Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Notch Signaling Reprograms Glial Lipid Metabolism to Promote Hypoxia Resistance.

bioRxiv : the preprint server for biology·2026

Same author

Systems modelling of mitochondrial dynamics in different exercise regimes.

The Journal of physiology·2026

Same author

Filling the Gaps: Generating 4D Dense Cardiac Anatomy from Sparse CMR for Enhanced Tetralogy of Fallot Assessment.

Journal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance·2026

Same author

Neural implicit heart coordinates: 3D cardiac shape reconstruction from sparse segmentations.

Medical image analysis·2026

Same author

Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis.

bioRxiv : the preprint server for biology·2026

Same author

Statistical Atlas-Based Surrogate Model of Biventricular Wall Mechanics.

bioRxiv : the preprint server for biology·2026

Search research articles

Related Experiment Video

Updated: May 2, 2026

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

Published on: October 5, 2016

MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data.

Zhuohui Gan, Jianwu Wang, Nathan Salomonis

¹Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA. azambon@ucsd.edu.

BMC Bioinformatics

|March 14, 2014

Summary

This study introduces a new workflow for analyzing microarray data, simplifying complex bioinformatics tasks. The automated Meta-Analysis of Affymetrix Microarray Data (MAAMD) workflow saves time and computational resources for researchers.

More Related Videos

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

An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome

An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome

Published on: September 20, 2022

Related Experiment Videos

Last Updated: May 2, 2026

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

Published on: October 5, 2016

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

An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome

An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome

Published on: September 20, 2022

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Publicly accessible raw microarray data enables new analyses.
Analyzing raw microarray data is computationally intensive and requires specialized skills.
Automated workflows streamline processing, improve efficiency, and standardize analyses.

Purpose of the Study:

To develop an automated workflow for analyzing Affymetrix microarray data.
To standardize meta-analysis of multiple microarray datasets.
To simplify complex bioinformatics tasks for researchers.

Main Methods:

Developed Meta-Analysis of Affymetrix Microarray Data (MAAMD) workflow in Kepler.
Integrated R and AltAnalyze software tools.
Utilized user-editable CSV files for input parameters and file locations.

Main Results:

MAAMD automates data downloading, quality control, differential gene expression, clustering, and pathway analysis.
Successfully analyzed 4 GEO datasets from mice and drosophila.
Identified gene orthologs responding to hypoxia/hyperoxia in both species within one hour.

Conclusions:

MAAMD significantly reduces analysis time and required computational expertise.
Provides a standardized procedure for intra- and inter-dataset microarray analysis.
Facilitates novel bioinformatics discoveries from public microarray data.