Gene Mapping, Discovery, and Expression

1. Front Matter

   Pages i-xiii

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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

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.

• Allele
• DNA
• Microarray
• Promoter
• gene expression
• genes
• molecular biology
• transcription

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

  Minou Bina

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