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Nucleic Acids Research 2006 34(Database Issue):D632-D636; doi:10.1093/nar/gkj034
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Nucleic Acids Research, 2006, Vol. 34, Database issue D632-D636
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis

Hideya Kawaji1, Takeya Kasukawa1,2, Shiro Fukuda2, Shintaro Katayama2,*, Chikatoshi Kai2, Jun Kawai2,3, Piero Carninci2,3 and Yoshihide Hayashizaki2,3

1NTT Software Corporation Teisan Kannai Building 209, Yamashita-cho Naka-ku, Yokohama, Kanagawa, 231-8551, Japan 2Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan 3Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan

*To whom corresponding should be addressed. Tel: +81 45 503 9222; Fax: +81 45 503 9216; Email: rgscerg{at}gsc.riken.jp

Received August 15, 2005. Revised September 26, 2005. Accepted September 26, 2005.

Cap-analysis gene expression (CAGE) Basic and Analysis Databases store an original resource produced by CAGE, which measures expression levels of transcription starting sites by sequencing large amounts of transcript 5' ends, termed CAGE tags. Millions of human and mouse high-quality CAGE tags derived from different conditions in >20 tissues consisting of >250 RNA samples are essential for identification of novel promoters and promoter characterization in the aspect of expression profile. CAGE Basic Database is a primary database of the CAGE resource, RNA samples, CAGE libraries, CAGE clone and tag sequences and so on. CAGE Analysis Database stores promoter related information, such as counts of related transcripts, CpG islands and conserved genome region. It also provides expression profiles at base pair and promoter levels. Both databases are based on the same framework, CAGE tag starting sites, tag clusters for defining promoters and transcriptional units (TUs). Their associations and TU attributes are available to find promoters of interest. These databases were provided for Functional Annotation Of Mouse 3 (FANTOM3), an international collaboration research project focusing on expanding the transcriptome and subsequent analyses. Now access is free for all users through the World Wide Web at http://fantom3.gsc.riken.jp/.


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