Microarray Technology in Practice

By: Steve Russell, Lisa Meadows, Roslin Russell

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Paperback | 6 October 2008 | Edition Number 1

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464 Pages

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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

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Foreword and acknowledgments	p. ix
Introduction
Technology	p. 1
A Brief History	p. 4
A Brief Outline	p. 9
References	p. 13
The Basics of Experimental Design
Sources of Variation in Microarray Gene Expression Measurements	p. 18
Controls and Replicates	p. 21
Experimental Designs	p. 26
Summary	p. 32
References	p. 32
Designing and Producing Microarrays
Probe Selection	p. 36
cDNA and Amplicon Probes	p. 39
Oligonucleotide Probes	p. 40
Preparing Arrays	p. 55
Summary	p. 65
References	p. 65
Sample Collection and Labeling
Sample Collection and RNA Extraction	p. 72
RNA Quality Assessment	p. 73
cDNA Production	p. 76
Labeling Methods	p. 78
Signal Amplification	p. 84
RNA Amplification	p. 86
Amplification Methods Compared	p. 95
Quality Control for Fluorescently Labeled Samples	p. 97
Summary	p. 97
References	p. 98
Hybridization and Scanning
Hybridization	p. 102
Data Acquisition	p. 106
Finding Spots	p. 115
Method Comparison	p. 121
Data Extraction	p. 122
Quality Control Basics	p. 127
Summary	p. 129
References	p. 130
Data Preprocessing
Preprocessing Rationale	p. 136
Sources of Systematic Error	p. 138
Background Correction	p. 139
Data Filtering, Flagging and Weighting	p. 141
Treating Missing Values	p. 142
Data Transformation	p. 145
Dealing with Spatial Effects	p. 158
Print-Tip Group Loess Normalization	p. 161
Two-Dimensional (2D) Loess	p. 163
Composite Loess Normalization	p. 163
Weighted Loess Normalization	p. 165
Probe Replicates Used for Effective Normalization	p. 166
'Between-Array' Normalization	p. 167
Other Quality Control Considerations	p. 171
MicroArray Quality Control Consortium (MAQC)	p. 172
The External RNA Controls Consortium (ERCC)	p. 172
The EMERALD Consortium	p. 173
Preprocessing Affymetrix Genechip Data	p. 173
Probe Correction and Summarization	p. 178
Background Correction	p. 180
Normalization	p. 184
Summary	p. 185
References	p. 186
Differential Expression
Introduction	p. 191
Statistical Inference	p. 195
Parametric Statistics	p. 208
Linear Models for Microarray Data (LIMMA)	p. 221
Nonparametric Statistics	p. 239
Gene-Class Testing	p. 246
Summary	p. 257
References	p. 261
Clustering and Classification
Introduction	p. 272
Similarity Metrics	p. 274
Unsupervised Analysis Methods: Clustering and Partitioning	p. 276
Assessing Cluster Quality	p. 287
Dimensional Reduction	p. 291
Supervised Methods	p. 295
Assessing Model Quality	p. 300
Summary	p. 301
References	p. 302
Microarray Data Repositories and Warehouses
Introduction	p. 307
ArrayExpress	p. 309
Gene Expression Omnibus (GEO)	p. 313
Other Repositories and Warehouses	p. 322
Summary	p. 326
References	p. 328
Beyond Expression Arrays: Genome Analysis
Genome Arrays	p. 334
Exon Arrays	p. 336
Tiling Arrays	p. 337
Amplicon and BAC Arrays	p. 338
Oligonucleotide Tiles	p. 342
Using Tiling Arrays	p. 344
Analysis of Tiling Arrays	p. 354
Summary	p. 357
References	p. 358
Medical Applications of Microarray Technology
Introduction	p. 364
Investigating Pathogens: Malaria	p. 367
Expression Profiling Human Disease	p. 374
Array-CGH	p. 381
SNPs and Genotyping	p. 390
Summary	p. 399
References	p. 401
Other Array Technologies
Protein-Binding Arrays	p. 411
Cell and Tissue Arrays	p. 414
Protein Arrays	p. 418
Summary	p. 424
References	p. 425
Future Prospects
Arrays	p. 431
Labeling and Detection	p. 433
Imaging	p. 434
Analysis	p. 436
References	p. 437
Index	p. 441
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Microarray Technology in Practice

At a Glance

Paperback

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