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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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Exon Array Analyzer: a web interface for Affymetrix exon array analysis.

Pascal Gellert¹, Shizuka Uchida, Thomas Braun

¹Max-Planck-Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany.

Bioinformatics (Oxford, England)

|October 8, 2009

Summary

This summary is machine-generated.

The Exon Array Analyzer (EAA) is a user-friendly web server for identifying alternative splicing events using Affymetrix Exon Arrays. It successfully identified 885 differentially expressed probe sets in 649 genes, including heart-specific alternative splicing events.

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Alternative splicing is a key mechanism for generating proteomic diversity.
Analyzing alternative splicing events from high-throughput data requires specialized tools.
Affymetrix Exon Arrays provide a platform for genome-wide splicing analysis.

Purpose of the Study:

To develop and present the Exon Array Analyzer (EAA), a web server for identifying alternative splicing events.
To provide a user-friendly interface for analyzing Affymetrix Exon Array data.
To demonstrate the EAA's capability in identifying tissue-specific alternative splicing.

Main Methods:

The Exon Array Analyzer (EAA) web server implements the Splice Index algorithm.
Utilizes various filters to reduce false positive alternative splicing events.
Analyzes Affymetrix Exon Array data from 11 murine tissues.

Main Results:

Identified 885 differentially expressed probe sets in 649 genes.
Successfully detected 649 genes with differential alternative splicing.
Characterized heart-specific alternative splicing events by comparing heart tissue data with other tissues.

Conclusions:

The Exon Array Analyzer (EAA) is an effective tool for identifying alternative splicing events.
The EAA facilitates biological validation of splice events through detailed annotation and graphics.
The EAA demonstrates versatility in analyzing various tissue-specific splicing patterns.