使用Mint管道整合DNA甲基化和羟甲基化数据。
Integrating DNA Methylation and Hydroxymethylation Data with the Mint Pipeline.
作者信息
Cavalcante Raymond G, Patil Snehal, Park Yongseok, Rozek Laura S, Sartor Maureen A
机构信息
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.
Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania.
出版信息
Cancer Res. 2017 Nov 1;77(21):e27-e30. doi: 10.1158/0008-5472.CAN-17-0330.
DNA methylation (5mC) plays important roles in mammalian development, oncogenesis, treatment response, and responses to the environment. DNA hydroxymethylation (5hmC) is also an informative epigenetic mark with distinct roles in regulation and cancer. Gold-standard, widely used technologies (bisulfite conversion, followed by deep sequencing) cannot distinguish between 5mC and 5hmC. Therefore, additional experiments are required to differentiate the two marks, and methods are needed to analyze, integrate, and interpret these data. We developed the Methylation INTegration (mint) pipeline to support the comprehensive analysis of bisulfite conversion and immunoprecipitation-based methylation and hydroxymethylation assays, with additional steps toward integration, visualization, and interpretation. The pipeline is available as both a command line and a Galaxy graphical user interface tool. Both implementations require minimal configuration while remaining flexible to experiment specific needs. .
DNA甲基化（5mC）在哺乳动物发育、肿瘤发生、治疗反应及环境应答中发挥着重要作用。DNA羟甲基化（5hmC）也是一种具有调控和癌症相关独特作用的信息性表观遗传标记。金标准且广泛使用的技术（亚硫酸氢盐转化，随后进行深度测序）无法区分5mC和5hmC。因此，需要额外的实验来区分这两种标记，并且需要方法来分析、整合和解读这些数据。我们开发了甲基化整合（mint）流程，以支持对亚硫酸氢盐转化以及基于免疫沉淀的甲基化和羟甲基化检测进行全面分析，并增加了整合、可视化和解读的步骤。该流程既可以作为命令行工具，也可以作为Galaxy图形用户界面工具使用。两种实现方式都只需最少的配置，同时又能灵活满足特定实验需求。
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