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DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning
Published on: March 15, 2011
High correspondence between Affymetrix exon and standard expression arrays
Michał J Okoniewski1, Yvonne Hey, Stuart D Pepper
1The Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Manchester, UK. mokoniewski@picr.man.ac.uk
Biotechniques
|March 22, 2007
Summary
Exon arrays offer detailed gene expression data. This study validates the Affymetrix Exon 1.0 ST array, showing high correspondence with existing HG-U133 Plus2 arrays, confirming exon array reliability for gene expression analysis.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Gene expression arrays traditionally provide data at the gene level.
- Exon arrays were developed to offer more granular expression data, analyzing individual exons.
- Validating new array technologies against established ones is crucial for reliable biological research.
Purpose of the Study:
- To evaluate the performance and reliability of the Affymetrix GeneChip Human Exon 1.0 ST array.
- To compare gene expression data obtained from exon arrays with data from established HG-U133 Plus2 arrays.
- To establish confidence in exon array technology for comprehensive gene expression profiling.
Main Methods:
- Hybridization of replicated RNA samples from MCF7 and MCF10A human cell lines to both Exon 1.0 ST and HG-U133 Plus2 arrays.
- Development and application of three probe set mapping strategies for cross-comparison between the two array types.
- Statistical analysis of probe set correspondence and fold change preservation between array platforms.
Main Results:
- A high degree of correspondence was observed between the Exon 1.0 ST and HG-U133 Plus2 arrays across different mapping strategies.
- Over 80% of probe sets from the HG-U133 Plus2 array could be successfully mapped to the Exon 1.0 ST array.
- Fold changes were well-preserved for more than 96% of detected probe sets, indicating strong data consistency.
Conclusions:
- The Affymetrix Exon 1.0 ST array demonstrates high performance and reliability.
- The strong correlation with the validated HG-U133 Plus2 array provides significant confidence in the utility of exon arrays.
- Exon arrays are a valuable tool for comprehensive gene expression analysis at the exon level.
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