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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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

Tim Yates1, Michał J Okoniewski, Crispin J Miller

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

Nucleic Acids Research
|October 13, 2007
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Summary

X:Map is a genome annotation database that precisely maps Affymetrix exon array reporters to genomic features. This facilitates the analysis of alternative splicing and non-coding genes for comprehensive genomic studies.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Affymetrix exon arrays offer comprehensive coverage of the human, mouse, and rat genomes, targeting known and predicted exons.
  • These arrays extend beyond protein-coding regions to include other transcribed genomic areas, crucial for studying alternative splicing and non-coding genes.

Purpose of the Study:

  • To develop a genome annotation database (X:Map) that precisely associates Affymetrix exon array reporters with their targeted genomic features.
  • To facilitate the analysis and visualization of genomic data derived from exon arrays.

Main Methods:

  • Creation of the X:Map genome annotation database.
  • Development of a Google Maps-based interface for data browsing.
  • Association of array reporters with gene and genome structure.

Main Results:

  • X:Map provides essential information to link exon array reporters to specific genomic features.
  • The database enables detailed analysis of alternative splicing and non-coding gene functions.
  • A BioConductor package is available for advanced data analysis and visualization.

Conclusions:

  • X:Map is a valuable resource for researchers utilizing Affymetrix exon arrays.
  • The database enhances the exploitation of exon array data for comprehensive genomic and transcriptomic studies.