Functional genomics : methods and protocols / edited by Michael J. Brownstein and Arkady B. Khodursky.

Format:

Book

Contributor:

Brownstein, Michael J.

Khodursky, Arkady B.

Series:

Methods in molecular biology (Clifton, N.J.) ; v. 224.

Methods in molecular biology ; v. 224

Language:

English

Subjects (All):

DNA microarrays--Laboratory manuals.

DNA microarrays.

Genomics--Laboratory manuals.

Genomics.

Proteomics--Laboratory manuals.

Proteomics.

Oligonucleotide Array Sequence Analysis--methods.

Medical Subjects:

Genomics.

Oligonucleotide Array Sequence Analysis--methods.

Genre:

Laboratory manuals.

Physical Description:

xii, 258 pages : illustrations (some color) ; 24 cm.

Place of Publication:

Totowa, N.J. : Humana Press, [2003]

Summary:

As high-throughput methods become more available and routine, experimentalists and theoreticians must be prepared to take advantage of the analytical power these methods offer. In Functional Genomics: Methods and Protocols, leading experimentalists -- many pioneers in the field -- describe in step-by-step detail robust methods for microarray-based studies and provide expert guidance in optimal data analysis and informatics. Drawing on insights derived from their long experience in biology, neurobiology, cell biology, molecular biology, and statistics, the authors review each of the key methods and analytical techniques used in functional genomics. On the methods side, this includes 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 test statistic, and the assessment of observational significance, data reduction, and clustering. Additional chapters outline the many available approaches to data visualization and storage so crucial to the successful mining and examination of experimental results. Timely and cutting-edge, Functional Genomics: Methods and Protocols offers novice and advanced investigators in all biological fields a collection of highly practical, readily reproducible methods, data analysis techniques, and experimental design criteria that will ensure safe passage through one of the most demanding and fastest growing fields today.

Contents:

1 Fabrication of cDNA Microarrays / Charlie C. Xiang, Michael J. Brownstein 1

2 Nylon cDNA Expression Arrays / George Jokhadze, Stephen Chen, Claire Granger, Alex Chenchik 9

3 Plastic Microarrays: A Novel Array Support Combining the Benefits of Macro- and Microarrays / Alexander Munishkin, Konrad Faulstich, Vissarion Aivazachvili, Claire Granger, Alex Chenchik 31

4 Preparing Fluorescent Probes for Microarray Studies / Charlie C. Xiang, Michael J. Brownstein 55

5 Escherichia coli Spotted Double-Strand DNA Microarrays: RNA Extraction, Labeling, Hybridization, Quality Control, and Data Management / Arkady B. Khodursky, Jonathan A. Bernstein, Brian J. Peter, Virgil Rhodius, Volker F. Wendisch, Daniel P. Zimmer 61

6 Isolation of Polysomal RNA for Microarray Analysis / Yoav Arava 79

7 Parallel Analysis of Gene Copy Number and Expression Using cDNA Microarrays / Jonathan R. Pollack 89

8 Genome-wide Mapping of Protein-DNA Interactions by Chromatin Immunoprecipitation and DNA Microarray Hybridization / Jason D. Lieb 99

9 Statistical Issues in cDNA Microarray Data Analysis / Gordon K. Smyth, Yee Hwa Yang, Terry Speed 111

10 Experimental Design to Make the Most of Microarray Studies / M. Kathleen Kerr 137

11 Statistical Methods for Identifying Differentially Expressed Genes in DNA Microarrays / John D. Storey, Robert Tibshirani 149

12 Detecting Stable Clusters Using Principal Component Analysis / Asa Ben-Hur, Isabelle Guyon 159

13 Clustering in Life Sciences / Ying Zhao, George Karypis 183

14 A Primer on the Visualization of Microarray Data / Paul Fawcett 219

15 Microarray Databases: Storage and Retrieval of Microarray Data / Gavin Sherlock, Catherine A. Ball 235.

Notes:

Includes bibliographical references and index.

ISBN:

1588292916

OCLC:

51316953