Chapter 4. From CAGE to DeepCAGE: High-Throughput Transcription Start Site and Promoter Identification for Gene Network Analysis

  1. Prof. Dr. Günter Kahl4,5,
  2. Prof. Dr. Khalid Meksem6
  1. Matthias Harbers1,
  2. Thomas Werner2,
  3. Piero Carninci3

Published Online: 11 JUN 2008

DOI: 10.1002/9783527622542.ch4

Book Title

The Handbook of Plant Functional Genomics: Concepts and Protocols

The Handbook of Plant Functional Genomics: Concepts and Protocols

Additional Information

How to Cite

Harbers, M., Werner, T. and Carninci, P. (2008) From CAGE to DeepCAGE: High-Throughput Transcription Start Site and Promoter Identification for Gene Network Analysis, in The Handbook of Plant Functional Genomics: Concepts and Protocols (eds G. Kahl and K. Meksem), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527622542.ch4

Editor Information

  1. 4

    Mohrmühlgasse 3, 63500 Seligenstadt, Germany

  2. 5

    GenXPro GmbH, Frankfurt Innovation Center Biotechnology (FIZ), Altenhöferallee 3, 60438 Frankfurt am Main, Germany

  3. 6

    Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901-4415, USA

Author Information

  1. 1

    DNAFORM Inc., Leading Venture Plaza 2, 75-1 Ono-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan

  2. 2

    Genomatix Software GmbH, Bayerstrasse 85a, 80335 Munich, Germany

  3. 3

    RIKEN Genomic Sciences Center (GSC), Laboratory for Genome Exploration, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

Publication History

  1. Published Online: 11 JUN 2008
  2. Published Print: 10 JUN 2008

ISBN Information

Print ISBN: 9783527318858

Online ISBN: 9783527622542

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Keywords:

  • Cap analysis gene expression (CAGE);
  • computational analysis;
  • non-coding RNAs (ncRNAs);
  • tiling arrays;
  • regulatory networks

Summary

This chapter contains sections titled:

  • From Genomes to Transcriptomes

  • Addressing the Complexity of Transcriptomes

  • The Shift From CAGE to DeepCAGE

  • Applications of CAGE and DeepCAGE Libraries

  • Preparation of a DeepCAGE Library

  • CAGE Data Analysis and Genome Mapping Approaches

  • Expression Profiling: Putting CAGE Tags into a Biological Context

  • Perspectives

  • References

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