypothesis testing. It provides flexible functionalities for a variety of DM analyses.
摘要
亚硫酸氢盐测序（BS-seq）技术能够在单核苷酸分辨率下测量DNA甲基化。BS-seq数据分析中的一项关键任务是识别不同条件下的差异甲基化（DM）情况。在此，我们提供一个使用Bioconductor软件包DSS进行BS-seq DM分析的教程。DSS使用β-二项式模型来表征来自BS-seq的序列计数，并实现了用于假设检验的严格统计方法。它为各种DM分析提供了灵活的功能。
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本文引用的文献
1
Disease prediction by cell-free DNA methylation.
Brief Bioinform. 2019 Mar 25;20(2):585-597. doi: 10.1093/bib/bby029.
2
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Nucleic Acids Res. 2016 Jul 8;44(W1):W90-7. doi: 10.1093/nar/gkw377. Epub 2016 May 3.
3
HMM-DM: identifying differentially methylated regions using a hidden Markov model.
Stat Appl Genet Mol Biol. 2016 Mar;15(1):69-81. doi: 10.1515/sagmb-2015-0077.
4
HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher's exact test.
Stat Appl Genet Mol Biol. 2016 Mar;15(1):55-67. doi: 10.1515/sagmb-2015-0076.
5
Differential methylation analysis for BS-seq data under general experimental design.
Bioinformatics. 2016 May 15;32(10):1446-53. doi: 10.1093/bioinformatics/btw026. Epub 2016 Jan 27.
6
Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates.
Nucleic Acids Res. 2015 Dec 2;43(21):e141. doi: 10.1093/nar/gkv715. Epub 2015 Jul 15.
7
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Genome Biol. 2014;15(12):550. doi: 10.1186/s13059-014-0550-8.
8
Comprehensive analysis of DNA methylation data with RnBeads.
Nat Methods. 2014 Nov;11(11):1138-1140. doi: 10.1038/nmeth.3115. Epub 2014 Sep 28.
9
A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data.
Nucleic Acids Res. 2014 Apr;42(8):e69. doi: 10.1093/nar/gku154. Epub 2014 Feb 22.
10
DNA methyltransferase inhibition reverses epigenetically embedded phenotypes in lung cancer preferentially affecting polycomb target genes.
Clin Cancer Res. 2014 Feb 15;20(4):814-26. doi: 10.1158/1078-0432.CCR-13-1483. Epub 2013 Dec 13.
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