Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags

Kodzius, Rimantas; Matsumura, Yonehiro; Kasukawa, Takeya; Shimokawa, Kazuro; Fukuda, Shiro; Shiraki, Toshiyuki; Nakamura, Mari; Arakawa, Takahiro; Sasaki, Daisuke; Kawai, Jun; Harbers, Matthias; Carninci, Piero; Hayashizaki, Yoshihide

doi:10.1016/S0014-5793(04)00018-3

Next »FEBS Letters
Volume 559, Issue 1 , Pages 22-26, 13 February 2004

Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags

Edited by Takashi Gojobori

Rimantas Kodzius
- Genome Science Laboratory, RIKEN, Wako Main Campus, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
Yonehiro Matsumura
- Division of Genomic Information Resource Exploration, Science of Biological Supramolecular Systems, Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi-Ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Takeya Kasukawa
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Network Service Solution Business Group, NTT Software Corporation, 209 Yamashita-cho, Naka-ku, Yokohama, Kanagawa 231-8551, Japan
Kazuro Shimokawa
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Shiro Fukuda
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Toshiyuki Shiraki
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Mari Nakamura
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Takahiro Arakawa
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Daisuke Sasaki
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Jun Kawai
- Genome Science Laboratory, RIKEN, Wako Main Campus, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Matthias Harbers
- K.K. Dnaform, Tsukuba Branch, 3-1 Chuo 8-chome, Ami-machi, Inashiki-gun, Ibaraki 300-0332, Japan
Piero Carninci
- Genome Science Laboratory, RIKEN, Wako Main Campus, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Corresponding author. Fax: (81)-48-4624686
Yoshihide Hayashizaki
- Genome Science Laboratory, RIKEN, Wako Main Campus, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

Received 30 October 2003; received in revised form 26 December 2003; accepted 5 January 2004.

Abstract

The RIKEN expression array database (READ) provides comprehensive gene expression data for the mouse, which were obtained as relative values from microarray double-staining experiments with E17.5 mRNA as common reference. To assign absolute expression values for mouse transcripts within READ, we applied the E17.5 reference sample to CAGE (cap analysis of gene expression) and expressed sequence tag (EST) high-throughput tag sequencing. Newly assigned values within the READ database were validated by comparison to expression data from serial analysis of gene expression, CAGE and EST experiments. These experiments confirmed the great significance of the absolute expression values within the improved READ database. The new Absolute READ database on absolute expression data is available under http://genome.gsc.riken.jp/absolute.

Keywords: Gene expression, Cap analysis of gene expression, Serial analysis of gene expression, Microarray, Absolute value, Expressed sequence tag count

Abbreviations: CAGE, cap analysis of gene expression, E17.5, mouse embryo whole body mixed sex E17.5 RNA, EST, expressed sequence tag, FANTOM, functional annotation of mouse, READ, RIKEN expression array database, RTS, representative transcript set, SAGE, serial analysis of gene expression, tpm, transcripts per million, TU, transcriptional unit