Bioinformatics Advance Access originally published online on July 27, 2007
Bioinformatics 2007 23(18):2385-2390; doi:10.1093/bioinformatics/btm360
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AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets
1Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, 2Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, 4000 Reservoir Road, NW, Washington, DC 20007, 3Electrical & Computer Engineering and Institute for Advanced Studies, University of Maryland, College Park, College Park, MD 20742, 4Department of Information Systems, 5Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, MD 21050, 6Department of Bioinformatics, George Mason University, Fairfax, Virginia, 20110, 7Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892 and 8SRA International, 4300 Fair Lakes Court, Fairfax, VA 22033, USA
*To whom correspondence should be addressed.
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Abstract |
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Motivation: Affymetrix microarrays are widely used to measure global expression of mRNA transcripts. That technology is based on the concept of a probe set. Individual probes within a probe set were originally designated by Affymetrix to hybridize with the same unique mRNA transcript. Because of increasing accuracy in knowledge of genomic sequences, however, a substantial number of the manufacturer's original probe groupings and mappings are now known to be inaccurate and must be corrected. Otherwise, analysis and interpretation of an Affymetrix microarray experiment will be in error.
Results: AffyProbeMiner is a computationally efficient platform-independent tool that uses all RefSeq mature RNA protein coding transcripts and validated complete coding sequences in GenBank to (1) regroup the individual probes into consistent probe sets and (2) remap the probe sets to the correct sets of mRNA transcripts. The individual probes are grouped into probe sets that are ‘transcript-consistent’ in that they hybridize to the same mRNA transcript (or transcripts) and, therefore, measure the same entity (or entities). About 65.6 % of the probe sets on the HG-U133A chip were affected by the remapping. Pre-computed regrouped and remapped probe sets for many Affymetrix microarrays are made freely available at the AffyProbeMiner web site. Alternatively, we provide a web service that enables the user to perform the remapping for any type of short-oligo commercial or custom array that has an Affymetrix-format Chip Definition File (CDF). Important features that differentiate AffyProbeMiner from other approaches are flexibility in the handling of splice variants, computational efficiency, extensibility, customizability and user-friendliness of the interface.
Availability: The web interface and software (GPL open source license), are publicly-accessible at http://discover.nci.nih.gov/affyprobeminer.
Contact: hl224{at}georgetown.edu or barry{at}discover.nci.nih.gov
Associate Editor: Joaquin Dopazo
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Received on February 1, 2007; revised on June 20, 2007; accepted on July 9, 2007
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