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An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data
Michał J Okoniewski1, Tim Yates, Siân Dibben
1Bioinformatics Group, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Manchester M20 4BX, UK. mokoniewski@picr.man.ac.uk
Genome Biology
|May 15, 2007
Summary
Affymetrix exon arrays present analysis challenges. X:MAP and exonmap tools enable fine-grained genome-wide data analysis, providing gene, transcript, and exon summaries.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Affymetrix exon arrays offer comprehensive genome-wide coverage, targeting all known and predicted exons.
- High-throughput analysis of exon array data presents significant computational and statistical challenges.
Purpose of the Study:
- To introduce X:MAP, an annotation database, and exonmap, a BioConductor/R package.
- To facilitate fine-grained analysis of Affymetrix exon array data.
Main Methods:
- Utilizing the X:MAP annotation database for comprehensive genomic information.
- Employing the exonmap BioConductor/R package for data analysis.
- Applying standard statistical techniques for data summarization.
Main Results:
- The system supports the integration of genome-scale annotation.
- Enables the generation of gene-, transcript-, and exon-level summaries.
- Provides visualization tools for complex exon array data.
Conclusions:
- X:MAP and exonmap provide a robust framework for analyzing exon array data.
- The tools support detailed, genome-wide investigations at multiple biological levels.
- Facilitates advanced genomic data interpretation and discovery.
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