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DNA Microarrays

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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Updated: May 23, 2026

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Published on: September 18, 2020

MethLAB: a graphical user interface package for the analysis of array-based DNA methylation data.

Varun Kilaru¹, Richard T Barfield, James W Schroeder

¹Departments of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA.

|March 21, 2012

Summary

This summary is machine-generated.

Researchers developed MethLAB, a user-friendly R package for analyzing DNA methylation data from arrays. This tool efficiently handles large datasets, identifies methylation-phenotype associations, and controls for false discoveries, aiding complex trait and disease research.

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Area of Science:

Epigenetics
Genomics
Bioinformatics

Background:

DNA methylation changes are linked to complex traits and diseases.
Array-based methods generate large DNA methylation datasets.
Limited user-friendly software exists for analyzing this data.

Purpose of the Study:

To develop an accessible software package for analyzing array-based DNA methylation data.
To provide a flexible and efficient tool for researchers with varying programming experience.

Main Methods:

Developed MethLAB, an R package with a graphical user interface (GUI).
MethLAB reads and manipulates array-based methylation data.
Tests for methylation-phenotype associations using linear models and controls for false discovery rate (FDR).

Main Results:

MethLAB offers a user-friendly GUI for data manipulation.
It performs association testing between DNA methylation and phenotypes.
The software controls for multiple testing using FDR and generates publication-quality figures.

Conclusions:

MethLAB is a valuable open-source resource for DNA methylation data analysis.
It empowers users without programming experience to conduct flexible and powerful analyses.
Facilitates research into the role of DNA methylation in complex traits and diseases.