CAP-ANALYSIS GENE EXPRESSION (CAGE)<br> The Science of Decoding Gene Transcription

CAP-ANALYSIS GENE EXPRESSION (CAGE)
The Science of Decoding Gene Transcription

CONTENTS


FRONT MATTER PIERO CARNINCI	i
Cap Analysis Gene Expression (CAGE) Y. Hayashizaki	1
Tagging Transcription Starting Sites with CAGE Piero Carninci	7
Construction of CAGE Libraries Hiromi Nishiyori and Piero Carninci	21
Transcriptome and Genome Characterization Using Massively Parallel Paired End Tag (PET) Sequencing Analysis Chia-Lin Wei and Yijun Ruan	41
New Era of Genome-Wide Gene Expression Analysis Norihiro Maeda	61
Computational Tools to Analyze CAGE — Introduction to PART II Carsten O. Daub	79
Extraction and Quality Control of CAGE Tags Erik Arner and Timo Lassmann	83
Setting CAGE Tags in a Genomic Context Geoffrey J. Faulkner and Sean M. Grimmond	93
Using CAGE Data for Quantitative Expression Michiel De Hoon, Nicolas Bertin and Alistair M. Chalk	101
Databases for CAGE Visualization and Analysis Hideya Kawaji	123
Computational Methods to Identify Transcription Factor Binding Sites Using CAGE Information Vladimir B. Bajic, Sebastian Schmeier and Cameron Ross MacPherson	137
Transcription Regulatory Networks Analysis Using CAGE Jesper Tegnér, Johan Björkegren, Timothy Ravasi and Vladimir B. Bajic	153
Gene-Expression Ontologies and Tag-Based Expression Profiling Oliver Hofmann and Winston Hide	169
Lessons Learned from Genomic CAGE A. Sandelin and E. Valen	179
Future Challenges in CAGE Analysis E. Valen and A. Sandelin	197
Comparative Genomics and Mammalian Promoter Evolution Martin S. Taylor, Gregory Jordan and Colin A. Semple	209
The Impact of CAGE Data on Understanding Macrophage Transcriptional Biology David A. Hume, Kate Schroder and Katharine M. Irvine	227
BACK MATTER PIERO CARNINCI	245
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