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Nucleic Acids Res. 2008 Jan;36(Database issue):D780-6. Epub 2007 Oct 11.

X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

Author information

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

Abstract

Affymetrix exon arrays aim to target every known and predicted exon in the human, mouse or rat genomes, and have reporters that extend beyond protein coding regions to other areas of the transcribed genome. This combination of increased coverage and precision is important because a substantial proportion of protein coding genes are predicted to be alternatively spliced, and because many non-coding genes are known also to be of biological significance. In order to fully exploit these arrays, it is necessary to associate each reporter on the array with the features of the genome it is targeting, and to relate these to gene and genome structure. X:Map is a genome annotation database that provides this information. Data can be browsed using a novel Google-maps based interface, and analysed and further visualized through an associated BioConductor package. The database can be found at http://xmap.picr.man.ac.uk.

PMID:
17932061
PMCID:
PMC2238884
DOI:
10.1093/nar/gkm779
[Indexed for MEDLINE]
Free PMC Article

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