메뉴 건너뛰기




Volumn 1, Issue 12, 2002, Pages 951-960

The use and analysis of microarray data

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; COMPLEMENTARY DNA; COMPLEMENTARY RNA; DNA; RNA;

EID: 0036884167     PISSN: 14741776     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrd961     Document Type: Review
Times cited : (419)

References (52)
  • 1
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena, M., Shalon, D., Davis, R. W. & Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470 (1995).
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 2
    • 10544256600 scopus 로고    scopus 로고
    • Expression monitoring by hybridization to high-density oligonucleotide arrays
    • Lockhart, D. J. et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol. 14, 1675-1680 (1996).
    • (1996) Nature Biotechnol. , vol.14 , pp. 1675-1680
    • Lockhart, D.J.1
  • 4
    • 0034807713 scopus 로고    scopus 로고
    • Analysing gene expression data from DNA microarrays to identify candidate genes
    • Wu, T. D. Analysing gene expression data from DNA microarrays to identify candidate genes. J. Pathol. 195, 53-65 (2001).
    • (2001) J. Pathol. , vol.195 , pp. 53-65
    • Wu, T.D.1
  • 5
    • 0033570768 scopus 로고    scopus 로고
    • Normalization of array hybridization experiments in differential gene expression analysis
    • Eickhoff, B., Korn, B., Schick, M., Poustka, A. & van der Bosch, J. Normalization of array hybridization experiments in differential gene expression analysis. Nucleic Acids Res. 27, 33 (1999).
    • (1999) Nucleic Acids Res. , vol.27 , pp. 33
    • Eickhoff, B.1    Korn, B.2    Schick, M.3    Poustka, A.4    van der Bosch, J.5
  • 6
    • 17744401429 scopus 로고    scopus 로고
    • Centralization: A new method for the normalization of gene expression data
    • Zien, A., Aigner, T., Zimmer, R. & Lengauer, T. Centralization: a new method for the normalization of gene expression data. Bioinformatics 17 (Suppl. 1), S323-S331 (2001).
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Zien, A.1    Aigner, T.2    Zimmer, R.3    Lengauer, T.4
  • 7
    • 17744413236 scopus 로고    scopus 로고
    • Model-based analysis of oligonucleotide arrays: Model validation, design issues and standard error application
    • research0032.1-0032.11
    • Li, C. & Hung Wong, W. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.1-0032.11 (2001).
    • (2001) Genome Biol. , vol.2
    • Li, C.1    Hung Wong, W.2
  • 8
    • 0035233680 scopus 로고    scopus 로고
    • Sources of nonlinearity in cDNA microarray expression measurements
    • research0047.1-0047.7
    • Ramdas, L. et al. Sources of nonlinearity in cDNA microarray expression measurements. Genome Biol. 2, research0047.1-0047.7 (2001).
    • (2001) Genome Biol. , vol.2
    • Ramdas, L.1
  • 9
    • 0035875553 scopus 로고    scopus 로고
    • Issues in cDNA microarray analysis: Quality filtering, channel normalization, models of variations and assessment of gene effects
    • Tseng, G. C., On, M. K., Rohlin, L., Liao, J. C. & Wong, W. H. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res. 29, 2549-2557 (2001).
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2549-2557
    • Tseng, G.C.1    On, M.K.2    Rohlin, L.3    Liao, J.C.4    Wong, W.H.5
  • 10
    • 0034704768 scopus 로고    scopus 로고
    • Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx
    • 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, 301-310 (2000).
    • (2000) Curr. Biol. , vol.10 , pp. 301-310
    • Livesey, F.J.1    Furukawa, T.2    Steffen, M.A.3    Church, G.M.4    Cepko, C.L.5
  • 11
    • 0033573938 scopus 로고    scopus 로고
    • Global response of Saccharomyces cerevisiae to an alkylating agent
    • Jelinsky S. A. & Samson, L. D. Global response of Saccharomyces cerevisiae to an alkylating agent. Proc. Natl Acad. Sci. USA 96, 1486-1491 (1999).
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 1486-1491
    • Jelinsky, S.A.1    Samson, L.D.2
  • 12
    • 0032143452 scopus 로고    scopus 로고
    • Profiling expression patterns and isolating differentially expressed genes by cDNA microarray system with colorimetry detection
    • Chen, J. J. et al. Profiling expression patterns and isolating differentially expressed genes by cDNA microarray system with colorimetry detection. Genomics 51, 313-324 (1998).
    • (1998) Genomics , vol.51 , pp. 313-324
    • Chen, J.J.1
  • 13
    • 0034283071 scopus 로고    scopus 로고
    • Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis
    • Ishii, M. et al. Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis. Genomics 68, 136-143 (2000).
    • (2000) Genomics , vol.68 , pp. 136-143
    • Ishii, M.1
  • 14
    • 0034252527 scopus 로고    scopus 로고
    • Reproducibility of alternative probe synthesis approaches for gene expression profiling with arrays
    • Vernon, S. D. et al. Reproducibility of alternative probe synthesis approaches for gene expression profiling with arrays. J. Mol. Diagn. 2, 124-127 (2000).
    • (2000) J. Mol. Diagn. , vol.2 , pp. 124-127
    • Vernon, S.D.1
  • 15
    • 0035293021 scopus 로고    scopus 로고
    • Quantitative analysis of mRNA amplification by in vitro transcription
    • Baugh, L. R., Hill, A. A., Brown, E. L. & Hunter, C. P. Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res. 29, E29 (2001).
    • (2001) Nucleic Acids Res. , vol.29
    • Baugh, L.R.1    Hill, A.A.2    Brown, E.L.3    Hunter, C.P.4
  • 16
    • 0034536614 scopus 로고    scopus 로고
    • Analyzing high-density oligonucleotide gene expression array data
    • Schadt, E. E., Li, C., Su, C. & Wong, W. H. Analyzing high-density oligonucleotide gene expression array data. J. Cell. Biochem. 80, 192-202 (2000).
    • (2000) J. Cell. Biochem. , vol.80 , pp. 192-202
    • Schadt, E.E.1    Li, C.2    Su, C.3    Wong, W.H.4
  • 17
    • 0003576795 scopus 로고    scopus 로고
    • Comparison of Methods for Image Analysis on cDNA Microarray Data
    • (Univ. California, Berkeley)
    • Yang, Y. H., Buckley, M. J., Dudoff, S. & Speed, T. P. Comparison of Methods for Image Analysis on cDNA Microarray Data (Univ. California, Berkeley, 2000).
    • (2000)
    • Yang, Y.H.1    Buckley, M.J.2    Dudoff, S.3    Speed, T.P.4
  • 18
    • 0030575911 scopus 로고    scopus 로고
    • Laser capture microdissection
    • Emmert-Buck, M. R. et al. Laser capture microdissection. Science 274, 998-1001 (1996).
    • (1996) Science , vol.274 , pp. 998-1001
    • Emmert-Buck, M.R.1
  • 19
    • 0034050902 scopus 로고    scopus 로고
    • Systematic variation in gene expression patterns in human cancer cell lines
    • Ross, D. T. et al. Systematic variation in gene expression patterns in human cancer cell lines. Nature Genet. 24, 227-235 (2000).
    • (2000) Nature Genet. , vol.24 , pp. 227-235
    • Ross, D.T.1
  • 20
    • 0034710924 scopus 로고    scopus 로고
    • Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks
    • Butte, A. J., Tamayo, P., Slonim, D., Golub, T. R. & Kohane, I. S. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc. Natl Acad. Sci. USA 97, 12182-12186 (2000).
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 12182-12186
    • Butte, A.J.1    Tamayo, P.2    Slonim, D.3    Golub, T.R.4    Kohane, I.S.5
  • 21
    • 0036211063 scopus 로고    scopus 로고
    • Analysis of matched mRNA measurements from two different microarray technologies
    • Kuo, W. P., Jenssen, T. K., Butte, A. J., Ohno-Machado, L. & Kohane, I. S. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18, 405-412 (2002).
    • (2002) Bioinformatics , vol.18 , pp. 405-412
    • Kuo, W.P.1    Jenssen, T.K.2    Butte, A.J.3    Ohno-Machado, L.4    Kohane, I.S.5
  • 22
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher, V. G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116-5121 (2001).
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 23
    • 0035228213 scopus 로고    scopus 로고
    • Determining significant fold differences in gene expression analysis
    • Butte, A. J. et al. Determining significant fold differences in gene expression analysis. Pac. Symp. Biocomput. 6-17 (2001).
    • (2001) Pac. Symp. Biocomput. , pp. 6-17
    • Butte, A.J.1
  • 24
    • 0035222126 scopus 로고    scopus 로고
    • A nonparametric scoring algorithm for identifying informative genes from microarray data
    • Park, P. J., Pagano, M. & Bonetti, M. A nonparametric scoring algorithm for identifying informative genes from microarray data. Pac. Symp. Biocomput. 52-63 (2001).
    • (2001) Pac. Symp. Biocomput. , pp. 52-63
    • Park, P.J.1    Pagano, M.2    Bonetti, M.3
  • 25
    • 0035228759 scopus 로고    scopus 로고
    • Analysis of strain and regional variation in gene expression in mouse brain
    • research0042.10-0042.15
    • Pavlidis, P. & Noble, W. S. Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol. 2, research0042.10-0042.15 (2001).
    • (2001) Genome Biol. , vol.2
    • Pavlidis, P.1    Noble, W.S.2
  • 26
    • 0033569406 scopus 로고    scopus 로고
    • Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring
    • Golub, T. R. et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531-537 (1999).
    • (1999) Science , vol.286 , pp. 531-537
    • Golub, T.R.1
  • 27
    • 0003500248 scopus 로고
    • C4.5: Programs for Machine Learning
    • (Morgan Kaufmann, San Mateo, California)
    • Quinlan, J. C4.5: Programs for Machine Learning (Morgan Kaufmann, San Mateo, California, 1992).
    • (1992)
    • Quinlan, J.1
  • 28
    • 0003444646 scopus 로고
    • Parallel Distributed Processing: Explorations in the Microstructure of Cognition
    • & The Parallel Distributed Processing Research Group (MIT Press, Cambridge, Massachusetts)
    • Rumelhart, D., McClelland, J. & The Parallel Distributed Processing Research Group. Parallel Distributed Processing: Explorations in the Microstructure of Cognition (MIT Press, Cambridge, Massachusetts, 1986).
    • (1986)
    • Rumelhart, D.1    McClelland, J.2
  • 29
    • 0033636139 scopus 로고    scopus 로고
    • Support vector machine classification and validation of cancer tissue samples using microarray expression data
    • Furey, T. S. et al. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics 16, 906-914 (2000).
    • (2000) Bioinformatics , vol.16 , pp. 906-914
    • Furey, T.S.1
  • 30
    • 0034602774 scopus 로고    scopus 로고
    • Knowledge-based analysis of microarray gene expression data by using support vector machines
    • Brown, M. P. et al. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl Acad. Sci. USA 97, 262-267 (2000).
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 262-267
    • Brown, M.P.1
  • 31
    • 0035826360 scopus 로고    scopus 로고
    • Identifying marker genes in transcription profiling data using a mixture of feature relevance experts
    • Chow, M. L., Moler, E. J. & Mian, I. S. Identifying marker genes in transcription profiling data using a mixture of feature relevance experts. Physiol. Genomics 5, 99-111 (2001).
    • (2001) Physiol. Genomics , vol.5 , pp. 99-111
    • Chow, M.L.1    Moler, E.J.2    Mian, I.S.3
  • 32
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • Alter, O., Brown, P. O. & Boi D. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl Acad. Sci. USA 97, 10101-10106 (2000).
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 10101-10106
    • Alter, O.1    Brown, P.O.2    Boi, D.3
  • 33
    • 0033657261 scopus 로고    scopus 로고
    • Principal components analysis to summarize microarray experiments: Application to sporulation time series
    • Raychaudhuri, S., Stuart, J. M. & Altman, R. B. Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac. Symp. Biocomput. 455-466 (2000).
    • (2000) Pac. Symp. Biocomput. , pp. 455-466
    • Raychaudhuri, S.1    Stuart, J.M.2    Altman, R.B.3
  • 34
    • 0033757963 scopus 로고    scopus 로고
    • Metabolite profiling for plant functional genomics
    • Fiehn, O. et al. Metabolite profiling for plant functional genomics. Nature Biotechnol. 18, 1157-1161 (2000).
    • (2000) Nature Biotechnol. , vol.18 , pp. 1157-1161
    • Fiehn, O.1
  • 35
    • 0031915896 scopus 로고    scopus 로고
    • Large-scale temporal gene expression mapping of central nervous system development
    • Wen, X. et al. Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl Acad. Sci. USA 95, 334-339 (1998).
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 334-339
    • Wen, X.1
  • 36
    • 0033518877 scopus 로고    scopus 로고
    • Statistical analysis of array expression data as applied to the problem of tamoxifen resistance
    • Hilsenbeck, S. G. et al. Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. J. Natl Cancer Inst. 91, 453-459 (1999).
    • (1999) J. Natl. Cancer Inst. , vol.91 , pp. 453-459
    • Hilsenbeck, S.G.1
  • 37
    • 0033692876 scopus 로고    scopus 로고
    • Tissue classification with gene expression profiles
    • Ben-Dor, A. et al. Tissue classification with gene expression profiles. J. Comput. Biol. 7, 559-583 (2000).
    • (2000) J. Comput. Biol. , vol.7 , pp. 559-583
    • Ben-Dor, A.1
  • 38
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
    • Tamayo, P. et al. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA 96, 2907-2912 (1999).
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 2907-2912
    • Tamayo, P.1
  • 39
    • 0042863923 scopus 로고    scopus 로고
    • Analysis of gene expression data using self-organizing maps
    • Toronen, P., Kolehmainen, M., Wong, G. & Castren, E. Analysis of gene expression data using self-organizing maps. FEES Lett. 451, 142-146 (1999).
    • (1999) FEES Lett. , vol.451 , pp. 142-146
    • Toronen, P.1    Kolehmainen, M.2    Wong, G.3    Castren, E.4
  • 41
    • 0031616241 scopus 로고    scopus 로고
    • Reveal, a general reverse engineering algorithm for inference of genetic network architectures
    • Liang, S., Fuhrman, S. & Somogyi, R. Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac. Symp. Biocomput. 18-29 (1998).
    • (1998) Pac. Symp. Biocomput. , pp. 18-29
    • Liang, S.1    Fuhrman, S.2    Somogyi, R.3
  • 42
    • 0031630211 scopus 로고    scopus 로고
    • Genomic regulation modeled as a network with basins of attraction
    • Wuensche, A. Genomic regulation modeled as a network with basins of attraction. Pac. Symp. Biocomput. 89-102 (1998).
    • (1998) Pac. Symp. Biocomput. , pp. 89-102
    • Wuensche, A.1
  • 43
    • 0031635563 scopus 로고    scopus 로고
    • Modeling the normal and neoplastic cell cycle with 'realistic Boolean genetic networks': Their application for understanding carcinogenesis and assessing therapeutic strategies
    • Szallasi, Z. & Liang, S. Modeling the normal and neoplastic cell cycle with 'realistic Boolean genetic networks': their application for understanding carcinogenesis and assessing therapeutic strategies. Pac. Symp. Biocomput. 66-76 (1998).
    • (1998) Pac. Symp. Biocomput. , pp. 66-76
    • Szallasi, Z.1    Liang, S.2
  • 44
  • 46
    • 0033655775 scopus 로고    scopus 로고
    • Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements
    • Butte, A. J. & Kahane, I. S. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac. Symp. Biocomput. 418-429 (2000).
    • (2000) Pac. Symp. Biocomput. , pp. 418-429
    • Butte, A.J.1    Kahane, I.S.2
  • 47
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
    • Spellman, P. T. et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273-3297 (1998).
    • (1998) Mol. Biol. Cell , vol.9 , pp. 3273-3297
    • Spellman, P.T.1
  • 48
    • 0037533972 scopus 로고    scopus 로고
    • An Empirical Study of Principal-Components Analysis for Clustering Gene Expression Data
    • Technical Report UW-CSE-2000-11-03. (Univ. Washington, Washington DC)
    • Yeung, K. Y. & Ruzzo, W. L. An Empirical Study of Principal-Components Analysis for Clustering Gene Expression Data Technical Report UW-CSE-2000-11-03. (Univ. Washington, Washington DC, 2000).
    • (2000)
    • Yeung, K.Y.1    Ruzzo, W.L.2
  • 49
    • 0034598746 scopus 로고    scopus 로고
    • Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
    • Alizadeh, A. A. et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503-511 (2000).
    • (2000) Nature , vol.403 , pp. 503-511
    • Alizadeh, A.A.1
  • 50
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25, 25-29 (2000).
    • (2000) Nature Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 52
    • 0035733719 scopus 로고    scopus 로고
    • Show me the data!
    • Perou, C. M. Show me the data! Nature Genet. 29, 373 (2001).
    • (2001) Nature Genet. , vol.29 , pp. 373
    • Perou, C.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.