Russell / Meadows Microarray Technology in Practice

1. Auflage 2008
ISBN: 978-0-08-091976-8
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, 464 Seiten

Using chips composed of thousands of spots, each with the capability of holding DNA molecules corresponding to a given gene, DNA microarray technology has enabled researchers to measure simultaneously gene expression across the genome. As with other large-scale genomics approaches, microarray technologies are broadly applicable across disciplines of life and biomedical sciences, but remain daunting to many researchers. This guide is designed to demystify the technology and inform more biologists about this critically important experimental technique. - Cohesive overview of the technology and available platforms, followed by detailed discussion of experimental design and analysis of microarray experiments - Up-to-date description of normalization methods and current methods for sample amplification and labeling - Deep focus on oligonucleotide design, printing, labeling and hybridization, data acquisition, normalization, and meta-analysis - Additional uses of microarray technology such as ChIP (chromatin immunoprecipitation) with hybridization to DNA arrays, microarray-based comparative genomic hybridization (CGH), and cell and tissue arrays

Autoren/Hrsg.

Russell, Steve

Meadows, Lisa A.

Russell, Roslin R.

Inhaltsverzeichnis

1;Front Cover;1
2;Microarray Technology in Practice;4
3;Copyright Page;5
4;Table of Contents;6
5;Foreword and acknowledgments;10
6;Chapter 1. Introduction;12
6.1;1.1. Technology;12
6.2;1.2. A Brief History;15
6.3;1.3. A Brief Outline;20
6.4;References;24
7;Chapter 2. The Basics of Experimental Design;28
7.1;2.1. Sources of Variation in Microarray Gene Expression Measurements;29
7.2;2.2. Controls and Replicates;32
7.3;2.3. Experimental Designs;37
7.4;2.4. Summary;43
7.5;References;43
8;Chapter 3. Designing and Producing Microarrays;46
8.1;3.1. Probe Selection;47
8.2;3.2. cDNA and Amplicon Probes;50
8.3;3.3. Oligonucleotide Probes;51
8.4;3.4. Preparing Arrays;66
8.5;3.5. Summary;76
8.6;References;76
9;Chapter 4. Sample Collection and Labeling;82
9.1;4.1. Sample Collection and RNA Extraction;83
9.2;4.2. RNA Quality Assessment;84
9.3;4.3. cDNA Production;87
9.4;4.4. Labeling Methods;89
9.5;4.5. Signal Amplifi cation;95
9.6;4.6. RNA Amplifi cation;97
9.7;4.7. Amplifi cation Methods Compared;106
9.8;4.8. Quality Control for Fluorescently Labeled Samples;108
9.9;4.9. Summary;108
9.10;References;109
10;Chapter 5. Hybridization and Scanning;112
10.1;5.1. Hybridization;113
10.2;5.2. Data Acquisition;117
10.3;5.3. Finding Spots;126
10.4;5.4. Method Comparison;132
10.5;5.5. Data Extraction;133
10.6;5.6. Quality Control Basics;138
10.7;5.7. Summary;140
10.8;References;141
11;Chapter 6. Data Preprocessing;146
11.1;6.1. Preprocessing Rationale;147
11.2;6.2. Sources of Systematic Error;149
11.3;6.3. Background Correction;150
11.4;6.4. Data Filtering, Flagging and Weighting;152
11.5;6.5. Treating Missing Values;153
11.6;6.6. Data Transformation;156
11.7;6.7. Dealing with Spatial Effects;169
11.8;6.8. Print-Tip Group Loess Normalization;172
11.9;6.9. Two-Dimensional (2D) Loess;174
11.10;6.10. Composite Loess Normalization;174
11.11;6.11. Weighted Loess Normalization;176
11.12;6.12. Probe Replicates Used for Effective Normalization;177
11.13;6.13. ‘Between-Array’ Normalization;178
11.14;6.14. Other Quality Control Considerations;182
11.15;6.15. MicroArray Quality Control Consortium (MAQC);183
11.16;6.16. The External RNA Controls Consortium (ERCC);183
11.17;6.17. The EMERALD Consortium;184
11.18;6.18. Preprocessing Affymetrix Genechip Data;184
11.19;6.19. Probe Correction and Summarization;189
11.20;6.20. Background Correction;191
11.21;6.21. Normalization;195
11.22;6.22. Summary;196
11.23;References;197
12;Chapter 7. Differential Expression;202
12.1;7.1. Introduction;202
12.2;7.2. Statistical Inference;206
12.3;7.3. Parametric Statistics;219
12.4;7.4. Linear Models for Microarray Data (LIMMA);232
12.5;7.5. Nonparametric Statistics;250
12.6;7.6. Gene-Class Testing;257
12.7;7.7. Summary;268
12.8;References;272
13;Chapter 8. Clustering and Classification;282
13.1;8.1. Introduction;283
13.2;8.2. Similarity Metrics;285
13.3;8.3. Unsupervised Analysis Methods: Clustering and Partitioning;287
13.4;8.4. Assessing Cluster Quality;298
13.5;8.5. Dimensional Reduction;302
13.6;8.6. Supervised Methods;306
13.7;8.7. Assessing Model Quality;311
13.8;8.8. Summary;312
13.9;References;313
14;Chapter 9. Microarray Data Repositories and Warehouses;318
14.1;9.1. Introduction;318
14.2;9.2. ArrayExpress;320
14.3;9.3. Gene Expression Omnibus (GEO);324
14.4;9.4. Other Repositories and Warehouses;333
14.5;9.5. Summary;337
14.6;References;339
15;Chapter 10. Beyond Expression Arrays: Genome Analysis;344
15.1;10.1. Genome Arrays;345
15.2;10.2. Exon Arrays;347
15.3;10.3. Tiling Arrays;348
15.4;10.4. Amplicon and BAC Arrays;349
15.5;10.5. Oligonucleotide Tiles;353
15.6;10.6. Using Tiling Arrays;355
15.7;10.7. Analysis of Tiling Arrays;365
15.8;10.8. Summary;368
15.9;References;369
16;Chapter 11. Medical Applications of Microarray Technology;374
16.1;11.1. Introduction;375
16.2;11.2. Investigating Pathogens: Malaria;378
16.3;11.3. Expression Profi ling Human Disease;385
16.4;11.4. Array-CGH;392
16.5;11.5. SNPs and Genotyping;401
16.6;11.6. Summary;410
16.7;References;412
17;Chapter 12. Other Array Technologies;422
17.1;12.1. Protein-Binding Arrays;422
17.2;12.2. Cell and Tissue Arrays;425
17.3;12.3. Protein Arrays;429
17.4;12.4. Summary;435
17.5;References;436
18;Chapter 13. Future Prospects;442
18.1;13.1. Arrays;442
18.2;13.2. Labeling and Detection;444
18.3;13.3. Imaging;445
18.4;13.4. Analysis;447
18.5;References;448
19;Index;452