Functional Genomics: Methods and Protocols

ISBN-13: 9781588292919 / Angielski / Twarda / 2003 / 260 str.

Denis B. Conniffe; Michael J. Brownstein; Arkady B. Khodursky

Opis

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.

Recenzje

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

Spis treści

Fabrication of cDNA Microarrays Charlie C. Xiang and Michael J. Brownstein Nylon cDNA Expression Arrays George Jokhadze, Stephen Chen, Claire Granger, and Alex Chenchik Plastic Microarrays: A Novel Array Support Combining the Benefits of Macro- and Microarrays, Alexander Munishkin Konrad Faulstich, Vissarion Aivazachvili, Claire Granger, and Alex Chenchik Preparing Fluorescent Probes for Microarray Studies Charlie C. Xiang and Michael J. Brownstein 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, and Daniel P. Zimmer Isolation of Polysomal RNA for Microarray Analysis Yoav Arava Parallel Analysis of Gene Copy Number and Expression Using cDNA Microarrays Jonathan R. Pollack Genome-wide Mapping of Protein-DNA Interactions by Chromatin Immunoprecipitation and DNA Microarray Hybridization, Jason D. Lieb Statistical Issues in cDNA Microarray Data Analysis Gordon K. Smyth, Yee Hwa Yang, and Terry Speed Experimental Design to Make the Most of Microarray Studies M. Kathleen Kerr Statistical Methods for Identifying Differentially Expressed Genes in DNA Microarrays John D. Storey and Robert Tibshirani Detecting Stable Clusters Using Principal Component Analysis Asa Ben-Hur and Isabelle Guyon Clustering in Life Sciences Ying Zhao and George Karypis A Primer on the Visualization of Microarray Data Paul Fawcett Microarray Databases: Storage and Retrieval of Microarray Data Gavin Sherlock and Catherine A. Ball Index

Blurb

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 of 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.