Journal Article

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

Pascal Gellert, Shizuka Uchida and Thomas Braun

in Bioinformatics

Volume 25, issue 24, pages 3323-3324
Published in print December 2009 | ISSN: 1367-4803
Published online October 2009 | e-ISSN: 1460-2059 | DOI:
Exon Array Analyzer: a web interface for Affymetrix exon array analysis

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Summary: The Exon Array Analyzer (EAA) is a web server, which provides a user-friendly interface to identify alternative splicing events analyzed with Affymetrix Exon Arrays. The EAA implements the Splice Index algorithm to identify differential expressed exons. The use of various filters allows reduction of the number of false positive hits. Results are presented with detailed annotation information and graphics to identify splice events and to facilitate biological validations. To demonstrate the versatility of the EAA, we analyzed exon arrays of 11 different murine tissues using sample data provided by Affymetrix ( Data from the heart were compared with other tissues to identify exons that undergo heart-specific alternatively splicing, resulting in the identification of 885 differentially expressed probe sets in 649 genes.

Availability: The web interface is available at Detailed documentation is available on the EAA web site ( including screen shots, example analyzes and step by step instructions.


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1400 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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