Preface ....................................................... vii
Acknowledgments ................................................ ix
Editor ......................................................... xi
Contributors ................................................. xiii
Summary of Chapters .......................................... xvii
Chapter 1. Introduction to Gene Expression Profiling with
DNA Microarray Technology ........................... 1
Michael D. Kane
Chapter 2. Introduction to Large-Scale Gene Expression
Data Analysis ...................................... 11
Anbarasu Lourdusamy, Massimo Ubaldi, Laura
Soverchia, Gary Hardiman, and
Roberto Ciccocioppo
Chapter 3. The Statistical Design and Analysis of Gene
Expression Data .................................... 25
Sonia Jain
Chapter 4. Laboratory Automation for Microarray
Experimentation .................................... 33
Douglas N. Gurevitch
Chapter 5. How to Evaluate a Microarray Scanner ............... 41
Yaping Zong, Shanshan Zhang, Youxiang Wang,
and Yaxian Shi
Chapter 6. The Role of Substrates in Microarray
Experimentation and How to Choose
the Correct Coating for Microarraying .............. 53
Ruediger Dietrich, Daniel Haines, Rajendra
Redkar, and Alistair Rees
Chapter 7. Toward Highly Efficient Automated Hybridizations ... 71
Kris Pappaert, Johan Vanderhoeven, Gert
Desmet, and Paul Van Hummelen
Chapter 8. Characterization of Microarray Hybridization
Stoichiometry ...................................... 87
Richard J.D. Rouse and Gary Hardiman
Chapter 9. Data Normalization Selection ....................... 97
Phillip Stafford
Chapter 10. Methods for Assessing Microarray Performance ...... 119
Steffen G. Oeser, Shawn C. Baker, Eugene
Chudin, Kenneth Kuhn, and Timothy K. McDaniel
Chapter 11. Comparison of Different Normalization Methods
for Applied Biosystems Expression Array System .... 127
Catalin Barbacioru, Yulei Wang, Roger
Canales, Yongming Sun, David Keys,
Frances Chan, Kathryn Hunkapiller, Karen
Poulter, and Raymond R. Samaha
Chapter 12. A Systematic Comparison of Gene Expression
Measurements across Different Hybridization-
Based Technologies ................................ 145
Winston Patrick Kuo, Fang Liu, Tor-Kristian
Jensen, Shari L. Benson, Connie L. Cepko,
Eivind Hovig, and Lucila Ohno-Machado
Chapter 13. DNA Methylation Arrays: Methods and Analysis ...... 175
Natalie P. Thorne, John Carlo Marioni,
Vardhman K. Rakyan, Ashraf E.K. Ibrahim,
Charles E. Massie, C. Curtis, James D.
Brenton, Adele Murrell, and Simon Tavaré
Chapter 14. Electronic Microarrays: Progress toward DNA
Diagnostics ....................................... 207
Howard Reese, Dan Smolko, Paul Swanson,
and Dalibor Hodko
Chapter 15. New Applications for Microarrays .................. 225
Mark Andersen, Steve Warrick, and
Christopher Adams
Chapter 16. Development of an Oligonucleotide Microarray
for Mutational Analysis Using Single or
Multiple Sample Hybridization ..................... 243
Il-Jin Kim, Hio Chung Kang, and Jae-Gahb Park
Chapter 17. Development of an Integrated Molecular
Diagnostic Test to Identify Respiratory Viruses ... 259
Frédéric Raymond, Whei-Kuo Wu, and
Jacques Corbeil
Chapter 18. Microarrays in Neuroscience ....................... 271
Massimo Ubaldi, Wolfgang Sommer, Laura
Soverchia, Anbarasu Lourdusamy, Barbara
Ruggeri, Roberto Ciccocioppo, and
Gary Hardiman
Chapter 19. Optimization of Protein Array Fabrication for
Establishing High-Throughput Ultra-Sensitive
Microarray Assays for Cancer Research ............. 289
Gary Hardiman, C. Ramana Bhasker, and
Richard J.D. Rouse
Index ......................................................... 301
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