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相关概念视频

DNA Microarrays02:34

DNA Microarrays

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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
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相关实验视频

Updated: Jun 8, 2025

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies
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MethylCallR:一个对Illumina甲基化珠芯片的综合分析框架.

Hyun-Ho Yang1, Mi-Ryung Han2,3

  • 1Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea.

Scientific reports
|November 6, 2024
PubMed
概括

MethylCallR是一个新的R包,简化了使用Illumina甲基化微阵列进行表观全基因组关联研究 (EWAS). 它通过新的EPICv2BeadChip解决了这些挑战,使得DNA甲基化分析具有稳定性.

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Last Updated: Jun 8, 2025

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科学领域:

  • 基因组学和表观遗传学
  • 生物信息学和计算生物学

背景情况:

  • 基因甲基化对基因环境相互作用至关重要,通过表观基因组范围的关联研究 (EWAS) 来研究.
  • 照明甲基化EPICv2珠芯片 (EPICv2) 由于重复探头和改变探头名称等新功能而带来了挑战.
  • 现有的算法需要更新,EPICv2与旧的微阵列版本的预处理/集成仍然很复杂.

研究的目的:

  • 开发MethylCallR,这是一个开源的R包,用于标准化的EWAS,使用Illumina甲基化微阵列,包括EPICv2.
  • 为处理EPICv2特定特征提供解决方案,例如重复探头.
  • 为了促进不同Illumina甲基化微阵列版本之间的无集成和转换.

主要方法:

  • 开发MethylCallR,这是一个R包,为EWAS提供标准程序.
  • 在EPICv2中使用预设或定制数据来管理重复探测的功能.
  • 包含不同Illumina人类甲基化珠芯片类型的转换函数.
  • 应用MethylCallR用于异常样本检测和统计功率估计,以选择重要的探测器.

主要成果:

  • MethylCallR成功地标准化了Illumina甲基化微阵列的EWAS程序,包括EPICv2.
  • 该套件有效地处理重复的探测器,并促进跨不同微阵列版本的数据集成.
  • 使用MethylCallR对公开可用的数据进行分析,结果与之前的研究相似,验证了它的实用性.

结论:

  • MethylCallR提供了一个强大的,用户友好的解决方案,用于预处理和分析来自Illumina微阵列的DNA甲基化数据.
  • 它简化了与EPICv2 BeadChip相关的复杂任务,提高了EWAS的可靠性和可比性.
  • 该方案通过为DNA甲基化分析提供标准化工具,促进表观遗传学的可重复性研究.