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Authors describe application of a cDNA microarray-based comparative genomic hybridization (CGH) method in the analysis of DNA copy-number variation in breast cancer cell lines and tumors. Using a cDNA panel representing over 30,000 radiation-hybrid (RH)-mapped human genes, this novel assay was able to identify gene amplifications and deletions genome-wide and with high resolution, and compare alterations in DNA copy number and gene expression. Identification of gene amplifications and deletions will be extremely important for basic understanding and diagnosis of cancer.
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A DNA microarray containing 97% of the open reading frames predicted from the recently published complete sequence of the M. tuberculosis genome was used to monitor changes in M. tuberculosis gene expression in response to the antituberculous drug isoniazid. This study has identified several genes that encode proteins physiologically relevant to the drug's mode of action. Insights gained from this approach may help define new drug targets and suggest new antituberculosis therapies to combat the growing problem of drug resistant strains.
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In order to identify and analyze the expression of genes during Drosophila development, high-density DNA microarrays containing several thousand Drosophila melanogaster genes were constructed. Besides identifying differentially expressed genes known to be active during metamorphosis, this genome-based approach has uncovered many genes of unknown function that may be involved in the control and execution of metamorphosis.
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White K.P., Rifkin S.A., Hurban P., Hogness D.S. Microarray analysis of Drosophila development during metamorphosis. Science. 286:1999;2179-2184. In order to identify and analyze the expression of genes during Drosophila development, high-density DNA microarrays containing several thousand Drosophila melanogaster genes were constructed. Besides identifying differentially expressed genes known to be active during metamorphosis, this genome-based approach has uncovered many genes of unknown function that may be involved in the control and execution of metamorphosis.
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The temporal program of gene expression during a physiological response of human fibroblasts to serum, was explored with a cDNA microarray representing about 8600 different human genes. Gene clustering on the basis of their temporal expression pattern has revealed transcriptional program related to the physiology of wound repair, suggesting that fibroblasts play a larger role in this complex multicellular response than previously anticipated.
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Iyer V.R., Eisen M.B., Ross D.T., Schuler G., Moore T., Lee J.C.F., Trent J.M., Staudt L.M., Hudson J. Jr., Boguski M.S.et al. The transcriptional program in the response of human fibroblasts to serum. Science. 283:1999;83-87. The temporal program of gene expression during a physiological response of human fibroblasts to serum, was explored with a cDNA microarray representing about 8600 different human genes. Gene clustering on the basis of their temporal expression pattern has revealed transcriptional program related to the physiology of wound repair, suggesting that fibroblasts play a larger role in this complex multicellular response than previously anticipated.
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Science
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Iyer, V.R.1
Eisen, M.B.2
Ross, D.T.3
Schuler, G.4
Moore, T.5
Lee, J.C.F.6
Trent, J.M.7
Staudt, L.M.8
Hudson J., Jr.9
Boguski, M.S.10
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38
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0033539169
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Microarray analysis of replicative senescence
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Shelton D.N., Chang E., Whittier P.S., Choi D., Funk W.D. Microarray analysis of replicative senescence. Curr Biol. 9:1999;939-945.
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Curr Biol
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Shelton, D.N.1
Chang, E.2
Whittier, P.S.3
Choi, D.4
Funk, W.D.5
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39
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0033610079
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Gene expression profile of aging and its retardation by caloric restriction
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Gene expression during the aging process was analyzed in skeletal muscle of mice with high-density oligonucleotide arrays representing 6347 genes. This study has revealed that aging resulted in a differential gene expression pattern indicative of a marked stress response and lower expression of metabolic and biosynthetic genes. Transcriptional patterns of calorie-restricted animals suggest that caloric restriction retards the aging process by causing a metabolic shift toward increased protein turnover and decreased macromolecular damage.
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Lee C.K., Klopp R.G., Weindruch R., Prolla T.A. Gene expression profile of aging and its retardation by caloric restriction. Science. 285:1999;1390-1393. Gene expression during the aging process was analyzed in skeletal muscle of mice with high-density oligonucleotide arrays representing 6347 genes. This study has revealed that aging resulted in a differential gene expression pattern indicative of a marked stress response and lower expression of metabolic and biosynthetic genes. Transcriptional patterns of calorie-restricted animals suggest that caloric restriction retards the aging process by causing a metabolic shift toward increased protein turnover and decreased macromolecular damage.
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(1999)
Science
, vol.285
, pp. 1390-1393
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Lee, C.K.1
Klopp, R.G.2
Weindruch, R.3
Prolla, T.A.4
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40
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0034603061
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Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles
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Roberts C.J., Nelson B., Marton M.J., Stoughton R., Meyer M.R., Bennett H.A., He Y.D., Dai H., Walker W.L., Hughes T.R.et al. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science. 287:2000;873-880.
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Science
, vol.287
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Roberts, C.J.1
Nelson, B.2
Marton, M.J.3
Stoughton, R.4
Meyer, M.R.5
Bennett, H.A.6
He, Y.D.7
Dai, H.8
Walker, W.L.9
Hughes, T.R.10
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41
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0033607212
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Activation changes the spectrum but not the diversity of genes expressed by T cells
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Teague T.K., Hildeman D., Kedl R.M., Mitchell T., Rees W., Schaefer B.C., Bender J., Kappler J., Marrack P. Activation changes the spectrum but not the diversity of genes expressed by T cells. Proc Natl Acad Sci USA. 96:1999;12691-12696.
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Proc Natl Acad Sci USA
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Teague, T.K.1
Hildeman, D.2
Kedl, R.M.3
Mitchell, T.4
Rees, W.5
Schaefer, B.C.6
Bender, J.7
Kappler, J.8
Marrack, P.9
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42
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0033991207
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Differential gene expression between human neurons and neuronal progenitor cells in culture: An analysis of arrayed cDNA clones in NTera2 human embryonal carcinoma cell line as a model system
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Satoh J., Kuroda Y. Differential gene expression between human neurons and neuronal progenitor cells in culture: an analysis of arrayed cDNA clones in NTera2 human embryonal carcinoma cell line as a model system. J Neurosci Methods. 94:2000;155-164.
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J Neurosci Methods
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Satoh, J.1
Kuroda, Y.2
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43
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0033000676
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Differences in brain gene expression between sleep and waking as revealed by mRNA differential display and cDNA microarray technology
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Cirelli C., Tononi G. Differences in brain gene expression between sleep and waking as revealed by mRNA differential display and cDNA microarray technology. J Sleep Res. 8:1999;44-52.
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J Sleep Res
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Cirelli, C.1
Tononi, G.2
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44
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0033539498
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CDNA microarrays detect activation of a myogenic transcription program by the PAX3-FKHR fusion oncogene
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Khan J., Bittner M.L., Saal L.H., Teichmann U., Azorsa D.O., Gooden G.C., Pavan W.J., Trent J.M., Meltzer P.S. cDNA microarrays detect activation of a myogenic transcription program by the PAX3-FKHR fusion oncogene. Proc Natl Acad Sci USA. 96:1999;13264-13269.
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(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 13264-13269
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Khan, J.1
Bittner, M.L.2
Saal, L.H.3
Teichmann, U.4
Azorsa, D.O.5
Gooden, G.C.6
Pavan, W.J.7
Trent, J.M.8
Meltzer, P.S.9
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45
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0034606682
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Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays
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To obtain a more comprehensive view of the global effects of HIV infection of CD4-positive T-cells at the mRNA level, expression pattern of 1500 cDNAs at two and three days postinfection (p.i.) with HIV-1 was analyzed by cDNA microarray. Genes involved in T-cell signaling, subcellular trafficking, and transcriptional regulation, as well as several uncharacterized genes, were among those found to be differentially expressed at three days p.i. This study provides a framework for future studies of how HIV-1 infection alters expression in affected cells.
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Geiss G.K., Bumgarner R.E., An M.C., Agy M.B., van 't Wout A.B., Hammersmark E., Carter V.S., Upchurch D., Mullins J.I., Katze M.G. Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays. Virology. 266:2000;8-16. To obtain a more comprehensive view of the global effects of HIV infection of CD4-positive T-cells at the mRNA level, expression pattern of 1500 cDNAs at two and three days postinfection (p.i.) with HIV-1 was analyzed by cDNA microarray. Genes involved in T-cell signaling, subcellular trafficking, and transcriptional regulation, as well as several uncharacterized genes, were among those found to be differentially expressed at three days p.i. This study provides a framework for future studies of how HIV-1 infection alters expression in affected cells.
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(2000)
Virology
, vol.266
, pp. 8-16
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Geiss, G.K.1
Bumgarner, R.E.2
An, M.C.3
Agy, M.B.4
Van't Wout, A.B.5
Hammersmark, E.6
Carter, V.S.7
Upchurch, D.8
Mullins, J.I.9
Katze, M.G.10
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46
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0032882174
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Analysis of gene expression in mutiple sclerosis lesions using cDNA microarrays
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The expression pattern of over 5000 genes was comparatively analyzed in normal white matter with that found in acute lesions from the brain of a single multiple sclerosis (MS) patient. Sixty-two differentially expressed genes were identified, some of which may be associated with the MS disease process.
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Whitney L.W., Becker K.G., Tresser N.J., Caballero-Ramos C.I., Munson P.J., Prabhu V.V., Trent J.M., McFarland H.F., Biddison W.E. Analysis of gene expression in mutiple sclerosis lesions using cDNA microarrays. Ann Neurol. 46:1999;425-428. The expression pattern of over 5000 genes was comparatively analyzed in normal white matter with that found in acute lesions from the brain of a single multiple sclerosis (MS) patient. Sixty-two differentially expressed genes were identified, some of which may be associated with the MS disease process.
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(1999)
Ann Neurol
, vol.46
, pp. 425-428
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Whitney, L.W.1
Becker, K.G.2
Tresser, N.J.3
Caballero-Ramos, C.I.4
Munson, P.J.5
Prabhu, V.V.6
Trent, J.M.7
McFarland, H.F.8
Biddison, W.E.9
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47
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13044304179
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Distinctive gene expression patterns in human mammary epithelial cells and breast cancers
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Perou C.M., Jeffrey S.S., van de Rijn M., Rees C.A., Eisen M.B., Ross D.T., Pergamenschikov A., Williams C.F., Zhu S.X., Lee J.C.et al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci USA. 96:1999;9212-9217.
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(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 9212-9217
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Perou, C.M.1
Jeffrey, S.S.2
Van De Rijn, M.3
Rees, C.A.4
Eisen, M.B.5
Ross, D.T.6
Pergamenschikov, A.7
Williams, C.F.8
Zhu, S.X.9
Lee, J.C.10
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48
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0033571118
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In vivo gene expression profile analysis of human breast cancer progression
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This report describes the combined use of laser capture microdissection and high-throughput cDNA microarrays to monitor in vivo gene expression levels in purified normal, invasive, and metastatic breast cell populations from a single patient. This powerful new approach provides a unique opportunity to elucidate gene expression profiles of cells from various stages of tumor progression as it occurs in situ.
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Sgroi D.C., Teng S., Robinson G., LeVangie R., Hudson J.R. Jr., Elkahloun A.G. In vivo gene expression profile analysis of human breast cancer progression. Cancer Res. 59:1999;5656-5661. This report describes the combined use of laser capture microdissection and high-throughput cDNA microarrays to monitor in vivo gene expression levels in purified normal, invasive, and metastatic breast cell populations from a single patient. This powerful new approach provides a unique opportunity to elucidate gene expression profiles of cells from various stages of tumor progression as it occurs in situ.
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(1999)
Cancer Res
, vol.59
, pp. 5656-5661
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Sgroi, D.C.1
Teng, S.2
Robinson, G.3
LeVangie, R.4
Hudson J.R., Jr.5
Elkahloun, A.G.6
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49
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0033580456
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Monitoring gene expression profile changes in ovarian carcinomas using cDNA microarray
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Wang K., Gan L., Jeffery E., Gayle M., Gown A.M., Skelly M., Nelson P.S., Ng W.V., Schummer M., Hood L., Mulligan J. Monitoring gene expression profile changes in ovarian carcinomas using cDNA microarray. Gene. 229:1999;101-108.
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(1999)
Gene
, vol.229
, pp. 101-108
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Wang, K.1
Gan, L.2
Jeffery, E.3
Gayle, M.4
Gown, A.M.5
Skelly, M.6
Nelson, P.S.7
Ng, W.V.8
Schummer, M.9
Hood, L.10
Mulligan, J.11
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50
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0033589283
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Hormone therapy failure in human prostate cancer: Analysis by complementary DNA and tissue microarrays
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A new strategy for the identification of differentially expressed genes in hormone-refractory human prostate cancer is described. Expression of 5184 genes in hormone-refractory and hormone-sensitive prostate cancer was analyzed by cDNA microarray. To validate cDNA microarray results on clinical specimens, a tissue microarray of benign prostatic hyperplasia, primary prostate cancer and hormone-refractory prostate cancer specimens was constructed and used for immunohistochemical detection of protein expression. The combination of cDNA and tissue microarrays should enables rapid identification of genes associated with progression of prostate cancer to the hormone-refractory state.
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Bubendorf L., Kolmer M., Kononen J., Koivisto P., Mousses S., Chen Y., Mahlamaki E., Schraml P., Moch H., Willi N.et al. Hormone therapy failure in human prostate cancer: analysis by complementary DNA and tissue microarrays. J Natl Cancer Inst. 91:1999;1758-1764. A new strategy for the identification of differentially expressed genes in hormone-refractory human prostate cancer is described. Expression of 5184 genes in hormone-refractory and hormone-sensitive prostate cancer was analyzed by cDNA microarray. To validate cDNA microarray results on clinical specimens, a tissue microarray of benign prostatic hyperplasia, primary prostate cancer and hormone-refractory prostate cancer specimens was constructed and used for immunohistochemical detection of protein expression. The combination of cDNA and tissue microarrays should enables rapid identification of genes associated with progression of prostate cancer to the hormone-refractory state.
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(1999)
J Natl Cancer Inst
, vol.91
, pp. 1758-1764
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Bubendorf, L.1
Kolmer, M.2
Kononen, J.3
Koivisto, P.4
Mousses, S.5
Chen, Y.6
Mahlamaki, E.7
Schraml, P.8
Moch, H.9
Willi, N.10
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51
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0033569406
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Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring
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A genomics approach to cancer classification based on gene expression monitoring by DNA microarrays is described and applied to human acute leukemias. A class discovery procedure automatically discovered the distinction between acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) without previous knowledge of these classes. An automatically derived class predictor was able to determine the class of new leukemia cases. The results demonstrate the feasibility of cancer classification based solely on gene expression monitoring, independent of previous biological knowledge.
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Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeek M., Mesirov J.P., Coller H., Loh M.L., Downing J.R., Caligiuri M.A.et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 286:1999;531-537. A genomics approach to cancer classification based on gene expression monitoring by DNA microarrays is described and applied to human acute leukemias. A class discovery procedure automatically discovered the distinction between acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) without previous knowledge of these classes. An automatically derived class predictor was able to determine the class of new leukemia cases. The results demonstrate the feasibility of cancer classification based solely on gene expression monitoring, independent of previous biological knowledge.
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(1999)
Science
, vol.286
, pp. 531-537
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Golub, T.R.1
Slonim, D.K.2
Tamayo, P.3
Huard, C.4
Gaasenbeek, M.5
Mesirov, J.P.6
Coller, H.7
Loh, M.L.8
Downing, J.R.9
Caligiuri, M.A.10
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52
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0034598746
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Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
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This study describes a systematic characterization of gene expression in diffuse large B-cell lymphoma (DLBCL). Using cDNA microarrays authors have identified two molecularly distinct forms of DLBCL, one with gene expression pattern characteristic for germinal center B cells and the other for activated peripheral blood B cells. Interestingly, expression pattern coincided well with the outcome of two forms of DLBCL, where patients with germinal center B-like DLBCL had a significantly better overall survival than those with activated B-like DLBCL.
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Alizadeh A.A., Eisen M.B., Davis R.E.et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 403:2000;503-511. This study describes a systematic characterization of gene expression in diffuse large B-cell lymphoma (DLBCL). Using cDNA microarrays authors have identified two molecularly distinct forms of DLBCL, one with gene expression pattern characteristic for germinal center B cells and the other for activated peripheral blood B cells. Interestingly, expression pattern coincided well with the outcome of two forms of DLBCL, where patients with germinal center B-like DLBCL had a significantly better overall survival than those with activated B-like DLBCL.
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(2000)
Nature
, vol.403
, pp. 503-511
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Alizadeh, A.A.1
Eisen, M.B.2
Davis, R.E.3
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53
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84984934048
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DNA microarrays in drug discovery and development
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Debouck C., Goodfellow P.N. DNA microarrays in drug discovery and development. Nat Genet. 21:1999;48-50.
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(1999)
Nat Genet
, vol.21
, pp. 48-50
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Debouck, C.1
Goodfellow, P.N.2
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54
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0032901303
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Microarrays and toxicology: The advent of toxicogenomics
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Nuwaysir E.F., Bittner M., Trent J., Barrett J.C., Afshari C.A. Microarrays and toxicology: the advent of toxicogenomics. Mol Carcinog. 24:1999;153-159.
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(1999)
Mol Carcinog
, vol.24
, pp. 153-159
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Nuwaysir, E.F.1
Bittner, M.2
Trent, J.3
Barrett, J.C.4
Afshari, C.A.5
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55
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0033214657
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Application of complementary DNA microarray technology to carcinogen identification, toxicology, and drug safety evaluation
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Afshari C.A., Nuwaysir E.F., Barrett J.C. Application of complementary DNA microarray technology to carcinogen identification, toxicology, and drug safety evaluation. Cancer Res. 59:1999;4759-4760.
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(1999)
Cancer Res
, vol.59
, pp. 4759-4760
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Afshari, C.A.1
Nuwaysir, E.F.2
Barrett, J.C.3
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56
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0033602367
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DNA microarray technology: The anticipated impact on the study of human disease
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Khan J., Bittner M.L., Chen Y., Meltzer P.S., Trent J.M. DNA microarray technology: the anticipated impact on the study of human disease. Biochim Biophys Acta. 1423:1999;M17-M28.
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(1999)
Biochim Biophys Acta
, vol.1423
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Khan, J.1
Bittner, M.L.2
Chen, Y.3
Meltzer, P.S.4
Trent, J.M.5
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