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Gene Mapping, Discovery, and Expression

Methods and Protocols

  • Book
  • © 2006

Overview

Editors:
  1. Minou Bina

    1. Department of Chemistry, Purdue University, West Lafayette, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

Part of the book series: Methods in Molecular Biology (MIMB, volume 338)

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Use of Genome Browsers to Locate Your Favorite Genes

    • Minou Bina
    Pages 1-7

  3. Methods for Identifying and Mapping Recent Segmental and Gene Duplications in Eukaryotic Genomes

    • Razi Khaja, Jeffrey R. MacDonald, Junjun Zhang, Stephen W. Scherer
    Pages 9-20

  4. Identification and Mapping of Paralogous Genes on a Known Genomic DNA Sequence

    • Minou Bina
    Pages 21-29

  5. Quantitative DNA Fiber Mapping in Genome Research and Construction of Physical Maps

    • Heinz-Ulrich G. Weier, Lisa W. Chu
    Pages 31-57

  6. PRINS for Mapping Single-Copy Genes

    • Avirachan T. Tharapel, Stephen S. Wachtel
    Pages 59-67

  7. VISTA Family of Computational Tools for Comparative Analysis of DNA Sequences and Whole Genomes

    • Inna Dubchak, Dmitriy V. Ryaboy
    Pages 69-89

  8. Computational Prediction of cis-Regulatory Modules from Multispecies Alignments Using Galaxy, Table Browser, and GALA

    • Laura Elnitski, David King, Ross C. Hardison
    Pages 91-103

  9. Comparative Promoter Analysis in Vertebrate Genomes With the CORG Workbench

    • Christoph Dieterich, Martin Vingron
    Pages 105-118

  10. cis-Regulatory Region Analysis Using BEARR

    • Vinsensius Berlian Vega
    Pages 119-127

  11. A Database of 9-Mers from Promoter Regions of Human Protein-Coding Genes

    • Minou Bina, Phillip Wyss, Syed Rehan Shah
    Pages 129-134

  12. A Program Toolkit for the Analysis of Regulatory Regions of Genes

    • Phillip Wyss, Sheryl A. Lazarus, Minou Bina
    Pages 135-152

  13. Analysis of Allele-Specific Gene Expression

    • Julian C. Knight
    Pages 153-165

  14. Construction of microRNA-Containing Vectors for Expression in Mammalian Cells

    • Yoko Fukuda, Hiroaki Kawasaki, Kazunari Taira
    Pages 167-173

  15. Mining Microarray Data at NCBI’s Gene Expression Omnibus (GEO)*

    • Tanya Barrett, Ron Edgar
    Pages 175-190

  16. The Stanford Microarray Database

    • Jeremy Gollub, Catherine A. Ball, Gavin Sherlock
    Pages 191-208

  17. Detecting Nucleosome Ladders on Unique DNA Sequences in Mouse Liver Nuclei

    • Tomara.J. Fleury, Alfred Cioffi, Arnold Stein
    Pages 209-223

  18. DNA Methyltransferase Probing of DNA-Protein Interactions

    • Scott A. Hoose, Michael P. Kladde
    Pages 225-244

  19. Protein Binding Microarrays (PBMs) for Rapid, High-Throughput Characterization of the Sequence Specificities of DNA Binding Proteins

    • Michael F. Berger, Martha L. Bulyk
    Pages 245-260

  20. Quantitative Profiling of Protein-DNA Binding on Microarrays

    • Jiannis Ragoussis, Simon Field, Irina A. Udalova
    Pages 261-279
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Keywords

About this book

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.

Editors and Affiliations

  • Department of Chemistry, Purdue University, West Lafayette, USA

    Minou Bina

Bibliographic Information

  • Book Title: Gene Mapping, Discovery, and Expression

  • Book Subtitle: Methods and Protocols

  • Editors: Minou Bina

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1385/1597450979

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2006

  • Hardcover ISBN: 978-1-58829-575-0Published: 01 April 2006

  • Softcover ISBN: 978-1-61737-651-1Published: 09 December 2010

  • eBook ISBN: 978-1-59745-097-3Published: 04 February 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 334

  • Number of Illustrations: 93 b/w illustrations, 1 illustrations in colour

  • Topics: Biochemistry, general, Cell Biology

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