Microarray Analysis

Microarray data resulting from intramural NCT toxicogenomics experiments are currently captured in the NIEHS MicroArray Project System (MAPS). MAPS is a laboratory management information system developed at NIEHS (Bushel et al. 2001) in which ~40 data fields are defined to manage microarray project information; detail experimental design; track clones, sample preparation, labelling, and hybridization; and survey the quality control and assurance of processed microarray chips. The NMG currently produces a Yeast Chip v. 1 (6.2 K clones) and four mammalian chips: the Human ToxChip v. 3. (2.2 K clones), the Rat ToxChip v. 2. (6.8 K clones), and human and mouse oligonucleotide discovery chips (17.0 K and 16.0 K oligonucleotides, respectively). Gene accession numbers for each gene or EST on each chip are automatically updated biweekly at http://www.ncbi.nlm.nih.gov/UniGene/to reflect the current build of the National Center for Biotechnology Information (NCBI) Uni-

Fig. 10.3 Components of the microarray image and data analysis process. AIMS = analysis information management system; LIMS = laboratory information management system

Gene. Hundreds of thousands of novel EST sequences have been included in NCBI's UniGene. NMG cDNA chips include a substantial proportion of ESTs, thus offering the potential to discover novel genes involved in important biological or toxicological outcomes and disease processes. To provide some perspective on the information management requirements of gene expression analysis, the image and data analysis processes for microarray experiments are illustrated in Figure 10.3.

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