DDT December 2005.qxp

1689 www.drugdiscoverytoday.com The first attempts at global analysis of gene expression were undertaken in the mid-1970s with studies of the hybridization of an mRNA pool with radioactively labeled cDNA. Interest in gene expression increased steadily during the 1980s, and in the 1990s a new era of high throughput gene expression studies unfolded with the development of microarrays [1,2]. Although microarrays are relatively new, their penetration has been phenomenal. Biologists and physicians have enthusiastically embraced this technology, and are currently producing an unprecedented quantity of microarray data. As of March 2005, for example, the Stanford microarray database (SMD) [3] contained sets of images for ~54,000 microarrays, relating to the biology of 35 organisms. The database has been growing exponentially since its inception. Microarrays allow studies of gene expression on a massively parallel scale; a single microarray experiment can provide information on the expression of thousands of genes. More specifically, a microarray experiment is designed to compare the transcriptional activity of a set of genes under two conditions (hereafter called ‘reference’ and ‘experimental’). The outcome is a quantitative measure of the relative change of expression of each gene in an experimental condition compared with the reference condition. Currently, a few variants of microarray technology exist. To simplify the discussion in this review, we will describe the so-called cDNA microarrays. Proprietary technologies developed by Affymetrix and NimbleGen Systems employ somewhat different strategies – although the general principles remain the same. cDNA microarrays are fabricated on a glass or a nylon substrate by specialized high-speed robots. The fabrication process creates thousands of microscopic spots containing DNA probes that are immobilized in the substrate. The DNA probes are chosen to hybridize to unique sequences in the genes being studied. The mRNA from the two different conditions is obtained separately and reverse transcriptase is used to transcribe the mRNA into cDNA. The cDNA is labeled with a green or red dye, depending on which conditions it corresponds to. The microarray chip is then exposed to a mix of the two populations of cDNAs. A given strand of cDNA will hybridize with the DNA probe that was selected from the gene that produced that transcript. The chip is then washed to remove any unbound cDNAs (see [1,2] for more details on the protocols). The microarray chip is finally scanned using a confocal laser or a chargecoupled device (CCD) to generate two digital images, Yu Luo* Stefano Lonardi** Department of Computer Science & Engineering, University of California, Riverside, CA 92521, USA *e-mail: [email protected] **e-mail: [email protected] Storage and transmission of microarray images