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

Yates T, Okoniewski MJ, Miller CJ - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

Show MeSH
Genes selected as alternatively spliced between MCF7 and MCF10A cell lines, coloured by fold change. Each row corresponds to a gene, each rectangle, an exon. Exons are arranged in position order. Exons targeted by multiple probesets are drawn with these stacked horizontally within the exon. White rectangles correspond to exons with missing data. Fold change colouring ranges from 2−5 (intense blue; up in MCF7) to 25 (intense red; up in MCF10A).
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Figure 3: Genes selected as alternatively spliced between MCF7 and MCF10A cell lines, coloured by fold change. Each row corresponds to a gene, each rectangle, an exon. Exons are arranged in position order. Exons targeted by multiple probesets are drawn with these stacked horizontally within the exon. White rectangles correspond to exons with missing data. Fold change colouring ranges from 2−5 (intense blue; up in MCF7) to 25 (intense red; up in MCF10A).

Mentions: A BioConductor package, ‘exonmap’, can connect to the database (via the Rdbi package) in order to extract annotation data for use within a full statistical analysis environment. The package provides a series of functions allowing mappings to be made between probeset, exon, transcript and gene identifiers, and filterings to be performed to include/exclude exon, intron and intergenic probesets and those that are non-specific to the genome. Additional functions allow genome features to be retrieved according to physical location. Finally, a set of visualization functions can be used to map expression data onto genomic features (Figures 3 and 4).Figure 3.


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

Yates T, Okoniewski MJ, Miller CJ - Nucleic Acids Res. (2007)

Genes selected as alternatively spliced between MCF7 and MCF10A cell lines, coloured by fold change. Each row corresponds to a gene, each rectangle, an exon. Exons are arranged in position order. Exons targeted by multiple probesets are drawn with these stacked horizontally within the exon. White rectangles correspond to exons with missing data. Fold change colouring ranges from 2−5 (intense blue; up in MCF7) to 25 (intense red; up in MCF10A).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238884&req=5

Figure 3: Genes selected as alternatively spliced between MCF7 and MCF10A cell lines, coloured by fold change. Each row corresponds to a gene, each rectangle, an exon. Exons are arranged in position order. Exons targeted by multiple probesets are drawn with these stacked horizontally within the exon. White rectangles correspond to exons with missing data. Fold change colouring ranges from 2−5 (intense blue; up in MCF7) to 25 (intense red; up in MCF10A).
Mentions: A BioConductor package, ‘exonmap’, can connect to the database (via the Rdbi package) in order to extract annotation data for use within a full statistical analysis environment. The package provides a series of functions allowing mappings to be made between probeset, exon, transcript and gene identifiers, and filterings to be performed to include/exclude exon, intron and intergenic probesets and those that are non-specific to the genome. Additional functions allow genome features to be retrieved according to physical location. Finally, a set of visualization functions can be used to map expression data onto genomic features (Figures 3 and 4).Figure 3.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

Show MeSH