Bioinformatics Division/Center for Synthetic and Systems Biology, Tsinghua National Laboratory for Information Science and Technology (TNLIST), Department of Automation, Tsinghua University, Beijing, China.
PLoS One. 2013 Sep 5;8(9):e74275. doi: 10.1371/journal.pone.0074275. eCollection 2013.
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/.
DNA 甲基化对于许多重要的生物过程和人类疾病至关重要。Illumina Infinium HumanMethylation450 Beadchip 是一种最近开发的平台，可研究超过 480,000 个 CpG 位点和少数 CHG 位点的全基因组 DNA 甲基化状态，具有高质量的数据。为了分析这个有前途的平台的数据，我们开发了 FastDMA，可用于识别显著差异甲基化的探针。除了单个探针分析，FastDMA 还可以进行基于区域的分析，以识别差异甲基化区域（DMRs）。统一的统计模型，协方差分析（ANCOVA），用于在 FastDMA 中进行所有分析。我们将 FastDMA 应用于来自癌症基因组图谱（TCGA）的三个大型 DNA 甲基化数据集，发现不同类型癌症中有许多差异甲基化的基因组位点。在测试数据集上，FastDMA 显示出比当前工具更高的计算效率。FastDMA 可以通过集成的管道和高效的计算效率，为大规模 DNA 甲基化研究的数据分析提供便利。该软件可通过 http://bioinfo.au.tsinghua.edu.cn/software/fastdma/ 免费获得。
