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. 2005 Nov 10;33(20):e175.
doi: 10.1093/nar/gni179.

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

Manhong Dai  1 , Pinglang Wang, Andrew D Boyd, Georgi Kostov, Brian Athey, Edward G Jones, William E Bunney, Richard M Myers, Terry P Speed, Huda Akil, Stanley J Watson, Fan Meng
Affiliations

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

Manhong Dai et al. Nucleic Acids Res. .

Abstract

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 approximately 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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Figure 1
Figure 1
Hierarchical clustering of probe set definition similarity based on differentially expressed gene lists derived from the GSE974 data set using different probe set definitions and analysis methods.
See this image and copyright information in PMC

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