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

Ting Yu Chang, Yin Yi Li, Chih Hung Jen, Tsun Po Yang, Chi Hung Lin, Ming Ta Hsu, Hsei Wei Wang*

*Corresponding author for this work

Research output: Contribution to journalArticle

13 Scopus citations

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, 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 Affymetrixexon array data. The simplicity, flexibility and brevity of easyExon make it a valuable tool for AS event identification in genomic research.

Original languageEnglish
Article number432
JournalBMC Bioinformatics
Volume9
DOIs
StatePublished - 14 Oct 2008

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