This is 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 Biology[trademark]" 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.