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Related Concept Videos

DNA Microarrays02:34

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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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Related Experiment Video

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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
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mHapBrowser: a comprehensive database for visualization and analysis of DNA methylation haplotypes.

Yuyang Hong1, Leiqin Liu1, Yan Feng1

  • 1Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.

Nucleic Acids Research
|October 13, 2023
PubMed
Summary

mHapBrowser visualizes DNA methylation haplotypes (mHaps), offering new insights beyond mean methylation. This database aids in understanding gene expression and disease classification using phased methylation patterns.

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Area of Science:

  • Epigenetics
  • Genomics
  • Bioinformatics

Background:

  • DNA methylation is a key epigenetic regulator of gene expression.
  • Bisulfite sequencing provides single-base resolution of methylation.
  • Current databases lack analysis of phased methylation patterns (mHaps).

Purpose of the Study:

  • Introduce mHapBrowser, a database for visualizing and analyzing DNA methylation haplotypes (mHaps).
  • Provide tools for comparing mHap patterns across diverse samples.
  • Facilitate downstream analysis of mHap data.

Main Methods:

  • Systematic processing of public bisulfite sequencing data from human, mouse, and rat tissues.
  • Generation of mHap format files for 6366 samples.
  • Integration with WashU Epigenome Browser for visualization and an online server for comparison.

Main Results:

  • mHapBrowser enables visualization of eight mHap metrics and comparison across samples.
  • Demonstrated association between mHap patterns and gene expression.
  • Showcased mHap patterns' role in lung cancer subtype differential expression and improved tumor classification from cell-free DNA.

Conclusions:

  • mHapBrowser provides a valuable resource for exploring DNA methylation haplotypes.
  • Phased methylation patterns offer insights beyond mean methylation levels.
  • mHap analysis has potential applications in gene regulation studies and disease diagnostics.