Exploiting microarrays to reveal differential gene expression in the nervous system.docVIP

Opinion Exploiting microarrays to reveal differential gene expression in the nervous system Robert S Griffin, Charles D Mills, Michael Costigan and Clifford J Woolf Address: Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA. Correspondence: Clifford J Woolf. E-mail: woolf.clifford@ Published: 29 January 2003 Genome Biology 2003, 4:105 The electronic version of this article is the complete one and can be found online at /2003/4/2/105 ? 2003 BioMed Central Ltd Abstract Microarrays have been used in a wide variety of experimental systems, but realizing their full poten- tial is contingent on sophisticated and rigorous experimental design and data analysis. This article highlights what is needed to get the most out of microarrays in terms of accurately and effectively revealing differential gene expression and regulation in the nervous system. The hypothesis-driven, single-gene analytic approach has dominated molecular neurobiology research and has been very successful. In grant submissions, the US National Insti- tutes of Health demand succinctly defined, closed hypothe- ses based on expected outcomes. Where does this leave experiments utilizing high-density microarrays, which do not fit this mold? The fact that microarray investigators do not know which genes or pathways will be discovered by their experiments is precisely the strength of microarrays. The ability to examine the expression profile of potentially the entire genome at once, without preconceptions, offers the possibility of completely novel and unexpected insights into entities as complex as the nervous system. But before these insights can be made, the practical problems of experi- mental design, data analysis, verification, and interpretation need to be addressed. transcription, amplification, labeling and hybridiz