ABSTRACT
Cellular control results from multivariate activity among cohorts of genes and their products. Since all three levels in the central dogma — DNA, RNA, and protein — interact, it is not possible to fully separate them, and ultimately information from all realms must be combined for full understanding; nevertheless, the high level of interactivity between levels insures that a significant amount of the system information is available in each of the levels, so that focused studies provide useful insights. Much current effort is focused at the RNA level owing to measurement considerations. High-throughput technologies make it possible to simultaneously measure the RNA abundances of tens of thousands of mRNAs. In particular, expression microarrays result from a complex biochemical-optical system incorporating robotic spotting and computer image formation [3]. These arrays are grids of thousands of different single-stranded DNA molecules attached to a surface to serve as probes. Two major kinds are those using synthesized oligonucleotides and those using spotted cDNAs (complementary-DNA molecules). The basic procedure is to extract RNA from cells, convert the RNA to single-stranded cDNA, attach fluorescent labels to the different cDNAs, allow the single-stranded cDNAs to hybridize to their complementary probes on the microarray, and then detect the resulting fluor-tagged hybrids via excitation of the attached fluors and image formation using a scanning confocal microscope. Relative RNA abundance is measured via measurement of signal intensity from the attached fluors. This intensity is obtained by image processing and statistical analysis, with particular attention often paid to the detection of high-or low-expressing genes [4], and beyond that to expression-based phenotype classification [5] and the discovery of multivariate inter-gene predictive relationships [6]. This chapter briefly discusses microarrays, their hybridization-based foundation, normalization, and ratio analysis. At this point in time there is an extensive literature on microarray technology, signal extraction, and basic data analysis. We refer those interested to the various books on the subject [7, 8, 9, 10].
