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Volumn 16, Issue 11, 2004, Pages 1370-1386

Cluster analysis for gene expression data: A survey

Author keywords

Clustering; Gene expression data; Microarray technology

Indexed keywords

CLUSTER ANALYSIS; CLUSTERING; GENE EXPRESSION DATA; MICROARRAY TECHNOLOGY;

EID: 13844276694     PISSN: 10414347     EISSN: None     Source Type: Journal    
DOI: 10.1109/TKDE.2004.68     Document Type: Review
Times cited : (1021)

References (77)
  • 2
    • 0034598746 scopus 로고    scopus 로고
    • Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
    • Feb.
    • A.A. Alizadeh et al., "Distinct Types of Diffuse Large B-Cell Lymphoma Identified by Gene Expression Profiling," Nature, vol. 403, pp. 503-511, Feb. 2000.
    • (2000) Nature , vol.403 , pp. 503-511
    • Alizadeh, A.A.1
  • 3
    • 0033536012 scopus 로고    scopus 로고
    • Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide array
    • June
    • U. Alon, N. Barkai, D.A. Notterman, K. Gish, S. Ybarra, D. Mack, and A.J. Levine, "Broad Patterns of Gene Expression Revealed by Clustering Analysis of Tumor and Normal Colon Tissues Probed by Oligonucleotide Array," Proc. Nat'l Academy of Science, vol. 96, no. 12, pp. 6745-6750, June 1999.
    • (1999) Proc. Nat'l Academy of Science , vol.96 , Issue.12 , pp. 6745-6750
    • Alon, U.1    Barkai, N.2    Notterman, D.A.3    Gish, K.4    Ybarra, S.5    Mack, D.6    Levine, A.J.7
  • 4
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • Aug.
    • O. Alter, P.O. Brown, and D. Bostein, "Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling," Proc. Nat'l Academy of Science, vol. 97, no. 18, pp. 10101-10106, Aug. 2000.
    • (2000) Proc. Nat'l Academy of Science , vol.97 , Issue.18 , pp. 10101-10106
    • Alter, O.1    Brown, P.O.2    Bostein, D.3
  • 5
    • 0347172110 scopus 로고    scopus 로고
    • OPTICS: Ordering points to identify the clustering structure
    • M. Ankerst, M.M. Breunig, H.-P. Kriegel, and J. Sander, "OPTICS: Ordering Points to Identify the Clustering Structure," Sigmod, pp. 49-60, 1999.
    • (1999) Sigmod , pp. 49-60
    • Ankerst, M.1    Breunig, M.M.2    Kriegel, H.-P.3    Sander, J.4
  • 7
    • 0032728081 scopus 로고    scopus 로고
    • Clustering gene expression patterns
    • A. Ben-Dor, R. Shamir, and Z. Yakhini, "Clustering Gene Expression Patterns," J. Computational Biology, vol. 6, nos. 3/4, pp. 281-297, 1999.
    • (1999) J. Computational Biology , vol.6 , Issue.3-4 , pp. 281-297
    • Ben-Dor, A.1    Shamir, R.2    Yakhini, Z.3
  • 8
    • 0000521616 scopus 로고    scopus 로고
    • Super-paramagnetic clustering of data
    • M. Blat, S. Wiseman, and E. Domany, "Super-Paramagnetic Clustering of Data," Physical Review Letters, vol. 76, pp. 3251-3255, 1996.
    • (1996) Physical Review Letters , vol.76 , pp. 3251-3255
    • Blat, M.1    Wiseman, S.2    Domany, E.3
  • 13
    • 0032561246 scopus 로고    scopus 로고
    • The transcriptional program of sporulation in budding yeast
    • S. Chu et al., "The Transcriptional Program of Sporulation in Budding Yeast," Science, vol. 282, no. 5389, pp. 699-705, 1998.
    • (1998) Science , vol.282 , Issue.5389 , pp. 699-705
    • Chu, S.1
  • 15
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale
    • J.L. DeRisi, V.R. Iyer, and P.O. Brown, "Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale," Science, pp. 680-686, 1997.
    • (1997) Science , pp. 680-686
    • DeRisi, J.L.1    Iyer, V.R.2    Brown, P.O.3
  • 16
    • 0001885544 scopus 로고    scopus 로고
    • Mining the gene expression matrix: Inferring gene relationships from large scale gene expression data
    • P. D'haeseleer, X. Wen, S. Fuhrman, and R. Somogyi, "Mining the Gene Expression Matrix: Inferring Gene Relationships From Large Scale Gene Expression Data," Information Processing in Cells and Tissues, pp. 203-212, 1998.
    • (1998) Information Processing in Cells and Tissues , pp. 203-212
    • D'Haeseleer, P.1    Wen, X.2    Fuhrman, S.3    Somogyi, R.4
  • 17
    • 0036377379 scopus 로고    scopus 로고
    • Analysis of gene expression profiles: Class discovery and leaf ordering
    • Apr.
    • C. Ding, "Analysis of Gene Expression Profiles: Class Discovery and Leaf Ordering," Proc. Int'l Conf. Computational Molecular Biology (RECOMB), pp. 27-136, Apr. 2002.
    • (2002) Proc. Int'l Conf. Computational Molecular Biology (RECOMB) , pp. 27-136
    • Ding, C.1
  • 20
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • Dec.
    • M.B. Eisen, P.T. Spellman, P.O. Brown, and D. Botstein, "Cluster Analysis and Display of Genome-Wide Expression Patterns," Proc. Nat'l Academy of Science, vol. 95, no. 25, pp. 14863-14868, Dec. 1998.
    • (1998) Proc. Nat'l Academy of Science , vol.95 , Issue.25 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3    Botstein, D.4
  • 21
    • 0032269108 scopus 로고    scopus 로고
    • How many clusters? which clustering method? Answers via model-based cluster analysis
    • C. Fraley and A.E. Raftery, "How Many Clusters? Which Clustering Method? Answers Via Model-Based Cluster Analysis," The Computer J., vol. 41, no. 8, pp. 578-588, 1998.
    • (1998) The Computer J. , vol.41 , Issue.8 , pp. 578-588
    • Fraley, C.1    Raftery, A.E.2
  • 22
    • 0034710876 scopus 로고    scopus 로고
    • Coupled two-way clustering analysis of gene microarray data
    • Oct.
    • G. Getz, E. Levine, and E. Domany, "Coupled Two-Way Clustering Analysis of Gene Microarray Data," Proc. Nat'l Academy of Science, vol. 97, no. 22, pp. 12079-12084, Oct. 2000.
    • (2000) Proc. Nat'l Academy of Science , vol.97 , Issue.22 , pp. 12079-12084
    • Getz, G.1    Levine, E.2    Domany, E.3
  • 23
    • 0036188158 scopus 로고    scopus 로고
    • Mixture modelling of gene expression data from microarray experiments
    • D. Ghosh and A.M. Chinnaiyan, "Mixture Modelling of Gene Expression Data from Microarray Experiments," Bioinformatics, vol. 18, pp. 275-286, 2002.
    • (2002) Bioinformatics , vol.18 , pp. 275-286
    • Ghosh, D.1    Chinnaiyan, A.M.2
  • 26
    • 0034515528 scopus 로고    scopus 로고
    • A clustering algorithm based on graph connectivity
    • E. Hartuv and R. Shamir, "A Clustering Algorithm Based on Graph Connectivity," Information Processing Letters, vol. 76, nos. 4-6, pp. 175-181, 2000.
    • (2000) Information Processing Letters , vol.76 , Issue.4-6 , pp. 175-181
    • Hartuv, E.1    Shamir, R.2
  • 27
    • 0035226961 scopus 로고    scopus 로고
    • Supervised harvesting of expression trees
    • Jan.
    • T. Hastie, R. Tibshirani, D. Boststein, and P. Brown, "Supervised Harvesting of Expression Trees," Genome Biology, vol. 2, no. 1, pp. 0003.1-0003.12, Jan. 2001.
    • (2001) Genome Biology , vol.2 , Issue.1
    • Hastie, T.1    Tibshirani, R.2    Boststein, D.3    Brown, P.4
  • 29
    • 0035108235 scopus 로고    scopus 로고
    • A hierarchical unsupervised growing neural network for clustering gene expression patterns
    • J. Herrero, A. Valencia, and J. Dopazo, "A Hierarchical Unsupervised Growing Neural Network for Clustering Gene Expression Patterns," Bioinformatics, vol. 17, pp. 126-136, 2001.
    • (2001) Bioinformatics , vol.17 , pp. 126-136
    • Herrero, J.1    Valencia, A.2    Dopazo, J.3
  • 30
    • 0032729435 scopus 로고    scopus 로고
    • Exploring expression data: Identification and analysis of coexpressed genes
    • L.J. Heyer, S. Kruglyak, and S. Yooseph, "Exploring Expression Data: Identification and Analysis of Coexpressed Genes," Genome Research, 1999.
    • (1999) Genome Research
    • Heyer, L.J.1    Kruglyak, S.2    Yooseph, S.3
  • 31
    • 0032729435 scopus 로고    scopus 로고
    • Exploring expression data: Identification and analysis of coexpressed genes
    • L.J. Heyer, S. Kruglyak, and S. Yooseph, "Exploring Expression Data: Identification and Analysis of Coexpressed Genes," Genome Research, vol. 9, no. 11, pp. 1106-1115, 1999.
    • (1999) Genome Research , vol.9 , Issue.11 , pp. 1106-1115
    • Heyer, L.J.1    Kruglyak, S.2    Yooseph, S.3
  • 32
    • 0035749210 scopus 로고    scopus 로고
    • Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA contros
    • A. Hill, E. Brown, M. Whitley, G. Tucker-Kellogg, C. Hunter, and D. Slonim, "Evaluation of Normalization Procedures for Oligonucleotide Array Data Based on Spiked cRNA Contros," Genome Biology, vol. 2, no. 12, pp. research0055.-1-0055.13, 2001.
    • (2001) Genome Biology , vol.2 , Issue.12
    • Hill, A.1    Brown, E.2    Whitley, M.3    Tucker-Kellogg, G.4    Hunter, C.5    Slonim, D.6
  • 34
    • 84893405732 scopus 로고    scopus 로고
    • Data clustering: A review
    • Sept.
    • A.K. Jain, M.N. Murty, and P.J. Flynn, "Data Clustering: A Review," ACM Computing Surveys, vol. 31, no. 3, pp. 254-323, Sept. 1999.
    • (1999) ACM Computing Surveys , vol.31 , Issue.3 , pp. 254-323
    • Jain, A.K.1    Murty, M.N.2    Flynn, P.J.3
  • 35
    • 0035156258 scopus 로고    scopus 로고
    • Assessing clusters and motifs from gene expression data
    • L.M. Jakt, L. Cao, K.S.E. Cheah, and D.K. Smith, "Assessing Clusters and Motifs from Gene Expression Data," Genome Research, vol. 11, pp. 1112-123, 2001.
    • (2001) Genome Research , vol.11 , pp. 1112-1123
    • Jakt, L.M.1    Cao, L.2    Cheah, K.S.E.3    Smith, D.K.4
  • 40
    • 0036012349 scopus 로고    scopus 로고
    • Plaid models for gene expression data
    • L. Lazzeroni and A. Owen, "Plaid Models for Gene Expression Data," Statistica Sinica, vol. 12, no. 1, pp. 61-86, 2002.
    • (2002) Statistica Sinica , vol.12 , Issue.1 , pp. 61-86
    • Lazzeroni, L.1    Owen, A.2
  • 41
    • 0035514007 scopus 로고    scopus 로고
    • Resampling methods for unsupervised estimation of cluster validity
    • E. Levine and E. Domany, "Resampling Methods for Unsupervised Estimation of Cluster Validity," Neural Computation, vol. 13, pp. 2573-2593, 2001.
    • (2001) Neural Computation , vol.13 , pp. 2573-2593
    • Levine, E.1    Domany, E.2
  • 42
    • 0036139278 scopus 로고    scopus 로고
    • Gene selection for sample classification based on gene expression data: Study of sensitivity to choice of parameters of the ga/knn method
    • L. Li, W. Leping, C.R. Weinberg, T.A. Darden, and L.G. Pedersen, "Gene Selection for Sample Classification Based on Gene Expression Data: Study of Sensitivity to Choice of Parameters of the ga/knn Method," Bioinformatics, vol. 17, pp. 1131-1142, 2001.
    • (2001) Bioinformatics , vol.17 , pp. 1131-1142
    • Li, L.1    Leping, W.2    Weinberg, C.R.3    Darden, T.A.4    Pedersen, L.G.5
  • 44
    • 10544256600 scopus 로고    scopus 로고
    • Expression monitoring by hybridization to high-density oligonucleotide arrays
    • D. Lockhart et al., "Expression Monitoring by Hybridization to High-Density Oligonucleotide Arrays," Nature Biotechnology, vol. 14, pp. 1675-1680, 1996.
    • (1996) Nature Biotechnology , vol.14 , pp. 1675-1680
    • Lockhart, D.1
  • 45
    • 0036203115 scopus 로고    scopus 로고
    • A mixture model-based approach to the clustering of microarray expression data
    • G.J. McLachlan, R.W. Bean, and D. Peel, "A Mixture Model-Based Approach to the Clustering of Microarray Expression Data," Bioinformatics, vol. 18, 413-422, 2002.
    • (2002) Bioinformatics , vol.18 , pp. 413-422
    • McLachlan, G.J.1    Bean, R.W.2    Peel, D.3
  • 46
  • 47
    • 0347079826 scopus 로고    scopus 로고
    • Analysis of molecular profile data using generative and discriminative methods
    • E.J. Moler, M.L. Chow, and I.S. Mian, "Analysis of Molecular Profile Data Using Generative and Discriminative Methods." Physiological Genomics, vol. 4, no. 2, pp. 109-126, 2000.
    • (2000) Physiological Genomics , vol.4 , Issue.2 , pp. 109-126
    • Moler, E.J.1    Chow, M.L.2    Mian, I.S.3
  • 48
    • 0032984045 scopus 로고    scopus 로고
    • Flow cytometric analysis of in vitro proinflammatory cytokine secretion in peripheral blood from multiple sclerosis patients
    • L.T. Nguyen et al., "Flow Cytometric Analysis of in Vitro Proinflammatory Cytokine Secretion in Peripheral Blood from Multiple Sclerosis Patients," J. Clinical Immunology, vol. 19, no. 3, pp. 179-185, 1999.
    • (1999) J. Clinical Immunology , vol.19 , Issue.3 , pp. 179-185
    • Nguyen, L.T.1
  • 49
    • 0035222126 scopus 로고    scopus 로고
    • A nonparametric scoring algorithm for identifying informative genes from microarray data
    • P.J. Park, M. Pagano, and M. Bonetti, "A Nonparametric Scoring Algorithm for Identifying Informative Genes from Microarray Data," Proc. Pacific Symp. Biocomputing, pp. 52-63, 2001.
    • (2001) Proc. Pacific Symp. Biocomputing , pp. 52-63
    • Park, P.J.1    Pagano, M.2    Bonetti, M.3
  • 52
    • 0032202775 scopus 로고    scopus 로고
    • Deterministic annealing for clustering, compression, classification, regression, and related optimization problems
    • K. Rose, "Deterministic Annealing for Clustering, Compression, Classification, Regression, and Related Optimization Problems," Proc. IEEE, vol. 96, pp. 2210-2239, 1998.
    • (1998) Proc. IEEE , vol.96 , pp. 2210-2239
    • Rose, K.1
  • 54
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a compolementatry DNA microarray
    • M.D. Schena, R. Shalon, R. Davis, and P. Brown, "Quantitative Monitoring of Gene Expression Patterns with a Compolementatry DNA Microarray," Science, vol. 270, pp. 467-470, 1995.
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.D.1    Shalon, R.2    Davis, R.3    Brown, P.4
  • 57
    • 0034062083 scopus 로고    scopus 로고
    • Analysis of large-scale gene expression data
    • G. Sherlock, "Analysis of Large-Scale Gene Expression Data," Current Opinion in Immunology, vol. 12, no. 2, pp. 201-205, 2000.
    • (2000) Current Opinion in Immunology , vol.12 , Issue.2 , pp. 201-205
    • Sherlock, G.1
  • 58
    • 0035116995 scopus 로고    scopus 로고
    • Meeting report: Making sense of microarrays
    • J.N. Siedow, "Meeting Report: Making Sense of Microarrays," Genome Biology, vol. 2, no. 2, pp. reports 4003.1-4003.2, 2001.
    • (2001) Genome Biology , vol.2 , Issue.2
    • Siedow, J.N.1
  • 60
    • 0001940940 scopus 로고
    • Clustering and classification: Background and current directions
    • J. Van Ryzin, ed., Academic Press
    • R.R. Sokal, "Clustering and Classification: Background and Current Directions," Classifincation and Clustering, J. Van Ryzin, ed., Academic Press, 1977.
    • (1977) Classifincation and Clustering
    • Sokal, R.R.1
  • 61
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization
    • P.T. Spellman et al., "Comprehensive Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces Cerevisiae by Microarray Hybridization," Molecular Biology of the Cell, vol. 9, no. 12, pp. 3273-3297, 1998.
    • (1998) Molecular Biology of the Cell , vol.9 , Issue.12 , pp. 3273-3297
    • Spellman, P.T.1
  • 62
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
    • Mar.
    • P. Tamayo, D. Solni, J. Mesirov, Q. Zhu, S. Kitareewan, E. Dmitrovsky, E.S. Lander, and T.R. Golub, "Interpreting Patterns of Gene Expression with Self-Organizing Maps: Methods and Application to Hematopoietic Differentiation," Proc. Nat'l Academy of Science, vol. 96, no. 6, pp. 2907-2912, Mar. 1999.
    • (1999) Proc. Nat'l Academy of Science , vol.96 , Issue.6 , pp. 2907-2912
    • Tamayo, P.1    Solni, D.2    Mesirov, J.3    Zhu, Q.4    Kitareewan, S.5    Dmitrovsky, E.6    Lander, E.S.7    Golub, T.R.8
  • 67
    • 0036728568 scopus 로고    scopus 로고
    • Primer on medical genomics part III: Microarray experiments and data analysis
    • A. Tefferi, E. Bolander, M. Ansell, D. Wieben, and C. Spelsberg, "Primer on Medical Genomics Part III: Microarray Experiments and Data Analysis," Mayo Clinic Proc., vol. 77, pp. 927-940, 2002.
    • (2002) Mayo Clinic Proc. , vol.77 , pp. 927-940
    • Tefferi, A.1    Bolander, E.2    Ansell, M.3    Wieben, D.4    Spelsberg, C.5
  • 68
    • 0034911875 scopus 로고    scopus 로고
    • An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles
    • J.G. Thomas, J.M. Olson, S.J. Tapscott, and L.P. Zhao, "An Efficient and Robust Statistical Modeling Approach to Discover Differentially Expressed Genes Using Genomic Expression Profiles," Genome Research, vol. 11, no. 7, pp. 1227-1236, 2001.
    • (2001) Genome Research , vol.11 , Issue.7 , pp. 1227-1236
    • Thomas, J.G.1    Olson, J.M.2    Tapscott, S.J.3    Zhao, L.P.4
  • 70
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Apr.
    • V.G. Tusher, R. Tibshirani, and G. Chu, "Significance Analysis of Microarrays Applied to the Ionizing Radiation Response," Proc. Nat'l Academy of Science, vol. 98, no. 9, pp. 5116-5121, Apr. 2001.
    • (2001) Proc. Nat'l Academy of Science , vol.98 , Issue.9 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 73
    • 0000959484 scopus 로고    scopus 로고
    • Cliff: Clustering of high-dimensional microarray data via iterative feature filtering using normalized cuts
    • E.P. Xing and R.M. Karp, "Cliff: Clustering of High-Dimensional Microarray Data via Iterative Feature Filtering Using Normalized Cuts," Bioinformatics, vol. 17, no. 1, pp. 306-315, 2001.
    • (2001) Bioinformatics , vol.17 , Issue.1 , pp. 306-315
    • Xing, E.P.1    Karp, R.M.2
  • 75
    • 0037533972 scopus 로고    scopus 로고
    • An empirical study on principal component analysis for clustering gene expression data
    • Dept. of Computer Science & Eng., Univ. of Washington
    • K.Y. Yeung and W.L. Ruzzo, "An Empirical Study on Principal Component Analysis for Clustering Gene Expression Data," Technical Report UW-CSE-2000-11-03, Dept. of Computer Science & Eng., Univ. of Washington, 2000.
    • (2000) Technical Report , vol.UW-CSE-2000-11-03
    • Yeung, K.Y.1    Ruzzo, W.L.2
  • 76
    • 0034782618 scopus 로고    scopus 로고
    • Model-based clustering and data transformations for gene expression data
    • K.Y. Yeung, C. Fraley, A. Murua, A.E. Raftery, and W.L. Ruzz, "Model-Based Clustering and Data Transformations for Gene Expression Data,"'Bioinformatics, vol. 17, pp. 977-987, 2001.
    • (2001) Bioinformatics , vol.17 , pp. 977-987
    • Yeung, K.Y.1    Fraley, C.2    Murua, A.3    Raftery, A.E.4    Ruzz, W.L.5
  • 77
    • 0035024021 scopus 로고    scopus 로고
    • Validating clustering for gene expression data
    • K.Y. Yeung, D.R. Haynor, and W.L. Ruzzo, "Validating Clustering for Gene Expression Data," Bioinformatics, vol. 17, no. 4, pp. 309-318, 2001.
    • (2001) Bioinformatics , vol.17 , Issue.4 , pp. 309-318
    • Yeung, K.Y.1    Haynor, D.R.2    Ruzzo, W.L.3


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