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AffyProbeMiner: a web resource for computing or retrieving accurately redefined
Affymetrix probe sets
Liu H, Zeeberg BR, Gang Q, Koru AG, Ferrucci A, Kahn A, Ryan MC, Nuhanovic A, Munson PJ, Reinhold WC,
Kane DW, Weinstein JN
Bioinformatics. 2007 Jul 27
Abstract:
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 RefSeqs 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 Ôtranscript-consistentÕ
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
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