Dna Microarray Technology And Data Analysis In Cancer Research

by Shaoguang Li, Dongguang Li

Overview

DNA microarray technology has become a useful technique in gene expression analysis for the development of new diagnostic tools and for the identification of disease genes and therapeutic targets for human cancers. Appropriate control for DNA microarray experiment and reliable analysis of the array data are key to performing the assay and utilizing the data correctly. The most difficult challenge has been the lack of a powerful method to analyze the data for all genes (more than 30,000 genes) simultaneously and to use the microarray data in a decision-making process. In this book, the authors describe DNA microarray technology and data analysis by pointing out current advantages and disadvantages of the technique and available analytical methods. Crucially, new ideas and analytical methods based on the authors' own experience in DNA microarray study and analysis are introduced. It is believed that this new way of interpreting and analyzing microarray data will bring us closer to success in decision-making using the information obtained through the DNA microarray technology.

Product Details

ISBN-13:	9789812790453
Publisher:	World Scientific Publishing Company, Incorporated
Publication date:	02/05/2009
Pages:	132
Product dimensions:	6.10(w) x 9.00(h) x 0.60(d)

Table of Contents

Preface v

Introduction of Authors vii

Chapter 1 DNA Microarray Technology 1

1.1 Experimental Procedure 2

1.2 Experimental Design 4

1.3 Quality Control 6

1.4 Interpretation of DNA Microarray Data 8

1.5 Advantages and Disadvantages 8

Chapter 2 Applications of DNA Microarray Technology in Cancer Research 11

2.1 Solid Tumors 11

2.2 Blood Cancers 12

2.3 Our DNA Microarray Study Using Mouse Model of BCR-ABL-Induced Leukemia 13

2.3.1 Leukemia mouse model study 15

2.3.2 Cell line study 19

Chapter 3 Current Analytical Methods of DNA Microarray Data 21

3.1 Experimental Design 21

3.2 Method 21

3.2.1 Robust multi-chip averaging (RMA) 21

3.2.2 iterPLIER 22

3.3 Quality Control Diagnostics 25

3.3.1 Saturation 25

3.3.2 Transformed intensities across arrays 28

3.3.3 Normalized intensities across arrays 29

3.3.4 Scatterplot of normalized intensities 30

3.3.5 Average MA plot of normalized intensities 31

3.4 Statistical Analysis 32

3.4.1 Analysis of variance (ANOVA) model 32

3.4.2 Contrasts 33

3.5 Coefficient of Variation Analysis 36

Chapter 4 A Novel Method for DNA Microarray Data Analysis: SDL Global Optimization Method 37

4.1 Research Subjects 38

4.2 Experimental Design 39

4.2.1 Rationale 39

4.3 Fold Change Analysis 40

4.4 More Information on SDL Global Optimization 51

4.4.1 Genetic algorithms (GAs) 53

4.4.2 SDL global optimization algorithms 54

Chapter 5 Applications of the SDL Global Optimization Method in DNA Microarray Data Analysis 55

5.1 Leukemia Cell Line Study 55

5.1.1 Introduction 55

5.1.2 Datasets 55

5.1.3 Analysis strategies 55

5.1.4 Discussion and conclusion 62

5.2 Analyses of Publicly Available HumanMicroarray Data 63

5.2.1 Introduction 63

5.2.2 Datasets 70

5.3 Overall Methodology 71

5.3.1 Orthogonal arrays (OAs) and sampling procedure 71

5.3.2 Objective function 74

5.3.3 Search space reduction for global search 76

5.3.4 Mathematical form of SDL optimization 80

5.3.5 Multi-subset class predictor 82

5.3.6 Validation (predicting through a voting mechanism) 83

5.4 Experimental Results 83

5.5 Discussion 90

5.6 Conclusion 99

Chapter 6 General Discussion and Future Directions 101

References 105

Index 117