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Nucleic Acids Research 2006 34(1):185-200; doi:10.1093/nar/gkj413
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Published online 5 January 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus

Maureen A. Sartor1,2,4, Aaron M. Zorn6, Jennifer A. Schwanekamp1,3, Danielle Halbleib1,3, Saikumar Karyala1,3, Michael L. Howell8, Gary E. Dean8,9, Mario Medvedovic1,2,4,5,7 and Craig R. Tomlinson1,3,4,7,*

1University of Cincinnati, Department of Environmental Health Cincinnati, OH, 45267-0056, USA 2Division of Biostatistics and Epidemiology, Children's Hospital Cincinnati, OH 45229-3039, USA 3Division of Environmental Genetics and Molecular Toxicology, Children's Hospital Cincinnati, OH 45229-3039, USA 4Center for Environmental Genetics, Children's Hospital Cincinnati, OH 45229-3039, USA 5Center for Genome Information, Children's Hospital Cincinnati, OH 45229-3039, USA 6Division of Developmental Biology, Children's Hospital Cincinnati, OH 45229-3039, USA 7Hyacinth Genomics, LLC 3431 Stettinius Avenue, Cincinnati, OH 45208, USA 8Protein Express, Inc. 9940 Reading Road, Cincinnati, OH 45241, USA 9Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati Cincinnati, OH, 45267-0524, USA

*To whom correspondence should be addressed. Tel: +1 603 650 7936; Fax: +1 603 650 6122; Email addresses: Craig.R.Tomlinson{at}Dartmouth.edu

Received September 13, 2005. Revised November 29, 2005. Accepted December 9, 2005.

The recent sequencing of a large number of Xenopus tropicalis expressed sequences has allowed development of a high-throughput approach to study Xenopus global RNA gene expression. We examined the global gene expression similarities and differences between the historically significant Xenopus laevis model system and the increasingly used X.tropicalis model system and assessed whether an X.tropicalis microarray platform can be used for X.laevis. These closely related species were also used to investigate a more general question: is there an association between mRNA sequence divergence and differences in gene expression levels? We carried out a comprehensive comparison of global gene expression profiles using microarrays of different tissues and developmental stages of X.laevis and X.tropicalis. We (i) show that the X.tropicalis probes provide an efficacious microarray platform for X.laevis, (ii) describe methods to compare interspecies mRNA profiles that correct differences in hybridization efficiency and (iii) show independently of hybridization bias that as mRNA sequence divergence increases between X.laevis and X.tropicalis differences in mRNA expression levels also increase.

Present address: Craig R. Tomlinson, Dartmouth College, Department of Medicine, Dartmouth Hitchcock Medical Center, One Medical Center Drive, Lebanon, NH 03756, USA.


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