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Comparative Study
. 2003 Jun;13(6B):1318-23.
doi: 10.1101/gr.1075103.

Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays

Hidemasa Bono  1 , Ken Yagi, Takeya Kasukawa, Itoshi Nikaido, Naoko Tominaga, Rika Miki, Yosuke Mizuno, Yasuhiro Tomaru, Hitoshi Goto, Hiroyuki Nitanda, Daisuke Shimizu, Hirochika Makino, Tomoyuki Morita, Junshin Fujiyama, Takehito Sakai, Takashi Shimoji, David A Hume, Yoshihide Hayashizaki, Yasushi Okazaki; RIKEN GER Group; GSL Members
Affiliations
Comparative Study

Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays

Hidemasa Bono et al. Genome Res. 2003 Jun.

Abstract

The number of known mRNA transcripts in the mouse has been greatly expanded by the RIKEN Mouse Gene Encyclopedia project. Validation of their reproducible expression in a tissue is an important contribution to the study of functional genomics. In this report, we determine the expression profile of 57,931 clones on 20 mouse tissues using cDNA microarrays. Of these 57,931 clones, 22,928 clones correspond to the FANTOM2 clone set. The set represents 20,234 transcriptional units (TUs) out of 33,409 TUs in the FANTOM2 set. We identified 7206 separate clones that satisfied stringent criteria for tissue-specific expression. Gene Ontology terms were assigned for these 7206 clones, and the proportion of 'molecular function' ontology for each tissue-specific clone was examined. These data will provide insights into the function of each tissue. Tissue-specific gene expression profiles obtained using our cDNA microarrays were also compared with the data extracted from the GNF Expression Atlas based on Affymetrix microarrays. One major outcome of the RIKEN transcriptome analysis is the identification of numerous nonprotein-coding mRNAs. The expression profile was also used to obtain evidence of expression for putative noncoding RNAs. In addition, 1926 clones (70%) of 2768 clones that were categorized as "unknown EST," and 1969 (58%) clones of 3388 clones that were categorized as "unclassifiable" were also shown to be reproducibly expressed.

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Figures

Figure 1
Figure 1
Pie charts for tissue profiling by Gene Ontology.
See this image and copyright information in PMC

References

    1. Alizadeh, A.A., Eisen, M.B., Davis, R.E., Ma, C., Lossos, I.S., Rosenwald, A., Boldrick, J.C., Sabet, H., Tran, T., Yu, X., et al. 2000. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403: 503-511. - PubMed
    1. Bono, H., Kasukawa, T., Hayashizaki, Y., and Okazaki, Y. 2002. READ: RIKEN Expression Array Database. Nucleic Acids Res. 30: 211-213. - PMC - PubMed
    1. Bono, H., Nikaido, I., Kasukawa, T., Hayashizaki, Y., RIKEN GER Group and GSL Members, and Okazaki, Y. 2003. Comprehensive analysis of the mouse metabolome based on the transcriptome. Genome Res. (this issue). - PMC - PubMed
    1. DeRisi, J.L., Iyer, V.R., and Brown, P.O. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686. - PubMed
    1. Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. 95: 14863-14868. - PMC - PubMed

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