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

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

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

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

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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

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.

Original language	English (US)
Pages (from-to)	22-26
Number of pages	5
Journal	FEBS Letters
Volume	559
Issue number	1-3
DOIs	https://doi.org/10.1016/S0014-5793(04)00018-3
State	Published - Feb 13 2004
Externally published	Yes

Bibliographical note

Funding Information:
We thank A. Hasegawa for database management and bioinformatic analysis, also Y. Mitsuiki for secretarial support. This work was supported by Research Grants for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government to Y.H., Research Grant for Advanced and Innovational Research Program in Life Science from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government to J.K. and Presidential Research Grant for Intersystem Collaboration of RIKEN to J.K. R.K. is the recipient of an INCO-JAPAN fellowship from the European Union.

Keywords

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

ASJC Scopus subject areas

Biophysics
Structural Biology
Biochemistry
Molecular Biology
Genetics
Cell Biology

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10.1016/S0014-5793(04)00018-3

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Kodzius, R., Matsumura, Y., Kasukawa, T., Shimokawa, K., Fukuda, S., Shiraki, T., Nakamura, M., Arakawa, T., Sasaki, D., Kawai, J., Harbers, M., Carninci, P., & Hayashizaki, Y. (2004). Absolute expression values for mouse transcripts: Re-annotation of the READ expression database by the use of CAGE and EST sequence tags. FEBS Letters, 559(1-3), 22-26. https://doi.org/10.1016/S0014-5793(04)00018-3

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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.",

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note = "Funding Information: We thank A. Hasegawa for database management and bioinformatic analysis, also Y. Mitsuiki for secretarial support. This work was supported by Research Grants for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government to Y.H., Research Grant for Advanced and Innovational Research Program in Life Science from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government to J.K. and Presidential Research Grant for Intersystem Collaboration of RIKEN to J.K. R.K. is the recipient of an INCO-JAPAN fellowship from the European Union.",

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Kodzius, R, Matsumura, Y, Kasukawa, T, Shimokawa, K, Fukuda, S, Shiraki, T, Nakamura, M, Arakawa, T, Sasaki, D, Kawai, J, Harbers, M, Carninci, P & Hayashizaki, Y 2004, 'Absolute expression values for mouse transcripts: Re-annotation of the READ expression database by the use of CAGE and EST sequence tags', FEBS Letters, vol. 559, no. 1-3, pp. 22-26. https://doi.org/10.1016/S0014-5793(04)00018-3

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AU - Harbers, Matthias

AU - Carninci, Piero

AU - Hayashizaki, Yoshihide

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

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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