PARENT SESSION
Organized Oral Session 2: At the Crossroads of Genomics and Ecology: The Potential for a Canary on a Chip
Organized by: RD Klaper
Tuesday, August 5. 1:30 PM to 5:00 PM, SITCC Meeting Room 106.

Microarray experiments for non-model organisms: Estimates of error rates for cross-species hybridizations.

Thomas, Michael^*,1, Perrone, Marc², Xiang, Bixia², Mazzari, Darrel², Li, Peigang², Carvan, Michael³, ¹ Department of Biological Sciences, Pocatello, ID, USA² Marquette University, Milwaukee, WI, USA³ Great Lakes WATER Institute, Milwaukee, WI

ABSTRACT- Microarrays are now routinely used in biomedical research as a tool for gene discovery and expression profiling. This tool has yet to be extensively used by researchers in evolutionary biology and ecology due to cost constraints and lack of species-specific arrays, despite its enormous potential. While the cost is becoming increasingly attractive, the lack of well characterized genomes make the second problem difficult to overcome. Few researchers are willing and capable of generating a cDNA library for their organism of interest, and (when constructed) these libraries are often poorly annotated, limiting their utility. One solution is the use of cross-species hybridizations - using a microarray slide from a sequenced and annotated model organism to explore gene expression in the organism of ecological interest. For example, a microarray slide from Rattus norvegicus , the lab rat, might be used to explore gene expression and behavior in Neotoma floridana , the eastern wood rat, or a Danio rerio (zebrafish) microarray slide might be used to examine gene expression and evolution among members of the Cichlidae of Lake Malawi. Understanding the expected error rate of such experiments, and the affect of evolutionary divergence on this error rate, is essential to an appropriate and meaningful interpretation. Without such understanding, researchers will be easily misled, wasting valuable resources. We conducted a computer simulation of cross-species microarray hybridization that allowed us to predict error rates (hybridization of non-homologues) that can be expected for these experiments. The results of this analysis allow us to make general recommendations for potential experiments, given a divergence time between the target species (of ecological interest) and probe species (from which the microarray slide is made).

Key words: expression, microarray, genomics