Functional Genomics

1. Front Matter

   Pages i-xii

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2. Fabrication of cDNA Microarrays

   • Charlie C. Xiang, Michael J. Brownstein

   Pages 1-7

3. Nylon cDNA Expression Arrays

   • George Jokhadze, Stephen Chen, Claire Granger, Alex Chenchik

   Pages 9-29

4. Plastic Microarrays

   • Alexander Munishkin, Konrad Faulstich, Vissarion Aivazachvili, Claire Granger, Alex Chenchik

   Pages 31-54

5. Preparing Fluorescent Probes for Microarray Studies

   • Charlie C. Xiang, Michael J. Brownstein

   Pages 55-60

6. Escherichia coli Spotted Double-Strand DNA Microarrays

   • Arkady B. Khodursky, Jonathan A. Bernstein, Brian J. Peter, Virgil Rhodius, Volker F. Wendisch, Daniel P. Zimmer

   Pages 61-78

7. Isolation of Polysomal RNA for Microarray Analysis

   • Yoav Arava

   Pages 79-87

8. Parallel Analysis of Gene Copy Number and Expression Using cDNA Microarrays

   • Jonathan R. Pollack

   Pages 89-97

9. Genome-wide Mapping of Protein-DNA Interactions by Chromatin Immunoprecipitation and DNA Microarray Hybridization

   • Jason D. Lieb

   Pages 99-109

10. Statistical Issues in cDNA Microarray Data Analysis

    • Gordon K. Smyth, Yee Hwa Yang, Terry Speed

    Pages 111-136

11. Experimental Design to Make the Most of Microarray Studies

    • M. Kathleen Kerr

    Pages 137-147

12. Statistical Methods for Identifying Differentially Expressed Genes in DNA Microarrays

    • John D. Storey, Robert Tibshirani

    Pages 149-157

13. Detecting Stable Clusters Using Principal Component Analysis

    • Asa Ben-Hur, Isabelle Guyon

    Pages 159-182

14. Clustering in Life Sciences

    • Ying Zhao, George Karypis

    Pages 183-218

15. A Primer on the Visualization of Microarray Data

    • Paul Fawcett

    Pages 219-234

16. Microarray Databases

    • Gavin Sherlock, Catherine A. Ball

    Pages 235-248

17. Back Matter

    Pages 249-258

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This collection of robust, readily reproducible methods for microarray-based studies includes expert guidance in the optimal data analysis and informatics. On the methods side are proven techniques for monitoring subcellular RNA localization en masse, for mapping chromosomes at the resolution of a single gene, and for surveying the steady-state genome-wide distribution of DNA binding proteins in vivo. For those workers dealing with massive data sets, the book discusses the methodological aspects of data analysis and informatics in the design of microarray experiments, the choice of test statistic, and the assessment of observational significance, data reduction, and clustering.

"....a good book, and it will be useful to microarray workers in their effots." - Journal of Chemical Neuroanatomy

• Laboratory of Genetics, NIMH/NHGRI, National Institutes of Health, Rockville

  Michael J. Brownstein

• Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul

  Arkady B. Khodursky

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