Nucleic Acids Research

Nucleic Acids Research 2005 33(20):e175; doi:10.1093/nar/gni179

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Published online 10 November 2005

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Methods Online

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data

Manhong Dai, Pinglang Wang, Andrew D. Boyd¹, Georgi Kostov¹, Brian Athey¹, Edward G. Jones², William E. Bunney³, Richard M. Myers⁴, Terry P. Speed⁵, Huda Akil, Stanley J. Watson and Fan Meng^*

Molecular and Behavioural Neuroscience Institute and Department of Psychiatry, University of Michigan Ann Arbor, MI 48109, USA ¹Michigan Center for Biological Information, University of Michigan Ann Arbor, MI 48105, USA ²Department of Psychiatry and Center for Neuroscience, University of California Davis, CA 95616, USA ³Department of Psychiatry and Human Behavior, University of California Irvine, CA 92697, USA ⁴Department of Genetics, Stanford University School of Medicine Stanford, CA 94305, USA ⁵Department of Statistics, University of California Berkeley, CA 94720, USA

^*To whom correspondence should be addressed. Tel: +1 734 615 7099; Fax: +1 734 647 4130; Email: mengf{at}umich.edu

Received September 26, 2005. Revised October 17, 2005. Accepted October 25, 2005.

Genome-wide expression profiling is a powerful tool for implicating novel gene ensembles in cellular mechanisms of health and disease. The most popular platform for genome-wide expression profiling is the Affymetrix GeneChip. However, its selection of probes relied on earlier genome and transcriptome annotation which is significantly different from current knowledge. The resultant informatics problems have a profound impact on analysis and interpretation the data. Here, we address these critical issues and offer a solution. We identified several classes of problems at the individual probe level in the existing annotation, under the assumption that current genome and transcriptome databases are more accurate than those used for GeneChip design. We then reorganized probes on more than a dozen popular GeneChips into gene-, transcript- and exon-specific probe sets in light of up-to-date genome, cDNA/EST clustering and single nucleotide polymorphism information. Comparing analysis results between the original and the redefined probe sets reveals 30–50% discrepancy in the genes previously identified as differentially expressed, regardless of analysis method. Our results demonstrate that the original Affymetrix probe set definitions are inaccurate, and many conclusions derived from past GeneChip analyses may be significantly flawed. It will be beneficial to re-analyze existing GeneChip data with updated probe set definitions.

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