Making Sense of Microchip Array Data

Microarray Analysis Software Packages Courtesy of SpotfireSpotfire's Array Explorer Gene expression profiling using DNA microarrays generates reams of data. But as is so often the case, it's not the quantity but the quality that matters: Gene expression data is useless unless biologically meaningful information can be extracted and presented in some readily understandable fashion. The production of this meaningful information, involving many facets of image processing, statistic

Written byMichael Brush

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The overall process begins with cDNA or oligonucleotides spotted in two-dimensional arrays onto glass slides or nylon membranes, or synthesized on biochips using technology borrowed from the semiconductor industry.¹ Messenger RNAs isolated from the test and reference tissues are labeled by reverse transcription with either a red or green fluorescent dye, mixed, and hybridized to the microarray. After washing, the bound fluorescent dyes on the arrays are interrogated by a laser, producing two images, one of each color. The resulting ratio of the red and green spots on the two images provides information about the changes in expression levels of the genes across experimental conditions.

Microarray data analysis software developers and companies have created numerous software packages designed to analyze the images and hybridization intensity data obtained from the arrays. These packages handle--with varying levels of complexity--the general problems associated with making sense of the gene expression data derived from ...

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