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Pollack J.R., Perou C.M., Alizadeh A.A., Eisen M.B., Pergamenschikov A., Williams C.F., Jeffrey S.S., Botstein D., Brown P.O. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet. 23:1999;41-46. This study shows that cDNA microarrays can be used to determine gene copy number by comparative genomic hybridization. Using the same array for copy number and expression measurements enables rapid mapping of regions of gene amplification in cancers. It also raises the possibility for finding mutational targets associated with copy-number loss and reduced expression.
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An oligonucleotide microarray designed to cover 600 SNPs yields allelic imbalance data on about 150 markers in analyses of tumor-cell DNA. However, the method cannot distinguish between loss and gain at a locus.
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Mei R., Galipeau P.C., Prass C., Berno A., Ghandour G., Patil N., Wolff R.K., Chee M.S., Reid B.J., Lockhart D.J. Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res. 10:2000;1126-1137. An oligonucleotide microarray designed to cover 600 SNPs yields allelic imbalance data on about 150 markers in analyses of tumor-cell DNA. However, the method cannot distinguish between loss and gain at a locus.
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Multiple genes at 17q23 undergo amplification and overexpression in breast cancer
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This study shows the potential of tissue microarrays to establish rapidly the rate of gene amplification at a series of loci on 17q23 in 372 breast cancers. This is an excellent illustration of the complementary application of tissue and expression microarrays.
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Positional cloning utilizing genomic DNA microarrays: The Niemann-Pick type C gene as a model system
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Christiano A.M., Amano S., Eichenfield L.F., Burgeson R.E., Uitto J. Premature termination codon mutations in the type VII collagen gene in recessive dystrophic epidermolysis bullosa result in nonsense-mediated mRNA decay and absence of functional protein. J Invest Dermatol. 109:1997;390-394.
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Acompound heterozygous one amino-acid insertion/nonsense mutation in the plectin gene causes epidermolysis bullosa simplex with plectin deficiency
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Bauer J.W., Rouan F., Kofler B., Rezniczek G.A., Kornacker I., Muss W., Hametner R., Klausegger A., Huber A., Pohla-Gubo G., et al. Acompound heterozygous one amino-acid insertion/nonsense mutation in the plectin gene causes epidermolysis bullosa simplex with plectin deficiency. Am J Pathol. 158:2001;617-625.
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19
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Nonsense mutations in the human β-globin gene lead to unexpected levels of cytoplasmic mRNA accumulation
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Romao L., Inacio A., Santos S., Avila M., Faustino P., Pacheco P., Lavinha J. Nonsense mutations in the human β-globin gene lead to unexpected levels of cytoplasmic mRNA accumulation. Blood. 96:2000;2895-2901.
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20
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A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes
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Liu H.X., Cartegni L., Zhang M.Q., Krainer A.R. A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nat Genet. 27:2001;55-58.
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Liu, H.X.1
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21
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0032725185
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The Tangier disease gene product ABC1 controls the cellular apolipoprotein-mediated lipid removal pathway
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This study illustrates the potential of using gene-expression analysis in concert with positional information to identify a hereditary disease gene.
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Lawn R.M., Wade D.P., Garvin M.R., Wang X., Schwartz K., Porter J.G., Seilhamer J.J., Vaughan A.M., Oram J.F. The Tangier disease gene product ABC1 controls the cellular apolipoprotein-mediated lipid removal pathway. J Clin Invest. 104:1999;R25-R31. This study illustrates the potential of using gene-expression analysis in concert with positional information to identify a hereditary disease gene.
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J Clin Invest
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Lawn, R.M.1
Wade, D.P.2
Garvin, M.R.3
Wang, X.4
Schwartz, K.5
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Seilhamer, J.J.7
Vaughan, A.M.8
Oram, J.F.9
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22
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0035171510
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X chromosome-specific cDNA arrays: Identification of genes that escape from X-inactivation and other applications
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The authors construct a specialized microarray containing 2423 cDNAs from the X chromosome. They confirm its utility with tests on samples containing varying numbers of X chromosomes. Notably, they can identify three genes contained within a male-viable deletion.
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Sudbrak R., Wieczorek G., Nuber U.A., Mann W., Kirchner R., Erdogan F., Brown C.J., Wohrle D., Sterk P., Kalscheuer V.M., et al. X chromosome-specific cDNA arrays: identification of genes that escape from X-inactivation and other applications. Hum Mol Genet. 10:2001;77-83. The authors construct a specialized microarray containing 2423 cDNAs from the X chromosome. They confirm its utility with tests on samples containing varying numbers of X chromosomes. Notably, they can identify three genes contained within a male-viable deletion.
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Hum Mol Genet
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Sudbrak, R.1
Wieczorek, G.2
Nuber, U.A.3
Mann, W.4
Kirchner, R.5
Erdogan, F.6
Brown, C.J.7
Wohrle, D.8
Sterk, P.9
Kalscheuer, V.M.10
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23
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0343717914
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High density lipoprotein deficiency and foam cell accumulation in mice with targeted disruption of ATP-binding cassette transporter-1
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The authors use gene-expression analysis in a mouse knockout model of Tangier disease. This study provides an example of the progress and problems in identifying pathways downstream of disease genes. It also illustrates the advantages of studying a disease model in the mouse for which target tissues can be readily obtained.
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McNeish J., Aiello R.J., Guyot D., Turi T., Gabel C., Aldinger C., Hoppe K.L., Roach M.L., Royer L.J., de Wet J., et al. High density lipoprotein deficiency and foam cell accumulation in mice with targeted disruption of ATP-binding cassette transporter-1. Proc Natl Acad Sci USA. 97:2000;4245-4250. The authors use gene-expression analysis in a mouse knockout model of Tangier disease. This study provides an example of the progress and problems in identifying pathways downstream of disease genes. It also illustrates the advantages of studying a disease model in the mouse for which target tissues can be readily obtained.
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Proc Natl Acad Sci USA
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McNeish, J.1
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Hoppe, K.L.7
Roach, M.L.8
Royer, L.J.9
De Wet, J.10
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24
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0034655590
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Leptin-specific patterns of gene expression in white adipose tissue
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This study demonstrates that a large proportion of the genes altered in mice carrying mutated leptin genes can indeed be placed in pathways credibly related to leptin function.
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Soukas A., Cohen P., Socci N.D., Friedman J.M. Leptin-specific patterns of gene expression in white adipose tissue. Genes Dev. 14:2000;963-980. This study demonstrates that a large proportion of the genes altered in mice carrying mutated leptin genes can indeed be placed in pathways credibly related to leptin function.
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Genes Dev
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Soukas, A.1
Cohen, P.2
Socci, N.D.3
Friedman, J.M.4
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25
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0034633783
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Misregulation of gene expression in primary fibroblasts lacking poly(ADP-ribose) polymerase
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This study explores the altered patterns of gene expression in mice deficient for poly(ADP-ribose) polymerase, and links the observed changes to pathways affecting cell cycle, DNA replication, the extracellular matrix and the cytoskeleton.
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Simbulan-Rosenthal C.M., Ly D.H., Rosenthal D.S., Konopka G., Luo R., Wang Z.Q., Schultz P.G., Smulson M.E. Misregulation of gene expression in primary fibroblasts lacking poly(ADP-ribose) polymerase. Proc Natl Acad Sci USA. 97:2000;11274-11279. This study explores the altered patterns of gene expression in mice deficient for poly(ADP-ribose) polymerase, and links the observed changes to pathways affecting cell cycle, DNA replication, the extracellular matrix and the cytoskeleton.
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Proc Natl Acad Sci USA
, vol.97
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Simbulan-Rosenthal, C.M.1
Ly, D.H.2
Rosenthal, D.S.3
Konopka, G.4
Luo, R.5
Wang, Z.Q.6
Schultz, P.G.7
Smulson, M.E.8
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26
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0034526621
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Microarray expression profiling identifies genes with altered expression in HDL-deficient mice
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Callow M.J., Dudoit S., Gong E.L., Speed T.P., Rubin E.M. Microarray expression profiling identifies genes with altered expression in HDL-deficient mice. Genome Res. 10:2000;2022-2029.
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Genome Res
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Callow, M.J.1
Dudoit, S.2
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Speed, T.P.4
Rubin, E.M.5
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28
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0034050902
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Systematic variation in gene expression patterns in human cancer cell lines
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The authors show that expression profiles determined by cDNA microarrays analysis can be used to cluster a variety of cancer cell lines into distinct disease categories.
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Ross D.T., Scherf U., Eisen M.B., Perou C.M., Rees C., Spellman P., Iyer V., Jeffrey S.S., Van de Rijn M., Waltham M., et al. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet. 24:2000;227-235. The authors show that expression profiles determined by cDNA microarrays analysis can be used to cluster a variety of cancer cell lines into distinct disease categories.
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Nat Genet
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Ross, D.T.1
Scherf, U.2
Eisen, M.B.3
Perou, C.M.4
Rees, C.5
Spellman, P.6
Iyer, V.7
Jeffrey, S.S.8
Van De Rijn, M.9
Waltham, M.10
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29
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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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By using a cDNA microarray (the 'lymphochip') optimized for relevant gene content, the authors are able to subclassify diffuse large B-cell lymphoma specimens into two groups. Of importance, they can relate these groups to normal B-cell differentiation and show that the group of patients with a germinal-center-like phenotype has a better prognosis.
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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. By using a cDNA microarray (the 'lymphochip') optimized for relevant gene content, the authors are able to subclassify diffuse large B-cell lymphoma specimens into two groups. Of importance, they can relate these groups to normal B-cell differentiation and show that the group of patients with a germinal-center-like phenotype has a better prognosis.
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Nature
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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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30
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0034601455
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Molecular classification of cutaneous malignant melanoma by gene expression profiling
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In this study, the potential of microarrays for class discovery is demonstrated by the identification of an unknown subset of melanoma samples with a characteristic gene-expression profile. By comparing this profile with that of an in vitro model of melanoma metastasis, the authors can predict biological properties (such as reduced motility) associated with this subset, which they confirm experimentally.
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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. In this study, the potential of microarrays for class discovery is demonstrated by the identification of an unknown subset of melanoma samples with a characteristic gene-expression profile. By comparing this profile with that of an in vitro model of melanoma metastasis, the authors can predict biological properties (such as reduced motility) associated with this subset, which they confirm experimentally.
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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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31
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0034680102
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Molecular portraits of human breast tumours
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The authors use cDNA microarrays to establish the gene-expression profile of breast cancer specimens. The results are striking and suggest distinct histogenesis for subsets of breast cancers. Along with Bittner et al. [30••], this study shows that two samples from the same patient tend to a greater similarity than any pair within a sample set.
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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. The authors use cDNA microarrays to establish the gene-expression profile of breast cancer specimens. The results are striking and suggest distinct histogenesis for subsets of breast cancers. Along with Bittner et al. [30••], this study shows that two samples from the same patient tend to a greater similarity than any pair within a sample set.
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(2000)
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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32
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0034326788
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Dysregulated expression of androgen-responsive and nonresponsive genes in the androgen-independent prostate cancer xenograft model CWR22-R1
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Amler L.C., Agus D.B., LeDuc C., Sapinoso M.L., Fox W.D., Kern S., Lee D., Wang V., Leysens M., Higgins B., et al. Dysregulated expression of androgen-responsive and nonresponsive genes in the androgen-independent prostate cancer xenograft model CWR22-R1. Cancer Res. 60:2000;6134-6141.
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Amler, L.C.1
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Fox, W.D.5
Kern, S.6
Lee, D.7
Wang, V.8
Leysens, M.9
Higgins, B.10
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33
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0034601487
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Genomic analysis of metastasis reveals an essential role for RhoC
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This paper shows the power of parallel gene-expression analysis to identify critical pathways and genes, in this case related to metastasis. RhoC is identified as a critical regulator of tumor-cell invasion in an in vivo model, an observation confirmed by expressing RhoC constructs.
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Clark E.A., Golub T.R., Lander E.S., Hynes R.O. Genomic analysis of metastasis reveals an essential role for RhoC. Nature. 406:2000;532-535. This paper shows the power of parallel gene-expression analysis to identify critical pathways and genes, in this case related to metastasis. RhoC is identified as a critical regulator of tumor-cell invasion in an in vivo model, an observation confirmed by expressing RhoC constructs.
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Nature
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Clark, E.A.1
Golub, T.R.2
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34
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Gene-expression profiles in hereditary breast cancer
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The authors investigate hereditary breast cancers arising in patients with BRCA1 or BRCA2 mutations to determine whether they have a characteristic gene-expression profile in comparison to sporadic tumors. This proves to be the case. BRCA1 tumors cluster together particularly strongly. A sporadic case that clusters in this group has methylation of the BRCA1 promoter and low expression of BRCA1. In addition to providing clues to the pathogenesis of hereditary breast cancer, these observations raise the possibility that gene-expression profiling may be used to classify tissue samples in complex diseases to aid gene discovery.
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Hedenfalk I., Duggan D., Chen Y., Radmacher M., Bittner M., Simon R., Meltzer P., Gusterson B., Esteller M., Kallioniemi O.P., et al. Gene-expression profiles in hereditary breast cancer. N Engl J Med. 344:2001;539-548. The authors investigate hereditary breast cancers arising in patients with BRCA1 or BRCA2 mutations to determine whether they have a characteristic gene-expression profile in comparison to sporadic tumors. This proves to be the case. BRCA1 tumors cluster together particularly strongly. A sporadic case that clusters in this group has methylation of the BRCA1 promoter and low expression of BRCA1. In addition to providing clues to the pathogenesis of hereditary breast cancer, these observations raise the possibility that gene-expression profiling may be used to classify tissue samples in complex diseases to aid gene discovery.
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N Engl J Med
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Hedenfalk, I.1
Duggan, D.2
Chen, Y.3
Radmacher, M.4
Bittner, M.5
Simon, R.6
Meltzer, P.7
Gusterson, B.8
Esteller, M.9
Kallioniemi, O.P.10
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35
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0035162594
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RefSeq and LocusLink: NCBI gene-centered resources
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Pruitt K.D., Maglott D.R. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 29:2001;137-140.
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Nucleic Acids Res
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Pruitt, K.D.1
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36
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Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
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Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25:2000;25-29.
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Nat Genet
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Ashburner, M.1
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Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
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37
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0034565168
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Genes, themes and microarrays: Using information retrieval for large- scale gene analysis
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Shatkay H., Edwards S., Wilbur W.J., Boguski M. Genes, themes and microarrays: using information retrieval for large- scale gene analysis. Proc Int Conf Intell Syst Mol Biol. 8:2000;317-328.
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Proc Int Conf Intell Syst Mol Biol
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Shatkay, H.1
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38
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0033655017
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Biobibliometrics: Information retrieval and visualization from co-occurrences of gene names in Medline abstracts
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Stapley BJ, Benoit G: Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pac Symp Biocomput 2000:529-540.
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Pac Symp Biocomput
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Stapley, B.J.1
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39
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0034571639
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A set-covering approach to specific search for literature about human genes
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Jenssen TK, Vinterbo S: A set-covering approach to specific search for literature about human genes. Proc AMIA Symp 2000:384-388.
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Proc AMIA Symp
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Jenssen, T.K.1
Vinterbo, S.2
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40
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Multivariate measurement of gene expression relationships
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Seungchan K., Dougherty E.K., Chen Y., Krishnamoorthy S., Meltzer P., Trent J.M., Bittner M. Multivariate measurement of gene expression relationships. Genomics. 67:2000;201-209.
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Genomics
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Seungchan, K.1
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Chen, Y.3
Krishnamoorthy, S.4
Meltzer, P.5
Trent, J.M.6
Bittner, M.7
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41
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0033677274
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Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function
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Akutsu T., Miyano S., Kuhara S. Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. J Comput Biol. 7:2000;331-343.
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J Comput Biol
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Akutsu, T.1
Miyano, S.2
Kuhara, S.3
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43
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0034568109
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'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns
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Hastie T, Tibshirani R, Eisen MB, Alizadeh A, Levy R, Staudt L, ChanWC, Botstein D, Brown P: 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. GenomeBiology.com 2000, 1.
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GenomeBiology.com
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Hastie, T.1
Tibshirani, R.2
Eisen, M.B.3
Alizadeh, A.4
Levy, R.5
Staudt, L.6
Chan, W.C.7
Botstein, D.8
Brown, P.9
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44
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0034602774
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Knowledge-based analysis of microarray gene expression data by using support vector machines
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Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D: Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA 2000, 97:262-267.
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Proc Natl Acad Sci USA
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Brown, M.P.1
Grundy, W.N.2
Lin, D.3
Cristianini, N.4
Sugnet, C.W.5
Furey, T.S.6
Ares M., Jr.7
Haussler, D.8
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45
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0035945567
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Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
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This study is an important step towards using microarrays to map regulatory elements in yeast. The authors take advantage of the complete sequence to construct arrays that allow them to identify 200 putative new targets for the transcription factors SBF and MBF.
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Iyer V.R., Horak C.E., Scafe C.S., Botstein D., Snyder M., Brown P.O. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 409:2001;533-538. This study is an important step towards using microarrays to map regulatory elements in yeast. The authors take advantage of the complete sequence to construct arrays that allow them to identify 200 putative new targets for the transcription factors SBF and MBF.
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Nature
, vol.409
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Iyer, V.R.1
Horak, C.E.2
Scafe, C.S.3
Botstein, D.4
Snyder, M.5
Brown, P.O.6
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46
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0034704248
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Genome-wide location and function of DNA binding proteins
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As in Iyer et al. [45••], the authors use microarrays to identify yeast genes directly regulated by two transcription factors, Gal4 and Ste12. Expression arrays lend themselves to identifying patterns of co-regulation, and these two studies take the next step of linking this information to genomic sequence.
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Ren B., Robert F., Wyrick J.J., Aparicio O., Jennings E.G., Simon I., Zeitlinger J., Schreiber J., Hannett N., Kanin E., et al. Genome-wide location and function of DNA binding proteins. Science. 290:2000;2306-2309. As in Iyer et al. [45••], the authors use microarrays to identify yeast genes directly regulated by two transcription factors, Gal4 and Ste12. Expression arrays lend themselves to identifying patterns of co-regulation, and these two studies take the next step of linking this information to genomic sequence.
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(2000)
Science
, vol.290
, pp. 2306-2309
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Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
Zeitlinger, J.7
Schreiber, J.8
Hannett, N.9
Kanin, E.10
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47
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0034704768
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Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx
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Livesey F.J., Furukawa T., Steffen M.A., Church G.M., Cepko C.L. Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol. 10:2000;301-310.
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Curr Biol
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Livesey, F.J.1
Furukawa, T.2
Steffen, M.A.3
Church, G.M.4
Cepko, C.L.5
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48
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0035252636
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High resolution deletion analysis of constitutional DNA from neurofibromatosis type 2 (NF2) patients using microarray-CGH
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This study shows the outstanding quantitative data that can be obtained with array-format comparative genomic hybridization when large-insert genomic clones are arrayed. The authors are able to map constitutional deletions in the NF2 locus with high resolution and precision. The potential of this approach for disease gene discovery is evident.
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Bruder C.E., Hirvela C., Tapia-Paez I., Fransson I., Segraves R., Hamilton G., Zhang X.X., Evans D.G., Wallace A.J., Baser M.E., et al. High resolution deletion analysis of constitutional DNA from neurofibromatosis type 2 (NF2) patients using microarray-CGH. Hum Mol Genet. 10:2001;271-282. This study shows the outstanding quantitative data that can be obtained with array-format comparative genomic hybridization when large-insert genomic clones are arrayed. The authors are able to map constitutional deletions in the NF2 locus with high resolution and precision. The potential of this approach for disease gene discovery is evident.
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(2001)
Hum Mol Genet
, vol.10
, pp. 271-282
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Bruder, C.E.1
Hirvela, C.2
Tapia-Paez, I.3
Fransson, I.4
Segraves, R.5
Hamilton, G.6
Zhang, X.X.7
Evans, D.G.8
Wallace, A.J.9
Baser, M.E.10
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49
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0034616930
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Functional discovery via a compendium of expression profiles
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Although this study involves expression data from yeast, it provides a valuable model for the integration of data from 300 conditions. Using this database, the authors can place eight anonymous genes into distinct functional pathways.
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Hughes T.R., Marton M.J., Jones A.R., Roberts C.J., Stoughton R., Armour C.D., Bennett H.A., Coffey E., Dai H., He Y.D., et al. Functional discovery via a compendium of expression profiles. Cell. 102:2000;109-126. Although this study involves expression data from yeast, it provides a valuable model for the integration of data from 300 conditions. Using this database, the authors can place eight anonymous genes into distinct functional pathways.
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(2000)
Cell
, vol.102
, pp. 109-126
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Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
Armour, C.D.6
Bennett, H.A.7
Coffey, E.8
Dai, H.9
He, Y.D.10
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50
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0035865260
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Experimental annotation of the human genome using microarray technology
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Shoemaker D.D., Schadt E.E., Armour C.D., He Y.D., Garrett-Engele P., McDonagh P.D., Loerch P.M., Leonardson A., Lum P.Y., Cavet G., et al. Experimental annotation of the human genome using microarray technology. Nature. 409:2001;922-927.
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Nature
, vol.409
, pp. 922-927
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Shoemaker, D.D.1
Schadt, E.E.2
Armour, C.D.3
He, Y.D.4
Garrett-Engele, P.5
McDonagh, P.D.6
Loerch, P.M.7
Leonardson, A.8
Lum, P.Y.9
Cavet, G.10
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