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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

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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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
07:50

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Published on: September 18, 2020

Methyl-Analyzer--whole genome DNA methylation profiling.

Yurong Xin1, Yongchao Ge, Fatemeh G Haghighi

  • 1Department of Psychiatry, Columbia University and New York State Psychiatric Institute, New York, NY 10032, USA.

Bioinformatics (Oxford, England)
|June 21, 2011
PubMed
Summary

Methyl-Analyzer is a Python package for analyzing genome-wide DNA methylation data from the Methyl-MAPS method. It processes sequencing data to estimate CpG methylation probabilities with single-base resolution.

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Area of Science:

  • Genomics
  • Epigenetics
  • Bioinformatics

Background:

  • DNA methylation is crucial for gene regulation and cellular function.
  • The Methyl-MAPS method provides comprehensive genome-wide DNA methylation profiles.
  • Accurate analysis of Methyl-MAPS data is essential for understanding epigenetic regulation.

Purpose of the Study:

  • To introduce Methyl-Analyzer, a novel Python package.
  • To enable efficient analysis of genome-wide DNA methylation data generated by Methyl-MAPS.
  • To provide single-base resolution CpG methylation probability estimates.

Main Methods:

  • Methyl-Analyzer is a Python package utilizing sequencing reads from methylated and unmethylated compartments.
  • It processes and integrates data from Methyl-MAPS, an enzymatic-based whole-genome DNA methylation profiling method.
  • The package analyzes >80% of CpG dinucleotides in mammalian genomes.

Main Results:

  • Methyl-Analyzer successfully processes and integrates Methyl-MAPS sequencing data.
  • The package estimates CpG methylation probabilities at single-base resolution.
  • It facilitates comprehensive analysis of whole-genome DNA methylation profiles.

Conclusions:

  • Methyl-Analyzer is a valuable tool for researchers studying epigenetics and gene regulation.
  • The package enhances the utility of the Methyl-MAPS method for large-scale DNA methylation analysis.
  • It supports the investigation of epigenetic mechanisms across mammalian genomes.