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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.]
| ABSTRACT |
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| Introduction |
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| Materials and Methods |
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SAGE.
Total RNA for use in the SAGE protocol was prepared from tissue or cell lines by ultracentrifugation over a cesium chloride gradient followed by mRNA selection by oligo(dT) cellulose (Life Technologies, Gaithersburg, MD). The SAGE libraries were constructed as described previously (3
, 7)
. For the brain libraries, 24 colonies were screened from each library before large-scale sequencing to ensure that they had an insert containing SAGE ditags. Approximately 2500 bacterial colonies were randomly picked by a robot and arrayed in 384-well plates. Plasmids from each colony were purified and sequenced as described previously (8)
. Transcript tags were extracted from the sequence files, using the SAGE software, v3.03. Tags matching linker sequence (approximately 4%) and duplicate ditags were excluded before analysis or posting on the web site. To estimate the total number of expressed genes in each library, the unique tags were matched to a list of presumed possible real tags.6
This list compromises only those tags that are unlikely to occur by random sequencing errors, in part, due to the number of times they were observed in a pool of 3.5 million transcripts. Statistical comparisons of transcript numbers and P values presented here were derived from the Monte-Carlo analysis in the SAGE software (5)
. SAGE tags from colon libraries were a combination of newly generated tags for this project or from a previous study (5)
.
Northern Blotting and RT-PCR.
For northern analysis, total RNA was isolated by ultracentrifugation over a cesium chloride gradient from five normal brain samples, seven glioblastoma primary tumors, three cell lines, and six xenografts. Radioactive labeled PCR probes were made from the following genes (with GenBank accession number in parentheses):
-glucosidase (X87237);
-actin and compared using autoradiography.
To confirm expression changes by PCR, total RNA was converted to random-primed cDNA using reverse-transcriptase for a panel of three normal brain samples, six glioblastoma primary tumors, two cell lines, and two xenografts. PCR of each cDNA was performed for 20, 25, 28, and 32 cycles using primers specific for
-actin, lipocortin (GenBank accession X05908), three ESTs (GenBank accessions AI302970, AI022985, and AA903288), and dynamin (GenBank accession L07807). The PCR reactions were normalized to the
-actin levels, and the products were compared on gel electrophoresis by band intensity to confirm large changes in gene expression between tumor and normal.
SAGEmap Informatics.
Tag-to-gene mapping was accomplished by first orienting GenBank sequences using polyadenylation signal and tail and placing the sequences into five "confidence" classes. In each of these confidence classes, tags were extracted from the ten-base tag directly 3'-adjacent to the 3'-most NlaIII site, and then linked to a UniGene cluster identifier, based on the sequences UniGene cluster assignment. This full mapping was used to provide the tag-to-gene and gene-to-tag information on the web site. In addition, a reliable tag-to-gene mapping was designed to reduce the effects of sequencing errors in EST GenBank entries. To correct for these errors, tag-gene pairings were first ordered by the frequency that a tag was observed in a particular cluster. Assuming the errors occur randomly and a sequencing error rate of 1% per base, 10 bases have roughly a 10% chance [1-(0.99)10] of having one or more errors. Therefore, the lowest 10% of the rank-ordered tag-gene pairings were eliminated. It was this mapping that is used to make tag-gene assignments for SAGE tag frequency on the web site. The above approach was written into an automatic algorithm, which is used to update SAGEmap weekly.
To avoid the random simulations required to assess statistical significance by the SAGE software (5)
, which would be impractical for an interactive web site, SAGEmap uses a previously described Bayesian approach (9)
. We have extended this method so that it can deal with unequal aggregate numbers of tags A and B from the two libraries being compared. For an mRNA species with concentrations y and z in these libraries, we study the quantity x = y ÷ (y + z), which we assume has a prior probability density f(x) over the interval zero to one. This function captures knowledge about the distribution of relative mRNA concentrations for the complete set of mRNA species. It is reasonable to assume that f(x) will peak at, and be symmetric about, 0.5 (5
, 10)
, and, for simplicity, f(x) may be taken proportional to xc(1 - x)c. Setting c = 1 has been proposed (9)
, but various data (5
, 10) suggest a greater concentration of x near 0.5, implying c = 3 is a more appropriate value. If a and b copies of a tag corresponding to a specific mRNA are sequenced from the two libraries, the posterior probability density for x (i.e., the density given these data) is proportional to g(x), given by the following equation (derivation omitted).
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L, where L = F ÷ (F + 1). The desired probability is simply the proportion of g(x), viewed as a density, that falls greater than L. The posterior probability that this is the case is given by the following equation.
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| Results and Discussion |
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Proper tag-to-gene mapping was obvious when the tag identified an accurate full-length sequence, such as most of the named GenBank entries. However, sequencing errors in ESTs can create ambiguity in the mapping process. To enhance tag-to-gene mapping for ESTs, an algorithm based on UniGene7 was constructed to ascertain mapping reliability. UniGene has sequence similarity clusters built from overlapping sequences and may have different tag sequences within the same cluster. However, SAGEmap takes into account the number of times a particular tag sequence is observed within each cluster, the orientation of the sequence, and the presence of a polyadenylation signal and tail. Thus, the likelihood that a particular tag is real and is not generated by sequencing errors is assessed and used for proper mapping.
We also constructed a tool for on-line statistical comparisons of tag populations for SAGEmap (Fig. 3A)
. This function allows comparisons between any possible combination of libraries and provides a confidence level for each differentially expressed tag. Desired fold differences can be specified to select the desired tags and libraries for comparison to suit the particular needs of an investigator. A virtual northern function is available that calculates the fractional representation of a particular gene in all of the posted libraries (Fig. 3B)
. In addition, tag frequencies and mapping information are downloadable for local analysis.
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SAGEmap is the first completely public database for quantitative gene expression comparisons and provides a central repository for SAGE data. Most major tumor types and normal tissues are planned for representation on this database as well as comparisons designed to provide insight into the major genetic pathways involved in malignant transformation (7 , 16, 17, 18) . Another practical advantage of this data is that they provide candidate tumor-specific genes for immune-based cancer therapy (19 , 20) . SAGEmap now makes some large-scale expression data and comparisons quickly accessible to any researcher with Internet access. These data demonstrate one aspect of the utility of a gene expression database that provides a prototype for future reporting and dissemination of quantitative gene expression data. It is hoped that the virtual experiments possible using this database will accelerate certain aspects of cancer research.
| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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1 Funding for this work was provided by Cancer Genome Anatomy Project (contract S98-146A). ![]()
2 These authors contributed equally to this work. ![]()
3 To whom requests for reprints should be addressed, at Duke University Medical Center, Box 3156, Durham, NC 27710. Phone: (919) 684-5343; Fax: (919) 681-2796; E-mail: greg.riggins{at}duke.edu ![]()
4 The abbreviations used are: CGAP, Cancer Genome Anatomy Project; SAGE, Serial Analysis of Gene Expression; EST, expressed sequence tag; GBM, glioblastoma multiforme; RT-PCR, reverse-transcriptase PCR; VEGF, vascular endothelial growth factor. ![]()
5 See http://www.ncbi.nlm.nih.gov/ncicgap. ![]()
6 V. E. Velculescu, S. L. Madden, L. Zhang, A. E. Lash, J. Yu, C. Rago, A. Lal, C. J. Wang, G. A. Beaudry, K. M. Ciriello, B. P. Cook, M. R. Dufault, A. T. Ferguson, Y. Gao, T. C. He, H. Hermeking, S. K. Hiraldo, P. M. Hwang, M. A. Lopez, H. F. Luderer, B. Mathews, J. M. Petroziello, K. Polyak, L. Zawel, W. Zhang, X. Zhang, W. Zhou, F. G. Haluska, J. Jen, S. Sukumar, G. M. Landes, G. J. Riggins, B. Vogelstein, and K. W. Kinzler. Analysis of human transcriptones, submitted for publication. ![]()
7 See http://www.ncbi.nlm.nih.gov/UniGene. ![]()
Received 7/20/99. Accepted 9/21/99.
| REFERENCES |
|---|
|
|
|---|
is a p53-regulated inhibitor of G2-M progression. Mol. Cell, 1: 3-11, 1997.[Medline]
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||||
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||||
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||||
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||||
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||||
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N. N. Khodarev, J. Yu, E. Labay, T. Darga, C. K. Brown, H. J. Mauceri, R. Yassari, N. Gupta, and R. R. Weichselbaum Tumour-endothelium interactions in co-culture: coordinated changes of gene expression profiles and phenotypic properties of endothelial cells J. Cell Sci., March 15, 2003; 116(6): 1013 - 1022. [Abstract] [Full Text] [PDF] |
||||
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||||
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O. Kabbarah, K. Pinto, D. G. Mutch, and P. J. Goodfellow Expression Profiling of Mouse Endometrial Cancers Microdissected from Ethanol-Fixed, Paraffin-Embedded Tissues Am. J. Pathol., March 1, 2003; 162(3): 755 - 762. [Abstract] [Full Text] [PDF] |
||||
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||||
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J. M. Ruijter, A. H. C. Van Kampen, and F. Baas Statistical evaluation of SAGE libraries: consequences for experimental design Physiol Genomics, October 29, 2002; 11(2): 37 - 44. [Abstract] [Full Text] [PDF] |
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T. Weinschenk, C. Gouttefangeas, M. Schirle, F. Obermayr, S. Walter, O. Schoor, R. Kurek, W. Loeser, K.-H. Bichler, D. Wernet, et al. Integrated Functional Genomics Approach for the Design of Patient-individual Antitumor Vaccines Cancer Res., October 15, 2002; 62(20): 5818 - 5827. [Abstract] [Full Text] [PDF] |
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J. Chen, M. Sun, S. Lee, G. Zhou, J. D. Rowley, and S. M. Wang Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags PNAS, September 17, 2002; 99(19): 12257 - 12262. [Abstract] [Full Text] [PDF] |
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L. Gillan, D. Matei, D. A. Fishman, C. S. Gerbin, B. Y. Karlan, and D. D. Chang Periostin Secreted by Epithelial Ovarian Carcinoma Is a Ligand for {alpha}V{beta}3 and {alpha}V{beta}5 Integrins and Promotes Cell Motility Cancer Res., September 15, 2002; 62(18): 5358 - 5364. [Abstract] [Full Text] [PDF] |
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K. Boon, E. C. Osorio, S. F. Greenhut, C. F. Schaefer, J. Shoemaker, K. Polyak, P. J. Morin, K. H. Buetow, R. L. Strausberg, S. J. de Souza, et al. An anatomy of normal and malignant gene expression PNAS, August 20, 2002; 99(17): 11287 - 11292. [Abstract] [Full Text] [PDF] |
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M. K. Tanwar, M. R. Gilbert, and E. C. Holland Gene Expression Microarray Analysis Reveals YKL-40 to Be a Potential Serum Marker for Malignant Character in Human Glioma Cancer Res., August 1, 2002; 62(15): 4364 - 4368. [Abstract] [Full Text] [PDF] |
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H. Scheel, S. Tomiuk, and K. Hofmann A common protein interaction domain links two recently identified epilepsy genes Hum. Mol. Genet., July 15, 2002; 11(15): 1757 - 1762. [Abstract] [Full Text] [PDF] |
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G. Trendelenburg, K. Prass, J. Priller, K. Kapinya, A. Polley, C. Muselmann, K. Ruscher, U. Kannbley, A. O. Schmitt, S. Castell, et al. Serial Analysis of Gene Expression Identifies Metallothionein-II as Major Neuroprotective Gene in Mouse Focal Cerebral Ischemia J. Neurosci., July 15, 2002; 22(14): 5879 - 5888. [Abstract] [Full Text] [PDF] |
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V. A. Kuznetsov, G. D. Knott, and R. F. Bonner General Statistics of Stochastic Process of Gene Expression in Eukaryotic Cells Genetics, July 1, 2002; 161(3): 1321 - 1332. [Abstract] [Full Text] [PDF] |
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C. Iseli, B. J. Stevenson, S. J. de Souza, H. B. Samaia, A. A. Camargo, K. H. Buetow, R. L. Strausberg, A. J.G. Simpson, P. Bucher, and C. V. Jongeneel Long-Range Heterogeneity at the 3' Ends of Human mRNAs Genome Res., July 1, 2002; 12(7): 1068 - 1074. [Abstract] [Full Text] [PDF] |
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C. P. Leo, S. Y. Hsu, and A. J. W. Hsueh Hormonal Genomics Endocr. Rev., June 1, 2002; 23(3): 369 - 381. [Abstract] [Full Text] [PDF] |
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A. Lal, C. A. Glazer, H. M. Martinson, H. S. Friedman, G. E. Archer, J. H. Sampson, and G. J. Riggins Mutant Epidermal Growth Factor Receptor Up-Regulates Molecular Effectors of Tumor Invasion Cancer Res., June 1, 2002; 62(12): 3335 - 3339. [Abstract] [Full Text] [PDF] |
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W. J. Kent, C. W. Sugnet, T. S. Furey, K. M. Roskin, T. H. Pringle, A. M. Zahler, and a. D. Haussler The Human Genome Browser at UCSC Genome Res., June 1, 2002; 12(6): 996 - 1006. [Abstract] [Full Text] [PDF] |
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L'H. Ouafik, S. Sauze, F. Boudouresque, O. Chinot, C. Delfino, F. Fina, V. Vuaroqueaux, C. Dussert, J. Palmari, H. Dufour, et al. Neutralization of Adrenomedullin Inhibits the Growth of Human Glioblastoma Cell Lines in Vitro and Suppresses Tumor Xenograft Growth in Vivo Am. J. Pathol., April 1, 2002; 160(4): 1279 - 1292. [Abstract] [Full Text] [PDF] |
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B. Ryu, J. Jones, N. J. Blades, G. Parmigiani, M. A. Hollingsworth, R. H. Hruban, and S. E. Kern Relationships and Differentially Expressed Genes among Pancreatic Cancers Examined by Large-scale Serial Analysis of Gene Expression Cancer Res., February 1, 2002; 62(3): 819 - 826. [Abstract] [Full Text] [PDF] |
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D. Zelenika, E. Adams, S. Humm, L. Graca, S. Thompson, S. P. Cobbold, and H. Waldmann Regulatory T Cells Overexpress a Subset of Th2 Gene Transcripts J. Immunol., February 1, 2002; 168(3): 1069 - 1079. [Abstract] [Full Text] [PDF] |
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C. Rosty, T. Ueki, P. Argani, M. Jansen, C. J. Yeo, J. L. Cameron, R. H. Hruban, and M. Goggins Overexpression of S100A4 in Pancreatic Ductal Adenocarcinomas Is Associated with Poor Differentiation and DNA Hypomethylation Am. J. Pathol., January 1, 2002; 160(1): 45 - 50. [Abstract] [Full Text] [PDF] |
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C. A. Iacobuzio-Donahue, B. Ryu, R. H. Hruban, and S. E. Kern Exploring the Host Desmoplastic Response to Pancreatic Carcinoma : Gene Expression of Stromal and Neoplastic Cells at the Site of Primary Invasion Am. J. Pathol., January 1, 2002; 160(1): 91 - 99. [Abstract] [Full Text] [PDF] |
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P. Argani, C. Iacobuzio-Donahue, B. Ryu, C. Rosty, M. Goggins, R. E. Wilentz, S. R. Murugesan, S. D. Leach, E. Jaffee, C. J. Yeo, et al. Mesothelin Is Overexpressed in the Vast Majority of Ductal Adenocarcinomas of the Pancreas: Identification of a New Pancreatic Cancer Marker by Serial Analysis of Gene Expression (SAGE) Clin. Cancer Res., December 1, 2001; 7(12): 3862 - 3868. [Abstract] [Full Text] [PDF] |
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G. Zhou, J. Chen, S. Lee, T. Clark, J. D. Rowley, and S. M. Wang The pattern of gene expression in human CD34+ stem/progenitor cells PNAS, November 20, 2001; 98(24): 13966 - 13971. [Abstract] [Full Text] [PDF] |
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B. N. Armbruster, S. S. R. Banik, C. Guo, A. C. Smith, and C. M. Counter N-Terminal Domains of the Human Telomerase Catalytic Subunit Required for Enzyme Activity in Vivo Mol. Cell. Biol., November 15, 2001; 21(22): 7775 - 7786. [Abstract] [Full Text] [PDF] |
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R. L. Strausberg and G. J. Riggins Navigating the human transcriptome PNAS, October 9, 2001; 98(21): 11837 - 11838. [Full Text] [PDF] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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. [Abstract] [Full Text] |
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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] |
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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. [Abstract] [Full Text] |
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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] |
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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] |
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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] |
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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. [Abstract] [Full Text] |
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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. [Abstract] [Full Text] |
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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. [Abstract] [Full Text] |
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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] |
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K. J. Martin and A. B. Pardee Identifying expressed genes PNAS, April 11, 2000; 97(8): 3789 - 3791. [Full Text] [PDF] |
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