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Published online 18 March 2004

Nucleic Acids Research, 2004, Vol. 32, No. 5 e51
Oxford University Press

Improving the sensitivity and specificity of gene expression analysis in highly related organisms through the use of electronic masks

Shailender Nagpal, Mazen W. Karaman, Michelle M. Timmerman1, Vincent V. Ho, Brian L. Pike and Joseph G. Hacia*

The Institute for Genetic Medicine, University of Southern California, 2250 Alcazar Street, IGM 240, Los Angeles, CA 90089, USA and 1 Department of Microbiology, 51 Newton Road, 3401 BSB, University of Iowa, Iowa City, IA 52242, USA

*To whom correspondence should be addressed. Tel: +1 323 442 3030; Fax: +1 323 442 2764; Email: hacia{at}usc.edu
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Received January 16, 2004; Revised and Accepted February 23, 2004

DNA microarrays are powerful tools for comparing gene expression profiles from closely related organisms. However, a single microarray design is frequently used in these studies. Therefore, the levels of certain transcripts can be grossly underestimated due to sequence differences between the transcripts and the arrayed DNA probes. Here, we seek to improve the sensitivity and specificity of oligonucleotide microarray-based gene expression analysis by using genomic sequence information to predict the hybridization efficiency of orthologous transcripts to a given microarray. To test our approach, we examine hybridization patterns from three Escherichia coli strains on E.coli K-12 MG1655 gene expression microarrays. We create electronic mask files to discard data from probes predicted to have poor hybridization sensitivity and specificity to cDNA targets from each strain. We increased the accuracy of gene expression analysis and identified genes that cannot be accurately interrogated in each strain using these microarrays. Overall, these studies provide guidelines for designing effective electronic masks for gene expression analysis in organisms where substantial genome sequence information is available.


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