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Bioinformatics Advance Access first published online on October 6, 2009
This version published online on October 12, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp577
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Pascal Gellert 1, Shizuka Uchida 1 and Thomas Braun 1,*

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

*To whom correspondence should be addressed. Thomas Braun, E-mail: Thomas.Braun{at}mpi-bn.mpg.de


  Abstract

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 (http://www.affymetrix.com). Data from the heart were compared to 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 http://EAA.mpi-bn.mpg.de/.

Contact: Thomas.Braun{at}mpi-bn.mpg.de

Supplementary information: Detailed documentation is available on the Exon Array Analyzer web site (http://EAA.mpi-bn.mpg.de/supp.php) including screen shots, example analyzes and step by step instructions.

Associate Editor: Dr. Trey Ideker

Received on July 27, 2009; revised on September 4, 2009; accepted on September 28, 2009

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