Table of Contents

1 DNA Arrays for Expression Measurement: An Historical Perspective.- 1 Introduction.- 2 The Forerunners: Colony Filters and Dot Blots.- 3 “High-Density” Filters.- 4 Colony Filters and Expression Analysis (Qualitative).- 5 Quantifying Expression with High-Density Filters.- 6 Miniaturisation: cDNA Microarrays.- 7 Miniaturisation: Oligonucleotide Chips.- 8 Data Acquisition, Storage and Mining.- 9 A (Provisional) Conclusion.- References.- 2 Expression Profiling with cDNA Microarrays: A User’s Perspective and Guide.- 1 Introduction.- 2 Expression Profiling with cDNA Microarrays: The Basics.- 3 Production of cDNA Microarrays.- 4 Conclusions.- 5 Protocols.- References.- 3 cDNA Microarrays on Nylon Membranes with Enzyme Colorimetrie Detection.- 1 Introduction.- 2 Fabrication of Microarrays on Nylon Membranes.- 3 Enzyme Colorimetrie Detection.- 4 Characteristics of the Microarray/CD System.- 5 Data Processing in the Microarray/CD System.- 6 Protocol 1: Preparation of cDNA Targets for Microarray Fabrication.- 7 Protocol 2: cDNA Complex Probe Labeling.- 8 Protocol 3: Array Hybridization and Color Development.- 9 Protocol 4: Modified Catalyzed Reporter Deposition (CARD) Method.- References.- 4 cDNA Macroarrays and Microarrays on Nylon Membranes with Radioactive Detection.- 1 Introduction.- 2 Manufacture of Nylon Arrays.- 3 Labelling and Hybridisation with Complex Probes from Total RNA.- 4 Signal Analysis.- 5 Protocol 1: Array Preparation.- 6 Protocol 2: RNA Preparation.- 7 Protocol 3: Labelling.- 8 Protocol 4: Hybridisation.- 9 Protocol 5: Data Processing.- References.- 5 Oligonucleotide Chips for Expression Analysis: Principles and Practical Procedures.- 1 Introduction.- 2 Principles.- 3 Bioinformatics.- 4 Conclusion.- References.- 6 Gene Expression Data Mining andAnalysis.- 1 Introduction.- 2 From Raw Data to Gene Expression Matrix.- 3 Gene Expression Matrix Analysis.- 4 Expression Profiler.- 5 Applications.- 6 From Gene Expression Data to Gene Regulatory Networks.- 7 Conclusions.- References.- 7 Future Trends in the Use of DNA Arrays for Expression Measurement.- 1 Introduction.- 2 Future Chips: How Complex?.- 3 From “Clone-Based” to “Sequence-Based Arrays”.- 4 From “Home-Made” Microarrays to Ready-Made Chips.- 5 From “Stand Alone” Array to Integrated “Lab-on-a-Chip”.- 6 From Fluorescent Labelling to Electrical Detection.- 7 Progress Towards More Sophisticated Data Interpretation and (Maybe) a Unified Expression Repository.- 8 Expression Measurement Is Here to Stay.- References.

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