Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays

doi:10.1073/pnas.041605498

Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays

^aLaboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama 230-0045, Japan; ^bGenome Science Laboratory, ⁱCenter for Biogenic Resources, RIKEN, Tsukuba Institute, Tsukuba 305-0074, Japan; ^cInstitute of Basic Medical Sciences and ^eBiological Sciences, University of Tsukuba, Ibaraki 305-8575, Japan; ^dDepartment of Biotechnology, University of Tokyo, Tokyo 113-8657, Japan; ^fCore Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Corporation; ^gSecond Department of Surgery, Yokohama City University School of Medicine, Yokohama 236-0004, Japan; ^hDepartment of Advanced Surgical Science and Technology, Graduate School of Medicine, Tohoku University, Sendai 980-8574, Japan; and Departments of ^jBiochemistry and ^kGenetics, Stanford University School of Medicine, Stanford, CA 94305

Communicated by Webster K. Cavenee, University of California at San Diego, La Jolla, CA (received for review November 8, 2000)

Abstract

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.

Footnotes

↵ 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.
↵ m To whom correspondence about all genome resources, including the RIKEN full-length cDNA bank, should be addressed at: RIKEN Genomic Science Center, Yokohama 230-0045, Japan. E-mail: yosihide{at}gsc.riken.go.jp.
Abbreviations:

En,

embryonic day n;

Nn,

postnatal day n;

EST,

expressed sequence tag;

FANTOM,

Functional Annotation of Mouse cDNAs;

CNS,

central nervous system