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Open Access Software

An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data

Michał J Okoniewski1*, Tim Yates1, Siân Dibben2 and Crispin J Miller1

Author affiliations

1 Bioinformatics Group, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Manchester M20 4BX, UK

2 Molecular Biology Core Facility, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Manchester M20 4BX, UK

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Citation and License

Genome Biology 2007, 8:R79  doi:10.1186/gb-2007-8-5-r79

Published: 11 May 2007

Abstract

Affymetrix exon arrays contain probesets intended to target every known and predicted exon in the entire genome, posing significant challenges for high-throughput genome-wide data analysis. X:MAP http://xmap.picr.man.ac.uk webcite, an annotation database, and exonmap http://www.bioconductor.org/packages/2.0/bioc/html/exonmap.html webcite, a BioConductor/R package, are designed to support fine-grained analysis of exon array data. The system supports the application of standard statistical techniques, prior to the use of genome scale annotation to provide gene-, transcript- and exon-level summaries and visualization tools.