Chapter 13: Analysis of Microarrays

Useful biological information about the genome of an organism can be determined by finding which genes are induced or repressed in a phase of the cell cycle, a development phase, or as an environmental response, such as in response to treatment with a hormone or exposure to high temperature. Sets of genes whose expression rises and falls under the same condition are likely to have a related biological function and perhaps a common regulatory relationship; e.g., they may have similar promoter sequences for binding transcription factors. In addition, a pattern of gene expression may be an indicator of abnormal cellular regulation and is, therefore, a useful tool in disease diagnosis. Because eukaryotic genomes are so large, microarray technology has been developed for studying regulation or sequence variation of thousands of genes or synthesized proteins at the same time. The major use of microarray technology has been to study gene expression by detecting mRNA levels in cells and tissues. In this type of analysis, many or most of the genes of an organism are represented by oligonucleotide sequences spread out in a high-density array on glass microscope slides or some other solid support medium. mRNA, extracted from cells or tissues, is copied into DNA and labeled with a fluorescent dye or some other means. The labeled mRNA or an mRNA mixture is then hybridized to the slide and the slide is scanned with a microscope to measure the amount of label over each spot. The amount of label is assumed to be proportional to the amount of each mRNA in the original biological sample. The data are then analyzed to identify genes whose expression is changing. This chapter provides a basis for planning experiments and for the subsequent analysis of microarray data. It also describes the most common techniques of microarray technology and the advantages and disadvantages of these methods.

Rapid changes are occurring in microarray technology and analysis. Supplementary material addressing these changes will be placed on the book Web site.