Microarray Bioinformatics

This book is a comprehensive guide to all of the mathematics, statistics and computing you will need to successfully operate DNA microarray experiments. It is written for researchers, clinicians, laboratory heads and managers, from both biology and bioinformatics backgrounds, who work with, or who intend to work with microarrays. The book covers all aspects of microarray bioinformatics, giving you the tools to design arrays and experiments, to analyze your data, and to share your results with your organisation or with the international community. There are chapters covering sequence databases, oligonucleotide design, experimental design, image processing, normalisation, identifying differentially expressed genes, clustering, classification and data standards. The book is based on the highly successful Microarray Bioinformatics course at Oxford University, and therefore is ideally suited for teaching the subject at postgraduate or professional level. Cover......Page 1 Title Page......Page 5 Copyright......Page 6 Dedication......Page 7 Contents......Page 9 Foreword......Page 11 Preface......Page 13 Acknowledgments......Page 15 CHAPTER ONE - Microarrays: Making Them and Using Them......Page 19 CHAPTER TWO - Sequence Databases for Microarrays......Page 37 CHAPTER THREE - Computer Design of Oligonucleotide Probes......Page 61 CHAPTER FOUR - Image Processing......Page 80 CHAPTER FIVE - Normalisation......Page 91 CHAPTER SIX - Measuring and Quantifying Microarray Variability......Page 118 CHAPTER SEVEN - Analysis of Differentially Expressed Genes......Page 128 COLOR PLATES......Page 146 CHAPTER EIGHT - Analysis of Relationships Between Genes, Tissues or Treatments......Page 165 CHAPTER NINE - Classification of Tissues and Samples......Page 209 CHAPTER TEN - Experimental Design......Page 237 CHAPTER ELEVEN - Data Standards, Storage and Sharing......Page 257 APPENDIX - MIAME Glossary......Page 279 INDEX......Page 285

DNA microarrays have revolutionized molecular biology and are becoming a standard tool in the field. Dov Stekel's book is a comprehensive guide to the mathematics, statistics, and computing required to use microarrays successfully. Unlike traditional molecular biology, the successful use of DNA microarrays requires the application of statistics and computing to design the arrays and experiments, and to analyze and manage the data. This book is written for researchers, clinicians, and laboratory managers.

"This book is a comprehensive guide to all of the mathematics, statistics and computing you will need to successfully operate DNA microarray experiments ... covers all aspects of microarray bioinformatics, giving you the tools to design arrays and experiments, to analyze your data, and to share your results with your organisation or with the international community."--Jacket DNA microarrays have revolutionised molecular biology and are becoming a standard tool in the field. Written for those from both laboratory and bioinformatics backgrounds, this book is a comprehensive guide to all of the mathematics, statistics and computing necessary to successfully carry out and analyze DNA microarray experiments.