Cover image for Gene mapping, discovery, and expression : methods and protocols
Title:
Gene mapping, discovery, and expression : methods and protocols
Series:
Methods in molecular biology ; 338
Publication Information:
Totowa, NJ : Humana Press, 2006
ISBN:
9781588295750
Added Author:

Available:*

Library
Item Barcode
Call Number
Material Type
Item Category 1
Status
Searching...
30000010149428 QH445.2 G46 2006 Open Access Book Book
Searching...

On Order

Summary

Summary

Completion of the sequence of the human genome represents an unpar- leled achievement in the history of biology. The project has produced nearly complete, highly accurate, and comprehensive sequences of genomes of s- eral organisms including human, mouse, drosophila, and yeast. Furthermore, the development of high-throughput technologies has led to an explosion of projects to sequence the genomes of additional organisms including rat, chimp, dog, bee, chicken, and the list is expanding. The nearly completed draft of genomic sequences from numerous species has opened a new era of research in biology and in biomedical sciences. In keeping with the interdisciplinary nature of the new scientific era, the chapters in Gene Mapping, Discovery, and Expression: Methods and Protocols recapitulate the necessity of integration of experimental and computational tools for solving - portant research problems. The general underlying theme of this volume is DNA sequence-based technologies. At one level, the book highlights the importance of databases, genome-browsers, and web-based tools for data access and ana- sis. More specifically, sequencing projects routinely deposit their data in p- licly available databases including GenBank, at the National Center of Biotechnology (NCBI) in the United States; EMBL, maintained by the European Bioinformatics Institute; and DDBJ, the DNA Data Bank of Japan. Currently, several browsers offer facile access to numerous genomic DNA sequences for gene mapping and data retrieval.


Table of Contents

Minou BinaRazi Khaja and Jeffrey R. MacDonald and Junjun Zhang and Stephen W. SchererMinou BinaHeinz-Ulrich G. Weier and Lisa W. ChuAvirachan T. Tharapel and Stephen S. WachtelInna Dubchak and Dmitriy V. RyaboyLaura Elnitski and David King and Ross C. HardisonChristoph Dieterich and Martin VingronVinsensius Berlian VegaMinou Bina and Phillip Wyss and Syed Rehan ShahPhillip Wyss and Sheryl A. Lazarus and Minou BinaJulian C. KnightYoko Fukuda and Hiroaki Kawasaki and Kazunari TairaTanya Barrett and Ron EdgarJeremy Gollub and Catherine A. Ball and Gavin SherlockTomara J. Fleury and Alfred Cioffi and Arnold SteinScott A. Hoose and Michael P. KladdeMichael F. Berger and Martha L. BulykJiannis Ragoussis and Simon Field and Irina A. UdalovaKenneth K. WuMariana Yaneva and Paul TempstPatrick Rodriguez and Harald Braun and Katarzyna E. Kolodziej and Ernie de Boer and Jennifer Campbell and Edgar Bonte and Frank Grosveld and Sjaak Philipsen and John Strouboulis
Prefacep. v
Contributorsp. xiii
1 Use of Genome Browsers to Locate Your Favorite Genesp. 1
2 Methods for Identifying and Mapping Recent Segmental and Gene Duplications in Eukaryotic Genomesp. 9
3 Identification and Mapping of Paralogous Genes on a Known Genomic DNA Sequencep. 21
4 Quantitative DNA Fiber Mapping in Genome Research and Construction of Physical Mapsp. 31
5 Prins for Mapping Single-Copy Genesp. 59
6 Vista Family of Computational Tools for Comparative Analysis of DNA Sequences and Whole Genomesp. 69
7 Computational Prediction of cis-Regulatory Modules from Multispecies Alignments Using Galaxy, Table Browser, and GALAp. 91
8 Comparative Promoter Analysis in Vertebrate Genomes with the CORG Workbenchp. 105
9 cis-Regulatory Region Analysis Using Bearrp. 119
10 A Database of 9-Mers from Promoter Regions of Human Protein-Coding Genesp. 119
11 A Program Toolkit for the Analysis of Regulatory Regions of Genesp. 135
12 Analysis of Allele-Specific Gene Expressionp. 153
13 Construction of microRNA-Containing Vectors for Expression in Mammalian Cellsp. 167
14 Mining Microarray Data at NCBI's Gene Expression Omnibus (GEO)p. 167
15 The Stanford Microarray Database: A User's Guidep. 191
16 Detecting Nucleosome Ladders on Unique DNA Sequences in Mouse Liver Nucleip. 209
17 DNA Methyltransferase Probing of DNA-Protein Interactionsp. 225
18 Protein Binding Microarrays (PBMs) for Rapid, High-Throughput Characterization of the Sequence Specificities of DNA Binding Proteinsp. 245
19 Quantitative Profiling of Protein-DNA Binding on Microarraysp. 261
20 Analysis of Protein-DNA Binding by Streptavidin-Agarose Pulldownp. 281
21 Isolation and Mass Spectrometry of Specific DNA Binding Proteinsp. 291
22 Isolation of Transcription Factor Complexes by In Vivo Biotinylation Tagging and Direct Binding to Streptavidin Beadsp. 305
Indexp. 325