By Piero Carninci
A consultant for clients of recent applied sciences, this quantity contains competently confirmed protocols, permitting readers to organize their samples for experiments. also, it offers a consultant for the bioinformatics instruments which are to be had for the research of the bought tags, together with the layout of the software program, the assets and internet details the place they are often downloaded. eventually, the publication presents examples of the applying of those applied sciences to spot promoters, annotate genomes, establish new RNAs and reconstruct types of transcriptional regulate. even though examples as a rule regard mammalians, the dialogue expands to different teams of eukaryotes, the place those methods are complementing genome sequencing.
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Extra info for Cap-Analysis Gene Expression (CAGE): The Science of Decoding Gene Transcription
Biotechnol. 22, 1146–1149 (2004).  M. Harbers and P. Carninci. Tag-based approaches for transcriptome research and genome annotation. Nat. Methods 2, 495–502 (2005).  P. Ng et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat. Methods 2, 105–111 (2005).  M. Simonis, J. Kooren and W. de Laat. An evaluation of 3C-based methods to capture DNA interactions. Nat. Methods 4, 895–901 (2007).  M. Zavolan et al. Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome.
3). through PET mapping on different orientations or different chromosomes. 27 One of them, BCAS4/BCAS3, has been verified through independent cytogenetic and genomic DNA sequencing approaches (Fig. 3). 25 Our data suggests that there are significant numbers of fusion genes that may have important biological functions and yet to be identified in many different cell types including stem cells and cancer cells. Indeed, GIS-PET is the only efficient system for large scale discovery in this uncharted territory.
11] P. Carninci, Constructing the landscape of the mammalian transcriptome. J. Exp. Biol. 210, 1497–1506 (2007).  T. Shiraki et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl. Acad. Sci. USA. 100, 1577–1581 (2003).  R. Kodzius et al. CAGE: Cap analysis of gene expression. Nat. Methods. 3, 211–222 (2006).  P. Carninci et al. Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA.
Cap-Analysis Gene Expression (CAGE): The Science of Decoding Gene Transcription by Piero Carninci