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Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies
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来自混合DNA样本的DNA甲基化数据的计算解卷.

Maísa R Ferro Dos Santos1,2, Edoardo Giuili1,2, Andries De Koker1,2

  • 1VIB-UGent Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Zwijnaarde, Belgium.

Briefings in bioinformatics
|May 19, 2024
PubMed
概括

本综述比较了25种用于DNA甲基化 (DNAm) 解卷的计算工具,以估计混合样本中的细胞比例. 它指导了基于数据类型和准确生物见解的可用性进行方法选择.

关键词:
基因组甲基化概况的DNA甲基化概况计算式解卷化解卷化工具比较 工具比较

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科学领域:

  • 计算生物学 计算生物学
  • 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
  • 生物信息学是一种生物信息学.

背景情况:

  • 大量DNA甲基化 (DNAm) 数据分析需要解卷以估计细胞类型比例.
  • 许多计算工具已经开发用于DNAm解卷,需要一个比较的概述.

研究的目的:

  • 综合审查和比较2012年至2023年间发表的25种DNA甲基化解卷积方法.
  • 评估数据生成平台,预处理和参考数据集对解卷性能的影响.
  • 为根据数据特征选择合适的解卷方法提供指导方针.

主要方法:

  • 25个DNA甲基化解卷积算法的系统审查和比较.
  • 将方法分为监督,无监督和混合方法.
  • 基于参考,部分参考和无参考的解卷策略的分析.

主要成果:

  • 详细比较的优点和局限性,为每一个25审查的解卷方法.
  • 评估微阵列与测序平台对解卷结果的影响.
  • 评估预处理步骤和对方法性能的参考数据集选择.

结论:

  • 选择DNA甲基化解卷化工具显著影响细胞类型比例估计.
  • 提供了指导方针,以帮助研究人员根据数据类型,可用性和实验背景选择最佳方法.
  • 这次审查是推动DNA甲基化数据分析的关键资源.