Systematic expression profiling of the mouse transcriptome using RIKEN cDNA mircoarrays

Bono, H., Yagi, K., Kasukawa, T., Nikaido, I., Tominaga, N., Miki, R., Mizuno, Y., Tomaru, Y., Goto, H., Nitanda, H., Shimizu, D., Makino, H., Morita, T., Fujiyama, J. and Sakai, T. (2003) Systematic expression profiling of the mouse transcriptome using RIKEN cDNA mircoarrays. Genome Research, 13 6B: 1318-1323. doi:10.1101/gr.1075103

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Author Bono, H.
Yagi, K.
Kasukawa, T.
Nikaido, I.
Tominaga, N.
Miki, R.
Mizuno, Y.
Tomaru, Y.
Goto, H.
Nitanda, H.
Shimizu, D.
Makino, H.
Morita, T.
Fujiyama, J.
Sakai, T.
Title Systematic expression profiling of the mouse transcriptome using RIKEN cDNA mircoarrays
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
Publication date 2003-06-01
Sub-type Article (original research)
DOI 10.1101/gr.1075103
Open Access Status File (Publisher version)
Volume 13
Issue 6B
Start page 1318
End page 1323
Total pages 6
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Language eng
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.
Keyword Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Genetics & Heredity
Functional Annotation
Q-Index Code C1
Institutional Status UQ
Additional Notes Authors of this document: Bono, H; Yagi, K; Kasukawa, T; Nikaido, I; Tominaga, N; Miki, R; Mizuno, Y; Tomaru, Y; Goto, H; Nitanda, H; Shimizu, D; Makino, H; Morita, T; Fujiyama, J; Sakai, T; Shimoji, T; Hume, DA; Hayashizaki, Y; Okazaki, Y; RIKEN GER Grp; GSL Members.

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2004 Higher Education Research Data Collection
Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 51 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 62 times in Scopus Article | Citations
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Created: Wed, 15 Aug 2007, 12:50:38 EST