mHapTk：用于分析 DNA 甲基化单倍型的综合工具包。

mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes.

机构信息

State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.

Department of Mathematics, Shanghai Normal University, Shanghai 200234, China.

出版信息

Bioinformatics. 2022 Nov 15;38(22):5141-5143. doi: 10.1093/bioinformatics/btac650.

DOI:10.1093/bioinformatics/btac650

PMID:36179079

Abstract

SUMMARY

Bisulfite sequencing remains the gold standard technique to detect DNA methylation profiles at single-nucleotide resolution. The DNA methylation status of CpG sites on the same fragment represents a discrete methylation haplotype (mHap). The mHap-level metrics were demonstrated to be promising cancer biomarkers and explain more gene expression variation than average methylation. However, most existing tools focus on average methylation and neglect mHap patterns. Here, we present mHapTk, a comprehensive python toolkit for the analysis of DNA mHap. It calculates eight mHap-level summary statistics in predefined regions or across individual CpG in a genome-wide manner. It identifies methylation haplotype blocks, in which methylations of pairwise CpGs are tightly correlated. Furthermore, mHap patterns can be visualized with the built-in functions in mHapTk or external tools such as IGV and deepTools.

AVAILABILITY AND IMPLEMENTATION

https://jiantaoshi.github.io/mhaptk/index.html.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

亚硫酸氢盐测序仍然是检测单核苷酸分辨率下 DNA 甲基化图谱的金标准技术。同一片段上 CpG 位点的 DNA 甲基化状态代表离散的甲基化单倍型（mHap）。mHap 水平的指标被证明是很有前途的癌症生物标志物，比平均甲基化能更好地解释基因表达的变化。然而，大多数现有的工具都集中在平均甲基化上，而忽略了 mHap 模式。在这里，我们提出了 mHapTk，这是一个用于分析 DNA mHap 的全面的 Python 工具包。它以预定义的区域或整个基因组范围内的单个 CpG 的方式计算八个 mHap 水平的汇总统计信息。它识别甲基化单倍型块，其中成对 CpG 的甲基化紧密相关。此外，mHap 模式可以使用 mHapTk 中的内置功能或外部工具（如 IGV 和 deepTools）进行可视化。