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[Cancer Research 59, 5403-5407, November 1, 1999]
© 1999 American Association for Cancer Research
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[Cancer Research 59, 5403-5407, November 1, 1999]
© 1999 American Association for Cancer Research

Advances in Brief

A Public Database for Gene Expression in Human Cancers1

Anita Lal2, Alex E. Lash2, Stephen F. Altschul, Victor Velculescu, Lin Zhang, Roger E. McLendon, Marco A. Marra, Christa Prange, Patrice J. Morin, Kornelia Polyak, Nickolas Papadopoulos, Bert Vogelstein, Kenneth W. Kinzler, Robert L. Strausberg and Gregory J. Riggins3

Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710 [A. L., R. E. M., G. J. R.]; National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland 20894 [A. E. L., S. F. A.]; The Johns Hopkins Oncology Center [V. V., K. W. K.], The Howard Hughes Medical Institute [L. Z., B. V.], and Department of Pathology [P. J. M.], Johns Hopkins University School of Medicine, Baltimore, Maryland 21231; Washington University Genome Sequencing Center, St. Louis, Missouri 63108 [M. A. M.]; The I.M.A.G.E. Consortium, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94550 [C. P.]; Laboratory of Biological Chemistry, Gerontology Research Center, National Institute on Aging, Baltimore, Maryland 21224 [P. J. M.]; Department of Adult Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115 [K. P.]; Department of Pathology, Columbia University, New York, New York 10032 [N. P.]; and Cancer Genome Anatomy Project, Office of the Director, National Cancer Institute, Bethesda, Maryland 20892 [R. L. S.]

A public database, SAGEmap, was created as a component of the Cancer Genome Anatomy Project to provide a central location for depositing, retrieving, and analyzing human gene expression data. This database uses serial analysis of gene expression to quantify transcript levels in both malignant and normal human tissues. By accessing SAGEmap (http://www.ncbi.nlm.nih.gov/SAGE) the user can compare transcript populations between any of the posted libraries. As an initial demonstration of the database’s utility, gene expression in human glioblastomas was compared with that of normal brain white matter. Of the 47,174 unique transcripts expressed in these two tissues, 471 (1.0%) were differentially expressed by more than 5-fold (P < 0.001). Classification of these genes revealed functions consistent with the biological properties of glioblastomas, in particular: angiogenesis, transcription, and cell cycle related genes.




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