A Public Database for Gene Expression in Human Cancers

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 theCancer Genome Anatomy Project to provide a central locationfor depositing, retrieving, and analyzing human gene expressiondata. This database uses serial analysis of gene expressionto quantify transcript levels in both malignant and normal humantissues. By accessing SAGEmap (http://www.ncbi.nlm.nih.gov/SAGE)the user can compare transcript populations between any of theposted libraries. As an initial demonstration of the database’sutility, gene expression in human glioblastomas was comparedwith that of normal brain white matter. Of the 47,174 uniquetranscripts expressed in these two tissues, 471 (1.0%) weredifferentially expressed by more than 5-fold (P < 0.001).Classification of these genes revealed functions consistentwith the biological properties of glioblastomas, in particular:angiogenesis, transcription, and cell cycle related genes.

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R. L. Strausberg and G. J. Riggins
Navigating the human transcriptome
PNAS, October 9, 2001; 98(21): 11837 - 11838.
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P. Buckhaults, C. Rago, B. St. Croix, K. E. Romans, S. Saha, L. Zhang, B. Vogelstein, and K. W. Kinzler
Secreted and Cell Surface Genes Expressed in Benign and Malignant Colorectal Tumors
Cancer Res., October 1, 2001; 61(19): 6996 - 7001.
[Abstract] [Full Text] [PDF]

A. Lal, H. Peters, B. St. Croix, Z. A. Haroon, M. W. Dewhirst, R. L. Strausberg, J. H. A. M. Kaanders, A. J. van der Kogel, and G. J. Riggins
Transcriptional Response to Hypoxia in Human Tumors
J Natl Cancer Inst, September 5, 2001; 93(17): 1337 - 1343.
[Abstract] [Full Text] [PDF]

H. M. Sowter, P. J. Ratcliffe, P. Watson, A. H. Greenberg, and A. L. Harris
HIF-1-dependent Regulation of Hypoxic Induction of the Cell Death Factors BNIP3 and NIX in Human Tumors
Cancer Res., September 1, 2001; 61(18): 6669 - 6673.
[Abstract] [Full Text] [PDF]

D. A. Porter, I. E. Krop, S. Nasser, D. Sgroi, C. M. Kaelin, J. R. Marks, G. Riggins, and K. Polyak
A SAGE (Serial Analysis of Gene Expression) View of Breast Tumor Progression
Cancer Res., August 1, 2001; 61(15): 5697 - 5702.
[Abstract] [Full Text] [PDF]

I. E. Krop, D. Sgroi, D. A. Porter, K. L. Lunetta, R. LeVangie, P. Seth, C. M. Kaelin, E. Rhei, M. Bosenberg, S. Schnitt, et al.
HIN-1, a putative cytokine highly expressed in normal but not cancerous mammary epithelial cells
PNAS, July 24, 2001; (2001) 171138398.
[Abstract] [Full Text] [PDF]

J. Y. Ljubimova, A. J. Lakhter, A. Loksh, W. H. Yong, M. S. Riedinger, J. H. Miner, L. M. Sorokin, A. V. Ljubimov, and K. L. Black
Overexpression of {alpha}4 Chain-containing Laminins in Human Glial Tumors Identified by Gene Microarray Analysis
Cancer Res., July 1, 2001; 61(14): 5601 - 5610.
[Abstract] [Full Text] [PDF]

K. Polyak and G. J. Riggins
Gene Discovery Using the Serial Analysis of Gene Expression Technique: Implications for Cancer Research
J. Clin. Oncol., June 1, 2001; 19(11): 2948 - 2958.
[Abstract] [Full Text] [PDF]

P. Argani, C. Rosty, R. E. Reiter, R. E. Wilentz, S. R. Murugesan, S. D. Leach, B. Ryu, H. G. Skinner, M. Goggins, E. M. Jaffee, et al.
Discovery of New Markers of Cancer through Serial Analysis of Gene Expression: Prostate Stem Cell Antigen Is Overexpressed in Pancreatic Adenocarcinoma
Cancer Res., June 1, 2001; 61(11): 4320 - 4324.
[Abstract] [Full Text] [PDF]

S. V. Anisimov, E. G. Lakatta, and K. R. Boheler
Discovering altered genomic expression patterns in heart: transcriptome determination by serial analysis of gene expression
Eur J Heart Fail, June 1, 2001; 3(3): 271 - 281.
[Abstract] [Full Text] [PDF]

G. J. Riggins and R. L. Strausberg
Genome and genetic resources from the Cancer Genome Anatomy Project
Hum. Mol. Genet., April 1, 2001; 10(7): 663 - 667.
[Abstract] [Full Text] [PDF]

H. Caron, B. v. Schaik, M. v. d. Mee, F. Baas, G. Riggins, P. v. Sluis, M.-C. Hermus, R. v. Asperen, K. Boon, P. A. Voûte, et al.
The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains
Science, February 16, 2001; 291(5507): 1289 - 1292.
[Abstract] [Full Text]

J. M. MARKERT, C. M. FULLER, G. Y. GILLESPIE, J. K. BUBIEN, L. A. MCLEAN, R. L. HONG, K. LEE, S. R. GULLANS, T. B. MAPSTONE, and D. J. BENOS
Differential gene expression profiling in human brain tumors
Physiol Genomics, February 7, 2001; 5(1): 21 - 33.
[Abstract] [Full Text] [PDF]

H. Huang, S. Colella, M. Kurrer, Y. Yonekawa, P. Kleihues, and H. Ohgaki
Gene Expression Profiling of Low-Grade Diffuse Astrocytomas by cDNA Arrays
Cancer Res., December 1, 2000; 60(24): 6868 - 6874.
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R. Chrast, H. S. Scott, M. P. Papasavvas, C. Rossier, E. S. Antonarakis, C. Barras, M. T. Davisson, C. Schmidt, X. Estivill, M. Dierssen, et al.
The Mouse Brain Transcriptome by SAGE: Differences in Gene Expression between P30 Brains of the Partial Trisomy 16 Mouse Model of Down Syndrome (Ts65Dn) and Normals
Genome Res., December 1, 2000; 10(12): 2006 - 2021.
[Abstract] [Full Text]

A. H. Charpentier, A. K. Bednarek, R. L. Daniel, K. A. Hawkins, K. J. Laflin, S. Gaddis, M. C. MacLeod, and C. M. Aldaz
Effects of Estrogen on Global Gene Expression: Identification of Novel Targets of Estrogen Action
Cancer Res., November 1, 2000; 60(21): 5977 - 5983.
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C. D. Hough, C. A. Sherman-Baust, E. S. Pizer, F. J. Montz, D. D. Im, N. B. Rosenshein, K. R. Cho, G. J. Riggins, and P. J. Morin
Large-Scale Serial Analysis of Gene Expression Reveals Genes Differentially Expressed in Ovarian Cancer
Cancer Res., November 1, 2000; 60(22): 6281 - 6287.
[Abstract] [Full Text]

K. W. Foster, A. R. Frost, P. McKie-Bell, C.-Y. Lin, J. A. Engler, W. E. Grizzle, and J. M. Ruppert
Increase of GKLF Messenger RNA and Protein Expression during Progression of Breast Cancer
Cancer Res., November 1, 2000; 60(22): 6488 - 6495.
[Abstract] [Full Text]

S.-i. Hashimoto, T. Suzuki, S. Nagai, T. Yamashita, N. Toyoda, and K. Matsushima
Identification of genes specifically expressed in human activated and mature dendritic cells through serial analysis of gene expression
Blood, September 15, 2000; 96(6): 2206 - 2214.
[Abstract] [Full Text] [PDF]

W. T. Loging, A. Lal, I-M. Siu, T. L. Loney, C. J. Wikstrand, M. A. Marra, C. Prange, D. D. Bigner, R. L. Strausberg, and G. J. Riggins
Identifying Potential Tumor Markers and Antigens by Database Mining and Rapid Expression Screening
Genome Res., September 1, 2000; 10(9): 1393 - 1402.
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D. Scheurle, M. P. DeYoung, D. M. Binninger, H. Page, M. Jahanzeb, and R. Narayanan
Cancer Gene Discovery Using Digital Differential Display
Cancer Res., August 1, 2000; 60(15): 4037 - 4043.
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J. M. Mariadason, G. A. Corner, and L. H. Augenlicht
Genetic Reprogramming in Pathways of Colonic Cell Maturation Induced by Short Chain Fatty Acids: Comparison with Trichostatin A, Sulindac, and Curcumin and Implications for Chemoprevention of Colon Cancer
Cancer Res., August 1, 2000; 60(16): 4561 - 4572.
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A. E. Lash, C. M. Tolstoshev, L. Wagner, G. D. Schuler, R. L. Strausberg, G. J. Riggins, and S. F. Altschul
SAGEmap: A Public Gene Expression Resource
Genome Res., July 1, 2000; 10(7): 1051 - 1060.
[Abstract] [Full Text]

K. J. Martin and A. B. Pardee
Identifying expressed genes
PNAS, April 11, 2000; 97(8): 3789 - 3791.
[Full Text] [PDF]