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

doi:10.1186/gb-2007-8-5-r79

Genome Biology
Volume 8
Issue 5

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

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

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

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

author email corresponding author email

Genome Biology 2007, 8:R79doi:10.1186/gb-2007-8-5-r79


Published:	11 May 2007

Subject areas: Bioinformatics, Genome studies

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.