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

2.00
Hdl Handle:
http://hdl.handle.net/10541/55037
Title:
X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.
Authors:
Yates, Tim; Okoniewski, Michal J; Miller, Crispin J
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.
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.
Citation:
X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis. 2008, 36 (Database issue):D780-6 Nucleic Acids Res.
Journal:
Nucleic Acids Research
Issue Date:
Jan-2008
URI:
http://hdl.handle.net/10541/55037
DOI:
10.1093/nar/gkm779
PubMed ID:
17932061
Type:
Article
Language:
en
ISSN:
1362-4962
Appears in Collections:
Applied Computational Biology and Bioinformatics; All Paterson Institute for Cancer Research

Full metadata record

DC FieldValue Language
dc.contributor.authorYates, Tim-
dc.contributor.authorOkoniewski, Michal J-
dc.contributor.authorMiller, Crispin J-
dc.date.accessioned2009-03-12T17:14:26Z-
dc.date.available2009-03-12T17:14:26Z-
dc.date.issued2008-01-
dc.identifier.citationX:Map: annotation and visualization of genome structure for Affymetrix exon array analysis. 2008, 36 (Database issue):D780-6 Nucleic Acids Res.en
dc.identifier.issn1362-4962-
dc.identifier.pmid17932061-
dc.identifier.doi10.1093/nar/gkm779-
dc.identifier.urihttp://hdl.handle.net/10541/55037-
dc.description.abstractAffymetrix 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.en
dc.language.isoenen
dc.subjectAffymetrix Exon Arraysen
dc.subjectGenomeen
dc.subject.meshAlternative Splicing-
dc.subject.meshAnimals-
dc.subject.meshChromosome Mapping-
dc.subject.meshComputer Graphics-
dc.subject.meshDatabases, Genetic-
dc.subject.meshExons-
dc.subject.meshGene Expression Profiling-
dc.subject.meshGenomics-
dc.subject.meshHumans-
dc.subject.meshInternet-
dc.subject.meshMice-
dc.subject.meshOligonucleotide Array Sequence Analysis-
dc.subject.meshRats-
dc.subject.meshSoftware-
dc.subject.meshUser-Computer Interface-
dc.titleX:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.en
dc.typeArticleen
dc.contributor.departmentCancer Research UK, Bioinformatics Group, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Withington, Manchester, M20 4BX, UK.en
dc.identifier.journalNucleic Acids Researchen

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