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CGED - Cancer Gene Expression Database


NAR Molecular Biology Database Collection entry number 431
Kato K.1, Yamashita R.1,2, Takagi T.3, Nakai K.2
1Taisho Laboratory of Functional Genomics, Nara Institute of Science and Technology, 8916-5, Takayama, Nara 630-0101, Japan.
2Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
3Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan

Database Description

CGED (Cancer Gene Expression Database) is a database containing gene expression profiles and accompanying clinical information. The data in CGED have been obtained through collaborative efforts made at the Nara Institute of Science and Technology and Osaka University School of Medicine to identify genes of clinical importance. The expression data have been obtained by a high-throughput RT-PCR technique (adaptor-tagged competitive PCR) (1), and patients were recruited mainly from a single hospital. The quality of the data has been demonstrated by successful identification of diagnostic genes (2-3). In CGED, the expression and clinical data are presented in a way useful for scientists interested in specific genes or biological functions. The data can be retrieved either using gene identifiers or by functional categories defined by Gene Ontology terms or the SwissProt annotation. Gene expression data are displayed in mosaic plots, and expression patterns of multiple genes, selected by names or similarity search of the patterns, can be compared. The sorting function enables users for easy recognition of relationships between gene expression and clinical parameters. Currently, data on breast, colorectal, and hepatocellular cancers are available.

Recent Developments

Data analysis of esophageal (squamous cell carcinoma) and thyroid cancers is now ongoing. In addition, expression data acquisition for lung cancer and glioma will be finished within the fiscal year 2003. These data will be deposited in CGED after completion of the data analysis. Some of the patients recruited for these studies are being clinically followed, and the clinical information will be regularly updated.

Acknowledgements

This work was partly supported by a Grant-in-Aid for Scientific Research on Priority Areas "Genome Information Science" from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

References

1. Kato, K. (1997) Adaptor-tagged competitive PCR: a novel method for measuring relative gene expression. Nucleic Acids Res. 25, 4694-4696.
2. Iwao, K., Matoba, R., Ueno, N., Ando, A., Miyoshi, Y., Matsubara, K., Noguchi, S. and Kato, K. (2002) Molecular classification of primary breast tumors possessing distinct prognostic properties. Hum. Mol. Genet. 11, 199-206.
3. Muro, S., Takemasa, I., Oba, S., Matoba, R., Ueno, N., Maruyama, M., Yamashita, R., Sekimoto, M., Yamamoto, H., Nakamori, S., Monden, M., Ishii, S., and Kato, K. (2003) Identification of expressed genes linked to the malignancy of human colorectal carcinoma by parametric clustering of quantitative expression data. Genome Biology 4, R21.
4. Kurokawa, Y., Matoba, R., Takemasa, I., Nakamori, S., Tsujie, M., Nagano, H., Dono, K., Umeshita, K., Sakon, M., Ueno, N., Kita, H., Oba, S., Ishii, S., Kato, K. and Monden, M. Molecular features of non-B, non-C hepatocellular carcinoma: a PCR-array gene expression profiling study. J. Hepatol., in press.

Subcategory: Cancer gene databases

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