Expression array approach

There are some important limitations to the expression array approach. Since this analysis examines only the transcriptome, it fails to identify the important regulatory points at the level of translation and enzyme activity [29], in addition to the processes of protein protein interaction. Currently, the expression arrays do not address the issue of alternative splicing, but there are new generations of arrays being produced to examine these events. 

The scientific basis of hybridization arraying as a technique for the determination of gene expression levels is shown in Figures 15.4 and 15.5. The two currently available systems use either immobilized oligonucleotides or immobilized cDNAs as mRNA hybridization targets, but both require preparation and fluorescent-labeling of the mRNAs prior to quantitation. A full description of these hybridization arraying approaches has been published and is also available on the Web (see Table 15.1). 

The simplest expression arrays consist of individual cDNA clones manually or robotically spotted onto nitrocellulose or nylon filters. Replicates of the clone arrays are then hybridized sequentially or in parallel with different radioactively labeled target cDNAs, and hybridization to each clone measured by Phosphor Imager or similar technologies (33-36). Our own laboratory used this simple approach to assess the efficacy of protocols to generate subtracted cDNA libraries (37). Filters with thousands of arrayed human or murine genes and the requisite analysis software have been commercially available for the past several years. 

Several different zinc-dependent enzymes have been investigated as potential markers of zinc status, but none have proved reliable. MT in blood cells has been suggested as a useful indicator of zinc status, assayed at either the protein or the mRNA level. MT expression is likely to be regulated by factors other than zinc and therefore may lack the specificity required of a good indicator. The gene-array approaches that have recently been used to determine the global effects of zinc deficiency within a tissue would appear to offer hope for the identification of an appropriate functional marker of zinc status. 

The method for estimating parameters from Monte Carlo simulation, described in mathematical detail by Reilly and Duever (in preparation), uses a Bayesian approach to establish the posterior distribution for the parameters based on a Monte Carlo model. The numerical nature of the solution requires that the posterior distribution be handled in discretised form as an array in computer storage using the method of Reilly 2). The stochastic nature of Monte Carlo methods implies that output responses are predicted by the model with some amount of uncertainty for which the term "shimmer" as suggested by Andres (D.B. Chambers, SENES Consultants Limited, personal communication, 1985) has been adopted. The model for the uth of n experiments can be expressed by... 

The ultimate goal of microarray-based expression analysis is to acquire a comprehension of the entire cellular process, in order to exploit and to standardize the multidi-menisional relations between genotype and phenotype. However, an increasingly important parameter, which has not yet been substantially taken into account, is the role of cellular translation. This means that mRNA expression data need to be correlated with the assortment of proteins actually present in the cell. One approach is based on the use of microarrays containing double-stranded DNA probes for the analysis of DNA-protein interaction and, thus, the detection and identification of DNA-binding proteins by means of fluorescence [130] or mass spectrometry analysis [131]. Moreover, substantial efforts are currently under way to develop protein, antibody, or even cell arrays, applicable to the cor-... 

Two features of expression profiling make it the most productive approach to study biological systems for the immediate future. First, the present efficiency with which investigators can obtain global and quantitative information with DNA arrays exceeds that of proteomic techniques. Second, RNA expression profiles provide an extremely precise and reproducible signature of the state of the cell that probably reflects albeit indirectly, the functional state of all proteins (Young, 2000, p. 13)-... 

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