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SECTION 1 Fundamentals of Expression Profiling Analysis Chapter 1 Preparation and Utilization of Microarrays.........................................................3 Sophie Wildsmith and Fiona Spence Chapter 2 Comparative Studies Using cDNA vs. Oligonucleotide Arrays ........................................17 Jiang Li and Jeffrey A. Johnson Chapter 3 Quality Control of Expression Profiling Data...................................................29 Andrew Hill and Maryann Whitley Chapter 4 An Introduction to Cluster Analysis ..............................................................45 Frederick Immermann and Youping Huang SECTION 2 Expression Profiling and Toxicology: The Advent of Toxicogenomics Chapter 5 Transcriptional Profiling in Toxicology...........................................................81 Julia Scheel, Marie-Charlotte von Brevern, and Thorsten Storck SECTION 3 Model Systems in Toxicogenomic Studies Chapter 6 Microarrays in Drug Metabolism and Toxicology: Rat Liver Responses to Prototypical CYP Inducers ...... ............................ ........ 101 David Gerhold, Jian Xu, and Thomas Rushmore Chapter 7 Characterization of Hepatocytes and Their Use as a Model System in Toxicogenomics ...........117 Thomas K. Baker, Marnie A. Higgins, Mark A. Carfagna, and Timothy P Ryan SECTION 4 Mechanistic Toxicogenomics Chapter 8 Molecular Signatures of Dioxin Toxicity .......................................................147 J. Kevin Kerzee, Craig R. Tomlinson, Jennifer L. Marlowe, and Alvaro Puga Chapter 9 Toxicogenomic Dissection of the Antioxidant Response............................................163 Jiang Li and Jeffrey A. Johnson Chapter 10 An Overview of Mechanistic Toxicogenomic Studies ...............................................183 Julia Scheel, Marie-Charlotte von Brevern, and Thorsten Storck SECTION 5 Predictive Toxicogenomics Chapter 11 Gene Expression Profile Databases in Toxicity Testing ..........................................213 Robert T Dunn II and Kyle L. Kolaja Chapter 12 Predictive Toxicogenomics .....................................................................225 Mark W Porter, Arthur L. Castle, Michael S. Orr, and Donna L. Mendrick Chapter 13 Unsupervised Hierarchical Clustering of Toxicants...............................................261 Jeffrey F Waring and Roger G. Ulrich Chapter 14 Toxicogenomic Analysis in Clinical Pharmacogenomic Studies......................................285 Michael E. Burczynski SECTION 6 The Future of Toxicogenomics Chapter 15 The Future of Toxicogenomics .................................................................. 299 John C. Rockett INDEX .......................................................................... .............. 319Library of Congress Subject Headings for this publication: Genetic toxicology, Genomics, Proteomics, Gene expression