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1
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0012949538
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Optimal gene expression analysis by microarrays
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A recent review of the microarray technology and analysis with commentary on clinical applications of this technology
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Miller L.D., Long P.M., Wong L., Mukherjee S., McShane L.M., Liu E.T. Optimal gene expression analysis by microarrays. Cancer Cell. 2:2002;353-361 A recent review of the microarray technology and analysis with commentary on clinical applications of this technology.
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Cancer Cell
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, pp. 353-361
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Miller, L.D.1
Long, P.M.2
Wong, L.3
Mukherjee, S.4
McShane, L.M.5
Liu, E.T.6
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2
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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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Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeck M., Mesirov J.P., Coller H., Loh M.L., Downing J.R., Caligiuri M.A., Bloomfield C.D., Lander E.S. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 286:1999;531-537.
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Science
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Golub, T.R.1
Slonim, D.K.2
Tamayo, P.3
Huard, C.4
Gaasenbeck, M.5
Mesirov, J.P.6
Coller, H.7
Loh, M.L.8
Downing, J.R.9
Caligiuri, M.A.10
Bloomfield, C.D.11
Lander, E.S.12
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3
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0035803371
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Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukaemia
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Rosenwald A., Alizadeh A.A., Widhopf G., Simon R., Davis R.E., Yu X., Yang L., Pickeral O.K., Rassenti L.Z., Powell J.et al. Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukaemia. J. Exp. Med. 194:2001;1639-1647.
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J. Exp. Med.
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Rosenwald, A.1
Alizadeh, A.A.2
Widhopf, G.3
Simon, R.4
Davis, R.E.5
Yu, X.6
Yang, L.7
Pickeral, O.K.8
Rassenti, L.Z.9
Powell, J.10
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4
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0036183437
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Gene expression profiling of lymphoid malignancies
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A comprehensive review of microarray studies in lymphoid malignancies
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Staudt L.M. Gene expression profiling of lymphoid malignancies. Annu. Rev. Medicine. 53:2002;303-318 A comprehensive review of microarray studies in lymphoid malignancies.
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(2002)
Annu. Rev. Medicine
, vol.53
, pp. 303-318
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Staudt, L.M.1
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5
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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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A classic paper; the first to identify clear array patterns in determining therapeutic response in malignant lympha
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Alizadeh A.A., Eisen M.B., Davis R.E., Ma C., Lossos I.S., Rosenwald A., Boldrick J.C., Sabet H., Tran T., Yu X.et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 403:2000;503-511 A classic paper; the first to identify clear array patterns in determining therapeutic response in malignant lymphoma.
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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
Ma, C.4
Lossos, I.S.5
Rosenwald, A.6
Boldrick, J.C.7
Sabet, H.8
Tran, T.9
Yu, X.10
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6
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18244409933
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Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning
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An excellent paper on the analysis and validation of expression markers derived from array data in diffuse large B cell lymphoma
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Shipp M.A., Ross K.N., Tamayo P., Weng A.P., Kutok J.L., Aguiar R.C., Gaasenbeek M., Angelo M., Reich M., Pinkus G.S.et al. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat. Med. 8:2002;68-74 An excellent paper on the analysis and validation of expression markers derived from array data in diffuse large B cell lymphoma.
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(2002)
Nat. Med.
, vol.8
, pp. 68-74
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Shipp, M.A.1
Ross, K.N.2
Tamayo, P.3
Weng, A.P.4
Kutok, J.L.5
Aguiar, R.C.6
Gaasenbeek, M.7
Angelo, M.8
Reich, M.9
Pinkus, G.S.10
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7
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0035845511
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Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
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A classic paper on the prognostic implications of expression patterns in Stage III breast cancers
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Sorlie T., Perou C.M., Tibshirani R., Aas T., Geisler S., Johnsen H., Hastie T., Eisen M.B., van de Rijn M., Jeffrey S.S.et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl. Acad. Sci. USA. 98:2001;10869-10874 A classic paper on the prognostic implications of expression patterns in Stage III breast cancers.
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(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 10869-10874
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Sorlie, T.1
Perou, C.M.2
Tibshirani, R.3
Aas, T.4
Geisler, S.5
Johnsen, H.6
Hastie, T.7
Eisen, M.B.8
Van de Rijn, M.9
Jeffrey, S.S.10
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8
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0035923583
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Diversity of gene expression in adenocarcinoma of the lung
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Garber M.E., Troyanskaya O.G., Schluens K., Petersen S., Thaesler Z., Pacyna-Gengelbach M., van de Rijn M., Rosen G.D., Perou C.M., Whyte R.I.et al. Diversity of gene expression in adenocarcinoma of the lung. Proc. Natl. Acad. Sci. USA. 98:2001;13784-13789.
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(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 13784-13789
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Garber, M.E.1
Troyanskaya, O.G.2
Schluens, K.3
Petersen, S.4
Thaesler, Z.5
Pacyna-Gengelbach, M.6
Van de Rijn, M.7
Rosen, G.D.8
Perou, C.M.9
Whyte, R.I.10
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9
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0035300437
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Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays
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Notterman D.A., Alon U., Sierk A.J., Levine A.J. Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays. Cancer Res. 61:2001;3124-3130.
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Cancer Res.
, vol.61
, pp. 3124-3130
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Notterman, D.A.1
Alon, U.2
Sierk, A.J.3
Levine, A.J.4
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10
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0037172983
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Transformation of follicular lymphoma to diffuse large-cell lymphoma: Alternative patterns with increased or decreased expression of c-myc and its regulated genes
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Lossos I.S., Alizadeh A.A., Diehn M., Warnke R., Thorstenson Y., Oefner P.J., Brown P.O., Botstein D., Levy R. Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes. Proc. Natl. Acad. Sci. USA. 99:2002;8886-8891.
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(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 8886-8891
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Lossos, I.S.1
Alizadeh, A.A.2
Diehn, M.3
Warnke, R.4
Thorstenson, Y.5
Oefner, P.J.6
Brown, P.O.7
Botstein, D.8
Levy, R.9
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11
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0034680102
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Molecular portraits of human breast tumours
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Perou C.M., Sorlie T., Eisen M.B., van de Rijn M., Jeffrey S.S., Rees C.A., Pollack J.R., Ross D.T., Johnsen H., Akslen L.A.et al. Molecular portraits of human breast tumours. Nature. 406:2000;747-752.
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Nature
, vol.406
, pp. 747-752
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Perou, C.M.1
Sorlie, T.2
Eisen, M.B.3
Van de Rijn, M.4
Jeffrey, S.S.5
Rees, C.A.6
Pollack, J.R.7
Ross, D.T.8
Johnsen, H.9
Akslen, L.A.10
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12
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13844311931
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Gene expression profiles derived from fine needle aspiration correlate with response to systemic chemotherapy in breast cancer
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This paper describes the gene-expression profile associated with response to doxorubicin and cyclophosphamide neo-adjuvant chemotherapy
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Sotiriou C., Powles T.J., Dowsett M., Jazaeri A.A., Feldman A.L., Assersohn L., Gadisetti C., Libutti S.K., Liu E.T. Gene expression profiles derived from fine needle aspiration correlate with response to systemic chemotherapy in breast cancer. Breast Cancer Res. 4:2002;R3 This paper describes the gene-expression profile associated with response to doxorubicin and cyclophosphamide neo-adjuvant chemotherapy.
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(2002)
Breast Cancer Res.
, vol.4
, pp. 3
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Sotiriou, C.1
Powles, T.J.2
Dowsett, M.3
Jazaeri, A.A.4
Feldman, A.L.5
Assersohn, L.6
Gadisetti, C.7
Libutti, S.K.8
Liu, E.T.9
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13
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0036645090
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Prospective molecular profiling of melanoma metastases suggests classifiers of immune responsiveness
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Wang E., Miller L.D., Ohnmacht G.A., Mocellin S., Perez-Diez A., Petersen D., Zhao Y., Simon R., Powell J.I., Asaki E.et al. Prospective molecular profiling of melanoma metastases suggests classifiers of immune responsiveness. Cancer Res. 62:2002;3581-3586.
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(2002)
Cancer Res.
, vol.62
, pp. 3581-3586
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Wang, E.1
Miller, L.D.2
Ohnmacht, G.A.3
Mocellin, S.4
Perez-Diez, A.5
Petersen, D.6
Zhao, Y.7
Simon, R.8
Powell, J.I.9
Asaki, E.10
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14
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0035985214
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Gene expression patterns in human liver cancers
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This is the most carefully performed work on liver cancers and describes the pattern of expression in multifocal cancers
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Chen X., Cheung S.T., So S., Fan S.T., Barry C., Higgins J., Lai K.M., Ji J.F., Dudoit S., Ng I.O.L.et al. Gene expression patterns in human liver cancers. Mol. Biol. Cell. 13:2002;1929-1939 This is the most carefully performed work on liver cancers and describes the pattern of expression in multifocal cancers.
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(2002)
Mol. Biol. Cell.
, vol.13
, pp. 1929-1939
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Chen, X.1
Cheung, S.T.2
So, S.3
Fan, S.T.4
Barry, C.5
Higgins, J.6
Lai, K.M.7
Ji, J.F.8
Dudoit, S.9
Ng, I.O.L.10
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15
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0037102254
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Identify metastasis-associated genes in hepatocellular carcinoma through clonality delineation for multinodular tumor
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Cheung S.T., Chen X., Guan X.Y., Wong S.Y., Tai L.S., Ng I.O.L., So S., Fan S.T. Identify metastasis-associated genes in hepatocellular carcinoma through clonality delineation for multinodular tumor. Cancer Res. 62:2002;4711-4721.
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(2002)
Cancer Res.
, vol.62
, pp. 4711-4721
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Cheung, S.T.1
Chen, X.2
Guan, X.Y.3
Wong, S.Y.4
Tai, L.S.5
Ng, I.O.L.6
So, S.7
Fan, S.T.8
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16
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0037076342
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Initiating oncogenic event determines gene-expression patterns of human breast cancer models
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An interesting paper that identifies the expression patterns of mouse tumours initiated by single onco-transgenes. It is among the first to show the importance of oncogenic pathways in determining the expression profiles of the resultant tumours
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Desai K.V., Xiao N., Wang W., Gangi L., Greene J., Powell J.I., Dickson R., Furth P., Hunter K., Kucherlapati R.et al. Initiating oncogenic event determines gene-expression patterns of human breast cancer models. Proc. Natl. Acad. Sci. USA. 99:2002;6967-6972 An interesting paper that identifies the expression patterns of mouse tumours initiated by single onco-transgenes. It is among the first to show the importance of oncogenic pathways in determining the expression profiles of the resultant tumours.
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(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 6967-6972
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Desai, K.V.1
Xiao, N.2
Wang, W.3
Gangi, L.4
Greene, J.5
Powell, J.I.6
Dickson, R.7
Furth, P.8
Hunter, K.9
Kucherlapati, R.10
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17
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0036798690
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CDNA microarray profiling of rat mammary gland carcinomas induced by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine and 7,12-dimethylbenz[a]anthracene
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Shan L., He M., Yu M., Qiu C., Lee N.H., Liu E.T., Snyderwine E.G. cDNA microarray profiling of rat mammary gland carcinomas induced by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine and 7,12-dimethylbenz[a]anthracene. Carcinogenesis. 23:2002;1561-1568.
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(2002)
Carcinogenesis
, vol.23
, pp. 1561-1568
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Shan, L.1
He, M.2
Yu, M.3
Qiu, C.4
Lee, N.H.5
Liu, E.T.6
Snyderwine, E.G.7
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18
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0036079155
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A bioinformatics-based strategy identifies c-Myc and Cdc25A as candidates for the Apmt mammary tumor latency modifiers
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An interesting use of murine genetic models to discover interacting genes in modifying tumour phenotype
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Cozma D., Lukes L., Rouse J., Qiu T.H., Liu E.T., Hunter K.W. A bioinformatics-based strategy identifies c-Myc and Cdc25A as candidates for the Apmt mammary tumor latency modifiers. Genome Res. 12:2002;969-975 An interesting use of murine genetic models to discover interacting genes in modifying tumour phenotype.
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(2002)
Genome Res.
, vol.12
, pp. 969-975
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Cozma, D.1
Lukes, L.2
Rouse, J.3
Qiu, T.H.4
Liu, E.T.5
Hunter, K.W.6
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19
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0037014795
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Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers
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This paper shows how array data generates unexpected hypotheses about the impact of susceptibility genes on a particular type of tumour
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Jazaeri A.A., Yee C.J., Sotiriou C., Brantley K.R., Boyd J., Liu E.T. Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers. J. Natl. Cancer Inst. 94:2002;990-1000 This paper shows how array data generates unexpected hypotheses about the impact of susceptibility genes on a particular type of tumour.
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(2002)
J. Natl. Cancer Inst.
, vol.94
, pp. 990-1000
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Jazaeri, A.A.1
Yee, C.J.2
Sotiriou, C.3
Brantley, K.R.4
Boyd, J.5
Liu, E.T.6
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20
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18744372123
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BRCA1 Supports XIST RNA Concentration on the Inactive X Chromosome
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A fascinating paper to be read along with that of Jazaeri et al. [21] giving a potential explanation for the array finding that genes on the X chromosome appear to be overexpressed in ovarian cancers from BRCA1 carriers
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Ganesan S., Silver D.P., Greenberg R.A., Avni D., Drapkin R., Miron A., Mok S.C., Randrianarison V., Brodie S., Salstrom J.et al. BRCA1 Supports XIST RNA Concentration on the Inactive X Chromosome. Cell. 111:2002;393-405 A fascinating paper to be read along with that of Jazaeri et al. [21] giving a potential explanation for the array finding that genes on the X chromosome appear to be overexpressed in ovarian cancers from BRCA1 carriers.
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(2002)
Cell
, vol.111
, pp. 393-405
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Ganesan, S.1
Silver, D.P.2
Greenberg, R.A.3
Avni, D.4
Drapkin, R.5
Miron, A.6
Mok, S.C.7
Randrianarison, V.8
Brodie, S.9
Salstrom, J.10
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21
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0034601455
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Molecular classification of cutaneous malignant melanoma by gene expression profiling
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Bittner M., Meltzer P., Chen Y., Jiang Y., Seftor E., Hendrix M., Radmacher M., Simon R., Yakhini Z., Ben-Dor A.et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature. 406:2000;536-540.
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(2000)
Nature
, vol.406
, pp. 536-540
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Bittner, M.1
Meltzer, P.2
Chen, Y.3
Jiang, Y.4
Seftor, E.5
Hendrix, M.6
Radmacher, M.7
Simon, R.8
Yakhini, Z.9
Ben-Dor, A.10
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22
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0036528247
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Wnt5a signaling directly affects cell motility and invasion of metastatic melanoma
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This paper describes the unique expression patterns associated with specific mutations associated with hereditary ovarian cancer
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Weeraratna A.T., Jiang Y., Hostetter G., Duray P., Bittner M., Trent J.M. Wnt5a signaling directly affects cell motility and invasion of metastatic melanoma. Cancer Cell. 1:2002;279-288 This paper describes the unique expression patterns associated with specific mutations associated with hereditary ovarian cancer.
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(2002)
Cancer Cell
, vol.1
, pp. 279-288
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Weeraratna, A.T.1
Jiang, Y.2
Hostetter, G.3
Duray, P.4
Bittner, M.5
Trent, J.M.6
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23
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0035923521
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Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses
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Bhattacharjee A., Richards W.G., Staunton J., Li C., Monti S., Vasa P., Ladd C., Beheshti J., Bueno R., Gillette M.et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc. Natl. Acad. Sci. USA. 98:2001;13790-13795.
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(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 13790-13795
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Bhattacharjee, A.1
Richards, W.G.2
Staunton, J.3
Li, C.4
Monti, S.5
Vasa, P.6
Ladd, C.7
Beheshti, J.8
Bueno, R.9
Gillette, M.10
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24
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0037126055
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Integrated classification of lung tumors and cell lines by expression profiling
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Virtanen C., Honjoh D., Kimura M., Shimane M., Miyoshi T., Nomura H., Jones M.H. Integrated classification of lung tumors and cell lines by expression profiling. Proc. Natl. Acad. Sci. USA. 99:2002;12357-12362.
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(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12357-12362
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Virtanen, C.1
Honjoh, D.2
Kimura, M.3
Shimane, M.4
Miyoshi, T.5
Nomura, H.6
Jones, M.H.7
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25
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19044391072
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Gene expression correlates of clinical prostate cancer behavior
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Singh D., Febbo P.G., Ross K., Jackson D.G., Manola J., Ladd C., Tamayo P., Renshaw A.A., D'Amico A.V., Richie J.P.et al. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell. 1:2002;203-209.
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(2002)
Cancer Cell
, vol.1
, pp. 203-209
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Singh, D.1
Febbo, P.G.2
Ross, K.3
Jackson, D.G.4
Manola, J.5
Ladd, C.6
Tamayo, P.7
Renshaw, A.A.8
D'Amico, A.V.9
Richie, J.P.10
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26
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0036682376
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Meta-analysis of microarrays: Interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer
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An excellent paper describing a meta-analysis approach to integrating results from multiple prostate cancer studies
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Rhodes D.R., Barrette T.R., Rubin M.A., Ghosh D., Chinnaiyan A.M. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res. 62:2002;4427-4433 An excellent paper describing a meta-analysis approach to integrating results from multiple prostate cancer studies.
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(2002)
Cancer Res.
, vol.62
, pp. 4427-4433
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Rhodes, D.R.1
Barrette, T.R.2
Rubin, M.A.3
Ghosh, D.4
Chinnaiyan, A.M.5
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27
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0036490145
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It's ALL in the diagnosis
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A short but excellent critique of the ALL array studies
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Staudt L.M. It's ALL in the diagnosis. Cancer Cell. 1:2002;109-110 A short but excellent critique of the ALL array studies.
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(2002)
Cancer Cell
, vol.1
, pp. 109-110
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Staudt, L.M.1
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28
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19044399684
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Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukaemia by gene expression profiling
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An excellent paper that comprehensively analyses the impact of expression profiling on the diagnosis and prognosis of patients with childhood ALL
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Yeoh E.J., Ross M.E., Shurtleff S.A., Williams W.K., Patel D., Mahfouz R., Behm F.G., Raimondi S.C., Relling M.V., Patel A.et al. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukaemia by gene expression profiling. Cancer Cell. 1:2002;133-143 An excellent paper that comprehensively analyses the impact of expression profiling on the diagnosis and prognosis of patients with childhood ALL.
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(2002)
Cancer Cell
, vol.1
, pp. 133-143
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Yeoh, E.J.1
Ross, M.E.2
Shurtleff, S.A.3
Williams, W.K.4
Patel, D.5
Mahfouz, R.6
Behm, F.G.7
Raimondi, S.C.8
Relling, M.V.9
Patel, A.10
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29
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17144474314
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Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukaemia
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Ferrando A.A., Neuberg D.S., Staunton J., Loh M.L., Huard C., Raimondi S.C., Behm F.G., Pui C.H., Downing J.R., Gilliland D.G. Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukaemia. Cancer Cell. 1:2002;75-87.
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(2002)
Cancer Cell
, vol.1
, pp. 75-87
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Ferrando, A.A.1
Neuberg, D.S.2
Staunton, J.3
Loh, M.L.4
Huard, C.5
Raimondi, S.C.6
Behm, F.G.7
Pui, C.H.8
Downing, J.R.9
Gilliland, D.G.10
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30
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0037142053
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The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma
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This is the definitive paper that follows up on the earlier observations defining prognostic subsets in DLBCL
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Rosenwald A., Wright G., Chan W.C., Connors J.M., Campo E., Fisher R.I., Gascoyne R.D., Muller-Hermelink H.K., Smeland E.B., Giltnane J.M.et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N. Engl. J. Med. 346:2002;1937-1947 This is the definitive paper that follows up on the earlier observations defining prognostic subsets in DLBCL.
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(2002)
N. Engl. J. Med.
, vol.346
, pp. 1937-1947
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Rosenwald, A.1
Wright, G.2
Chan, W.C.3
Connors, J.M.4
Campo, E.5
Fisher, R.I.6
Gascoyne, R.D.7
Muller-Hermelink, H.K.8
Smeland, E.B.9
Giltnane, J.M.10
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31
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18244409687
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Gene expression profiling predicts clinical outcome of breast cancer
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The first paper associating expression patterns with survival in untreated breast cancer patients
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van't Veer L.J., Dai H., van de Vijver M.J., He Y.D., Hart A.A., Mao M., Peterse H.L., van der Kooy K., Marton M.J., Witteveen A.T.et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature. 415:2002;530-536 The first paper associating expression patterns with survival in untreated breast cancer patients.
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(2002)
Nature
, vol.415
, pp. 530-536
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Van't Veer, L.J.1
Dai, H.2
Van de Vijver, M.J.3
He, Y.D.4
Hart, A.A.5
Mao, M.6
Peterse, H.L.7
Van der Kooy, K.8
Marton, M.J.9
Witteveen, A.T.10
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32
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18344378043
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Gene expression profiles of poor prognosis primary breast cancer correlate with survival
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Bertucci F., Nasser V., Granjeaud S., Eisinger F., Adelaide J., Tagett R., Loriod B., Giaconia A., Benziane A., Devilard E.et al. Gene expression profiles of poor prognosis primary breast cancer correlate with survival. Hum. Mol. Genet. 11:2002;863-872.
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(2002)
Hum. Mol. Genet.
, vol.11
, pp. 863-872
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Bertucci, F.1
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