Abstract
BackgroundAlternative 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.ResultsIn this study we present a Java-based freeware, 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.ConclusionEasyExon 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.
Highlights
Alternative RNA splicing greatly increases proteome diversity and thereby contribute to species- or tissue-specific functions
Step 3: Feature filtration Statistical filtration We developed Java classes to adopt the Affymetrix MIDAS and PAC alternative splicing algorithms for statistical filtration according to the Affymetrix White Paper[32]
Alternative splicing events in colorectal carcinoma Here we illustrate an example of applying easyExon to quickly identify AS events by analyzing a public accessible colorectal carcinoma dataset, which includes 10 pairs of tumor and normal samples[34]
Summary
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. 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
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