A collection of cutting-edge computational tools and experimental techniques to study how genes are regulated, and to reconstruct the regulatory networks through which various cell-types are produced. On the computational side, web-based technologies to localize genes, to access and retrieve data from microarray databases, to conduct comparative genomics, and to discover the potential "codes" in genomic DNA that may control the expression of protein-coding genes. Detailed experimental techniques described include methods for studying chromatin structure and allele-specific gene expression, methods for high-throughput analysis to characterize the transcription factor binding elements, and methods for isolating and identifying proteins that interact with DNA. The protocols follow the successful Methods in Molecular BiologyT series format, each offering step-by-step instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding pitfalls.
Use of Genome Browsers to Locate Your Favorite Genes Minou Bina Methods for Identifying and Mapping Recent Segmental and Gene Duplications in Eukaryotic Genomes Razi Khaja, Jeffrey R. MacDonald, Junjun Zhang, and Stephen W. Scherer Identification and Mapping of Paralogous Genes on a Known Genomic DNA Sequence Minou Bina Quantitative DNA Fiber Mapping in Genome Research and Construction of Physical Maps Heinz-Ulrich G. Weier and Lisa W. Chu PRINS for Mapping Single-Copy Genes Avirachan T. Tharapel and Stephen S. Wachtel VISTA Family of Computational Tools for Comparative Analysis of DNA Sequences and Whole Genomes Inna Dubchak and Dmitriy V. Ryaboy Computational Prediction of cis-Regulatory Modules from Multispecies Alignments Using Galaxy, Table Browser, and GALA Laura Elnitski, David King, and Ross C. Hardison Comparative Promoter Analysis in Vertebrate Genomes with the CORG Workbench Christoph Dieterich and Martin Vingron cis-Regulatory Region Analysis Using BEARR Vinsensius Berlian Vega A Database of 9-Mers from Promoter Regions of Human Protein-Coding Genes Minou Bina, Phillip Wyss, and Syed Rehan Shah A Program Toolkit for the Analysis of Regulatory Regions of Genes Phillip Wyss, Sheryl A. Lazarus, and Minou Bina Analysis of Allele-Specific Gene Expression Julian C. Knight Construction of microRNA-Containing Vectors for Expression in Mammalian Cells Yoko Fukuda, Hiroaki Kawasaki, and Kazunari Taira Mining Microarray Data at NCBI's Gene Expression Omnibus (GEO) Tanya Barrett and Ron Edgar The Stanford Microarray Database: A User's Guide Jeremy Gollub, Catherine A. Ball, and Gavin Sherlock Detecting Nucleosome Ladders on Unique DNA Sequences in Mouse Liver Nuclei Tomara J. Fleury, Alfred Cioffi, and Arnold Stein DNA Methyltransferase Probing of DNA-Protein Interactions Scott A. Hoose and Michael P. Kladde Protein Binding Microarrays (PBMs) for Rapid, High-Throughput Characterization of the Sequence Specificities of DNA Binding Proteins Michael F. Berger and Martha L. Bulyk Quantitative Profiling of Protein-DNA Binding on Microarrays Jiannis Ragoussis, Simon Field, and Irina A. Udalova Analysis of Protein-DNA Binding by Streptavidin-Agarose Pulldown Kenneth K. Wu Isolation and Mass Spectrometry of Specific DNA Binding Proteins Mariana Yaneva and Paul Tempst Isolation of Transcription Factor Complexes by In Vivo Biotinylation Tagging and Direct Binding to Streptavidin Beads Patrick Rodriguez, Harald Braun, Katarzyna E. Kolodziej, Ernie de Boer, Jennifer Campbell, Edgar Bonte, Frank Grosveld, Sjaak Philipsen, and John Strouboulis Index