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Vol. 10, Issue 11, 1817-1827, November 2000

RESOURCE
BodyMap: A Collection of 3' ESTs for Analysis of Human Gene Expression Information

Shoko Kawamoto,1 Junji Yoshii,2 Katsuya Mizuno,2 Kouichi Ito,1 Yasuhide Miyamoto,1 Tadashi Ohnishi,1 Ryo Matoba,1 Naohiro Hori,1 Yuhiko Matsumoto,1 Toshiyuki Okumura,1 Yuko Nakao,1 Hisae Yoshii,1 Junko Arimoto,1 Hiroko Ohashi,1 Hiroko Nakanishi,1 Ikko Ohno,1 Jun Hashimoto,1 Kota Shimizu,1 Kazuhisa Maeda,1 Hiroshi Kuriyama,1 Koji Nishida,1 Akiyo Shimizu-Matsumoto,1 Wakako Adachi,1 Reiko Ito,1 Satoshi Kawasaki,1 K.S. Chae,1 Katsuji Murakawa,1 Masahiro Yokoyama,1 Atsushi Fukushima,1 Teruyoshi Hishiki,1 Akihiko Nakaya,3 Jun Sese,3 Norikazu Monma,3 Hitoshi Nikaido,3 Shinichi Morishita,3 Kenichi Matsubara,4 and Kousaku Okubo5

1 Institute for Molecular and Cellular Biology, Osaka University, Osaka 565-0871, Japan; 2 Hitachi Software Engineering Co., Ltd., Yokohama 231-0015, Japan; 3 Department of Genome Knowledge Discovery System, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; 4 Internal Institute for Advanced Study, Kyoto 619-0225, Japan

BodyMap is a collection of site-directed 3' expressed sequence tags (ESTs) (gene signatures, GSs) that contains the transcript compositions of various human tissues and was the first systematic effort to acquire gene expression data. For the construction of BodyMap, cDNA libraries were made, preserving abundance information and histologic resolutions of tissue mRNAs. By sequencing 164,000 randomly selected clones, 88,587 GSs that represent chromosomally coded transcripts have been collected from 51 human organs and tissues. They were clustered into 18,722 independent 3' termini from transcripts, and more than 3000 of these were not found among ESTs assembled in UniGene (Build 75). Assessment of the prevalence of polyadenylation signals and comparison with GenBank cDNAs indicated that there was no significant contamination by internally primed cDNAs or genomic fragments but that there was a relatively high incidence (12%) of alternative polyadenylation sites. We evaluated the sensitivity and resolution of expression information in BodyMap by in silico Northern hybridization and selection of tissue-specific gene probes. BodyMap is a unique resource for estimation of the absolute abundance of transcripts and selection of gene probes for efficient hybridization-based gene expression profiling. [BodyMap data are available at http://bodymap.ims.u-tokyo.ac.jp.]

5 Corresponding author.

10:1817-1827 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
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