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First published online April 20, 2007
Journal of Experimental Biology 210, 1584-1592 (2007)
Published by The Company of Biologists 2007
doi: 10.1242/jeb.004333

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Review Article

Interpreting physiological responses to environmental change through gene expression profiling

Andrew Y. Gracey

Marine Environmental Biology, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA

e-mail: gracey{at}usc.edu

Accepted 12 March 2007

Identification of differentially expressed genes in response to environmental change offers insights into the roles of the transcriptome in the regulation of physiological responses. A variety of methods are now available to implement large-scale gene expression screens, and each method has specific advantages and disadvantages. Construction of custom cDNA microarrays remains the most popular route to implement expression screens in the non-model organisms favored by comparative physiologists, and we highlight some factors that should be considered when embarking along this path. Using a carp cDNA microarray, we have undertaken a broad, system-wide gene expression screen to investigate the physiological mechanisms underlying cold and hypoxia acclimation. This dataset provides a starting point from which to explore a range of specific mechanistic hypotheses at all levels of organization, from individual biochemical pathways to the level of the whole organism. We demonstrate the utility of two data analysis methods, Gene Ontology profiling and rank-based statistical methods, to summarize the probable physiological function of acclimation-induced gene expression changes, and to prioritize specific genes as candidates for further study.

Key words: acclimation, adaptation, gene expression, microarray

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Laura Blackburn
JEB 2007 210: ii. [Full Text]  

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