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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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Related Experiment Video

Updated: Aug 12, 2025

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies

Published on: May 6, 2022

Interactive DNA Methylation Array Analysis with ShinyÉPICo.

Octavio Morante-Palacios^1,2

¹Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain.

Methods in Molecular Biology (Clifton, N.J.)

|February 1, 2023

Summary

This summary is machine-generated.

ShinyÉPICo is a user-friendly tool for analyzing DNA methylation arrays. It simplifies the entire process, from raw data to identifying differentially methylated positions and regions.

Keywords:

DNA methylation Differentially Methylated Positions Differentially Methylated Regions Epigenetics Shiny Web Interface

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Area of Science:

Genomics
Epigenetics
Bioinformatics

Background:

DNA methylation arrays (450k and EPIC) are cost-effective for human DNA methylation analysis.
Analyzing these arrays requires specialized tools to manage raw data and identify significant changes.

Purpose of the Study:

To introduce ShinyÉPICo, an interactive, web-based graphical tool for analyzing Illumina DNA methylation arrays.
To provide a comprehensive guide for users to perform end-to-end analysis of methylation data.

Main Methods:

ShinyÉPICo processes raw data from Illumina 450k and EPIC methylation arrays.
The tool offers an interactive interface for selecting analysis parameters.
It guides users from initial data import to the final identification of differentially methylated positions/regions.

Main Results:

ShinyÉPICo enables complete analysis of DNA methylation array data.
Users can analyze data locally or on a server.
The tool facilitates the identification of differentially methylated positions and regions.

Conclusions:

ShinyÉPICo offers a comprehensive and accessible solution for DNA methylation array analysis.
The tool empowers researchers to efficiently analyze Illumina methylation data.
Understanding the available parameters is key to optimizing analysis outcomes.