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easyExon – A Java-based GUI tool for processing and visualization of Affymetrix exon array data

Ting-Yu Chang1, Yin-Yi Li1, Chih-Hung Jen4, Tsun-Po Yang1, Chi-Hung Lin145, Ming-Ta Hsu24 and Hsei-Wei Wang1345*

Author Affiliations

1 Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan

2 Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan

3 Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan

4 Veteran General Hospital-Yang Ming Genome Center, National Yang-Ming University, Taipei, Taiwan

5 Department of Education and Research, Taipei City Hospital, Taipei, Taiwan

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BMC Bioinformatics 2008, 9:432  doi:10.1186/1471-2105-9-432

Published: 14 October 2008

Abstract

Background

Alternative RNA splicing greatly increases proteome diversity and thereby contribute to species- or tissue-specific functions. The possibility to study alternative splicing (AS) events on a genomic scale using splicing-sensitive microarrays, including the Affymetrix GeneChip Exon 1.0 ST microarray (exon array), has appeared very recently. However, the application of this new technology is hindered by the lack of free and user-friendly software devoted to these novel platforms.

Results

In this study we present a Java-based freeware, easyExon http://microarray.ym.edu.tw/easyexon webcite, to process, filtrate and visualize exon array data with an analysis pipeline. This tool implements the most commonly used probeset summarization methods as well as AS-orientated filtration algorithms, e.g. MIDAS and PAC, for the detection of alternative splicing events. We include a biological filtration function according to GO terms, and provide a module to visualize and interpret the selected exons and transcripts. Furthermore, easyExon can integrate with other related programs, such as Integrate Genome Browser (IGB) and Affymetrix Power Tools (APT), to make the whole analysis more comprehensive. We applied easyExon on a public accessible colon cancer dataset as an example to illustrate the analysis pipeline of this tool.

Conclusion

EasyExon can efficiently process and analyze the Affymetrix exon array data. The simplicity, flexibility and brevity of easyExon make it a valuable tool for AS event identification in genomic research.