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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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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Updated: Apr 1, 2026

Performing Custom MicroRNA Microarray Experiments

Performing Custom MicroRNA Microarray Experiments

Published on: October 28, 2011

Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.

Janine Arloth¹, Daniel M Bader², Simone Röh¹

¹Translational Research Department, Max Planck Institute of Psychiatry, Kraepelinstrasse 2-10, 80804, Munich, Germany.

|October 2, 2015

Summary

This summary is machine-generated.

Microarray probe annotation accuracy is critical for reliable gene expression analysis. The Re-Annotator pipeline improves probe mapping by using updated databases, correcting annotation errors in existing microarray platforms.

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Last Updated: Apr 1, 2026

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Published on: October 28, 2011

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Microarray technology is widely used for high-throughput gene expression, methylation, and genotyping.
Accurate probe mapping is essential for reliable biological findings from microarrays.
Existing annotation tables from manufacturers are often outdated and inconsistent with current genome and transcriptome databases.

Purpose of the Study:

To develop and present Re-Annotator, a novel pipeline for re-annotating microarray probe sequences.
To enhance the accuracy of probe mapping for gene expression microarrays.
To provide a freely available tool and updated annotation files for specific microarray platforms.

Main Methods:

Developed the Re-Annotator pipeline utilizing a custom-built mRNA reference database.
Applied Re-Annotator to the Illumina Human-HT12 v4 microarray platform.
Compared Re-Annotator's performance against another re-annotation tool, ReMOAT, using computational experiments.

Main Results:

Approximately 25% of probes on the Illumina Human-HT12 v4 microarray showed discrepancies with the manufacturer's annotation.
Re-Annotator demonstrated improved re-annotation accuracy compared to the ReMOAT tool.
The pipeline is adaptable for various microarray types beyond gene expression.

Conclusions:

Thorough re-annotation of probe information is crucial for the validity of microarray analyses.
Re-Annotator offers a significant improvement in microarray probe re-annotation.
The Re-Annotator pipeline and associated annotation files are publicly accessible for broader scientific use.