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

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2006 Jan 7

PMID 16397297

Citations 25

Authors

Maureen A Sartor

Aaron M Zorn

Jennifer A Schwanekamp

Danielle Halbleib

Saikumar Karyala

Michael L Howell

Gary E Dean

Mario Medvedovic

Craig R Tomlinson

Affiliations

Soon will be listed here.

Abstract

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.

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