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a Laboratory for Genome Exploration Research Group,
RIKEN Genomic Sciences Center (GSC), Yokohama 230-0045, Japan;
b Genome Science Laboratory, i Center for
Biogenic Resources, RIKEN, Tsukuba Institute, Tsukuba 305-0074, Japan;
c Institute of Basic Medical Sciences and
e Biological Sciences, University of Tsukuba, Ibaraki
305-8575, Japan; d Department of Biotechnology, University
of Tokyo, Tokyo 113-8657, Japan; f Core Research for
Evolutional Science and Technology (CREST) of Japan Science and
Technology Corporation; g Second Department of Surgery,
Yokohama City University School of Medicine, Yokohama 236-0004, Japan; h Department of Advanced Surgical Science and
Technology, Graduate School of Medicine, Tohoku University, Sendai
980-8574, Japan; and Departments of j Biochemistry and
k Genetics, Stanford University School of Medicine,
Stanford, CA 94305
Communicated by Webster K. Cavenee, University of California at
San Diego, La Jolla, CA, December 22, 2000 (received for review November 8, 2000)
We have systematically characterized gene expression patterns in 49 adult and embryonic mouse tissues by using cDNA microarrays with 18,816 mouse cDNAs. Cluster analysis defined sets of genes that were expressed
ubiquitously or in similar groups of tissues such as digestive organs
and muscle. Clustering of expression profiles was observed in embryonic
brain, postnatal cerebellum, and adult olfactory bulb, reflecting
similarities in neurogenesis and remodeling. Finally, clustering genes
coding for known enzymes into 78 metabolic pathways revealed a
surprising coordination of expression within each pathway among
different tissues. On the other hand, a more detailed examination of
glycolysis revealed tissue-specific differences in profiles of key
regulatory enzymes. Thus, by surveying global gene expression by using
microarrays with a large number of elements, we provide insights into
the commonality and diversity of pathways responsible for the
development and maintenance of the mammalian body plan.
Applied Biological Sciences
Delineating developmental and metabolic pathways in
vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays
l
To whom reprint requests should be addressed at: RIKEN
Genomic Science Center, Yokohama 230-0045, Japan. E-mail:
okazaki{at}gsc.riken.go.jp.
www.pnas.org/cgi/doi/10.1073/pnas.041605498
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|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
 L. Smith and A. Greenfield DNA microarrays and development Hum. Mol. Genet., April 2, 2003; 12(90001): R1 - 8. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
 N.M. Svrakic, O. Nesic, M.R.K. Dasu, D. Herndon, and J.R. Perez-Polo Statistical Approach to DNA Chip Analysis Recent Prog. Horm. Res., January 1, 2003; 58(1): 75 - 93. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. A. Hume, I. L. Ross, S. R. Himes, R. T. Sasmono, C. A. Wells, and T. Ravasi The mononuclear phagocyte system revisited J. Leukoc. Biol., October 1, 2002; 72(4): 621 - 627. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Kaminski and N. Friedman Practical Approaches to Analyzing Results of Microarray Experiments Am. J. Respir. Cell Mol. Biol., August 1, 2002; 27(2): 125 - 132. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
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|
|
|
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|
|
|
|
|
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