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

FEBS Letters

Harbers, Matthias³  Shiraki, Toshiyuki²  Kawai, Jun¹  Matsumura, Yonehiro⁴  Carninci, Piero¹  Shimokawa, Kazuro²  Hayashizaki, Yoshihide¹  Kasukawa, Takeya²  Fukuda, Shiro²  Nakamura, Mari²  Kodzius, Rimantas¹  Sasaki, Daisuke²  Arakawa, Takahiro² 

[1] 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;K.K. Dnaform, Tsukuba Branch, 3-1 Chuo 8-chome, Ami-machi, Inashiki-gun, Ibaraki 300-0332, Japan;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

关键词: Gene expression;    Cap analysis of gene expression;    Serial analysis of gene expression;    Microarray;    Absolute value;    Expressed sequence tag count;    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;   

DOI  :  10.1016/S0014-5793(04)00018-3

学科分类：生物化学/生物物理

来源: John Wiley & Sons Ltd.

【 摘 要 】

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.

【 授权许可】

Unknown