NAR Molecular Biology Database Collection entry number 802
Kawaji H.1, Kasukawa T.1,2, Fukuda S.2, Katayama S.2, Kai C.2, Kawai J.2,3, Carninci P.2,3, and Hayashizaki Y.2,3
1NTT Software Corporation, Teisan Kannai Bldg. 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

Database Description

CAGE Basic and Analysis Databases store an original resource produced by CAGE (cap-analysis gene expression; 1), which measures expression levels of transcription starting sites (TSS) 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 over 20 tissues consisting of over 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, etc. 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 (CTSS), tag clusters (TC) for defining promoters, and transcriptional units (TU; 2). Their associations and TU attributes are available to find promoters of interest. These databases were provided for FANTOM3 (Functional Annotation Of Mouse 3; 3,4), an international collaboration research project focusing on expanding the transcriptome and subsequent analyses.


We would like to thank A. Hasegawa for data processing; K. Nakano, H. Murakami for building computational systems; K. Yoshida for support; and all members of the FANTOM consortium. This study was supported by Research Grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government to Y.H., a grant of the Genome Network Project from the Ministry of Education, Culture, Sports, Science and Technology, Japan. to Y.H., Grant for the Strategic Programs for R&D of RIKEN to Y.H.


1. Shiraki, T., Kondo, S., Katayama, S., Waki, K., Kasukawa, T., Kawaji, H., Kodzius, R., Watahiki, A., Nakamura, M., Arakawa, T. et al. (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl. Acad. Sci. U. S. A., 100, 15776-15781.
2. Kasukawa, T., Katayama, S., Kawaji, H., Suzuki, H., Hume, D.A. and Hayashizaki, Y. (2004) Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis. Genomics, 84, 913-921.
3. Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M.C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.
4. Katayama, S., Tomaru, Y., Kasukawa, T., Waki, K., Nakanishi, M., Nakamura, M., Nishida, H., Yap, C.C., Suzuki, M., Kawai, J. et al. (2005) Antisense transcription in the mammalian transcriptome. Science, 309, 1564-1566.

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