Description
Book SynopsisThis book is a guide for users of new technologies, as it includes accurately proven protocols, allowing readers to prepare their samples for experiments. Additionally, it is a guide for the bioinformatics tools that are available for the analysis of the obtained tags, including the design of the software, the sources and the Web. Finally, the book provides examples of the application of these technologies to identify promoters, annotate genomes, identify new RNAs and reconstruct models of transcriptional control. Although examples mainly concern mammalians, the discussion expands to other groups of eukaryotes, where these approaches are complementing genome sequencing.
Trade Review"This is a comprehensive introduction to a powerful and important new technique that is transforming our understanding of gene regulation. This volume contains everything you need to know to become an expert in CAGE, from library construction to bioinformatic analysis of the voluminous data sets."
—Gene E. Robinson, University of Illinois
Table of ContentsBrief Historical Perspective on Transcriptional Regulation. Preparation of CAGE Libraries: An Enabling Experimental Protocol. Ditags and PET-Technologies for Transcript Identification and Review Use of Ditags with Emphasis on Gene Identification. From Sequencing Output to CAGE Tags: A Chapter on the Extraction of CAGE Tags from the Raw Output of the Sequencing Machine. Using CAGE Data for Quantitative Expression. Compare CAGE Expression to Microarrays and qPCR. Identification of Isoforms. Promoter Analysis Databases. Construction and Tutorial of the CAGE Analysis Viewer and Genome Viewer. Transcriptional Network Analysis Using CAGE. Biological Examples of Alternative TSS/Promoters. Challenges in CAGE Analysis.
