This complete and practical manual on expression measurement using DNA arrays covers the existing methods (from nylon macroarrays to oligonucleotide chips) and includes detailed protocols. It has been written by practising scientists who have experienced the difficulties involved in actually using microarrays, and provides helpful advice and hints on setting up these powerful but sometimes tricky methods. Software, data mining procedures and probable future developments, which should be useful to any practising scientist interested in expression measurement, are also covered in this book.

Inhalt

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 and Analysis.- 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.