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Volumn 54, Issue 3, 2005, Pages 627-644

A Bayesian mixture model for differential gene expression

Author keywords

Density estimation; Dirichlet process; Gene expression; Microarrays; Mixture models; Nonparametric Bayes method

Indexed keywords


EID: 18444401138     PISSN: 00359254     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1467-9876.2005.05593.x     Document Type: Article
Times cited : (124)

References (38)
  • 1
    • 0033536012 scopus 로고    scopus 로고
    • Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
    • Alon, U., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S., Mack, D. and Levine, A. J. (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natn. Acad. Sci. USA, 96, 6745-6750.
    • (1999) Proc. Natn. Acad. Sci. USA , vol.96 , 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
  • 2
    • 0000708831 scopus 로고
    • Mixtures of Dirichlet processes with applications to Bayesian non-parametric problems
    • Antoniak, C. E. (1974) Mixtures of Dirichlet processes with applications to Bayesian non-parametric problems. Ann. Statist., 2, 1152-1174.
    • (1974) Ann. Statist. , vol.2 , pp. 1152-1174
    • Antoniak, C.E.1
  • 4
    • 0001677717 scopus 로고    scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (2002) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B, 57, 289-300.
    • (2002) J. R. Statist. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 5
    • 0002205556 scopus 로고    scopus 로고
    • Rao-Blackwellisation of sampling schemes
    • Casella, G. and Robert, C. P. (1996) Rao-Blackwellisation of sampling schemes. Biometrika, 83, 81-94.
    • (1996) Biometrika , vol.83 , pp. 81-94
    • Casella, G.1    Robert, C.P.2
  • 6
    • 18444377191 scopus 로고    scopus 로고
    • A class of new mixture models for differential gene expression in dna microarray data
    • Department of Statistics, University of Connecticut, Storrs
    • Chen, M. and Ibrahim, J. (2004) A class of new mixture models for differential gene expression in dna microarray data. Technical Report. Department of Statistics, University of Connecticut, Storrs.
    • (2004) Technical Report
    • Chen, M.1    Ibrahim, J.2
  • 7
    • 0031246430 scopus 로고    scopus 로고
    • Ratio-based decisions and the quantitative analysis of cDNA microarray images
    • Chen, Y., Dougherty, E. R. and Bittner, M. L. (1997) Ratio-based decisions and the quantitative analysis of cDNA microarray images. J. Biomed. Opt., 2, 364-374.
    • (1997) J. Biomed. Opt. , vol.2 , pp. 364-374
    • Chen, Y.1    Dougherty, E.R.2    Bittner, M.L.3
  • 11
    • 84950937290 scopus 로고
    • Bayesian density estimation and inference using mixtures
    • Escobar, M. D. and West, M. (1995) Bayesian density estimation and inference using mixtures. J. Am. Statist. Ass., 90, 577-588.
    • (1995) J. Am. Statist. Ass. , vol.90 , pp. 577-588
    • Escobar, M.D.1    West, M.2
  • 12
    • 0001120413 scopus 로고
    • A Bayesian analysis of some nonparametric problems
    • Ferguson, T. S. (1973) A Bayesian analysis of some nonparametric problems. Ann. Statist., 1, 209-230.
    • (1973) Ann. Statist. , vol.1 , pp. 209-230
    • Ferguson, T.S.1
  • 13
    • 0036017464 scopus 로고    scopus 로고
    • A computational approach for full nonparametric Bayesian inference under Dirichlet process mixture models
    • Gelfand, A. E. and Kottas, A. (2002) A computational approach for full nonparametric Bayesian inference under Dirichlet process mixture models. J. Comput. Graph. Statist., 11, 289-305.
    • (2002) J. Comput. Graph. Statist. , vol.11 , pp. 289-305
    • Gelfand, A.E.1    Kottas, A.2
  • 14
    • 0036020944 scopus 로고    scopus 로고
    • Operating characteristics and extensions of the false discovery rate procedure
    • Genovese, C. and Wasserman, L. (2002) Operating characteristics and extensions of the false discovery rate procedure. J. R. Statist. Soc. B, 64, 499-517.
    • (2002) J. R. Statist. Soc. B , vol.64 , pp. 499-517
    • Genovese, C.1    Wasserman, L.2
  • 15
    • 10844295316 scopus 로고    scopus 로고
    • Bayesian and frequentist multiple testing
    • (eds J. M. Bernardo, J. O. Berger, M. Bayarri, A. P. Dawid, D. Heckerman and A. F. M. Smith). Oxford: Oxford University Press
    • Genovese, C. and Wasserman, L. (2003) Bayesian and frequentist multiple testing. In Bayesian Statistics 7 (eds J. M. Bernardo, J. O. Berger, M. Bayarri, A. P. Dawid, D. Heckerman and A. F. M. Smith). Oxford: Oxford University Press.
    • (2003) Bayesian Statistics 7
    • Genovese, C.1    Wasserman, L.2
  • 16
    • 84972808999 scopus 로고
    • Estimating normal means with a conjugate style Dirichlet process prior
    • MacEachern, S. (1994) Estimating normal means with a conjugate style Dirichlet process prior. Communs Statist. Simuln Computn, 23, 727-741.
    • (1994) Communs Statist. Simuln Computn , vol.23 , pp. 727-741
    • MacEachern, S.1
  • 17
    • 0038524824 scopus 로고    scopus 로고
    • Efficient MCMC schemes for robust model extensions using encompassing Dirichlet process mixture models
    • (eds F. Ruggeri and D. Rios-Insua), New York: Springer
    • MacEachern, S. N. and Müller, P. (2000) Efficient MCMC schemes for robust model extensions using encompassing Dirichlet process mixture models. In Robust Bayesian Analysis (eds F. Ruggeri and D. Rios-Insua), pp. 295-316, New York: Springer.
    • (2000) Robust Bayesian Analysis , pp. 295-316
    • MacEachern, S.N.1    Müller, P.2
  • 18
    • 0036203115 scopus 로고    scopus 로고
    • A mixture model-based approach to the clustering of microarray expression data
    • McLachlan, G. J., Bean, R. W. and Peel, D. (2002) A mixture model-based approach to the clustering of microarray expression data. Bioinformatics, 18, 413-422.
    • (2002) Bioinformatics , vol.18 , pp. 413-422
    • McLachlan, G.J.1    Bean, R.W.2    Peel, D.3
  • 19
    • 0035378234 scopus 로고    scopus 로고
    • Microarrays: Lost in a storm of data?
    • Miles, M. (2001) Microarrays: lost in a storm of data? Nat. Rev. Neursci., 2, 441-443.
    • (2001) Nat. Rev. Neursci. , vol.2 , pp. 441-443
    • Miles, M.1
  • 20
    • 10844254626 scopus 로고    scopus 로고
    • Optimal sample size for multiple testing: The case of gene expression microarrays
    • to be published
    • Müller, P., Parmigiani, G., Robert, C. and Rouseau, J. (2004) Optimal sample size for multiple testing: the case of gene expression microarrays. J. Am. Statist. Ass., to be published.
    • (2004) J. Am. Statist. Ass.
    • Müller, P.1    Parmigiani, G.2    Robert, C.3    Rouseau, J.4
  • 21
    • 18444393420 scopus 로고    scopus 로고
    • A nonparametric Bayesian model for inference in related studies
    • in the press
    • Müller, P., Rosner, G., De Iorio, M. and MacEachern, S. (2005) A nonparametric Bayesian model for inference in related studies. Appl. Statist., 54, in the press.
    • (2005) Appl. Statist. , vol.54
    • Müller, P.1    Rosner, G.2    De Iorio, M.3    MacEachern, S.4
  • 22
    • 0034923013 scopus 로고    scopus 로고
    • On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data
    • Newton, M. A., Kendziorsky, C. M., Richmond, C. S., Blattner, F. R. and Tsui, K. W. (2001) On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J. Comput. Biol., 8, 37-52.
    • (2001) J. Comput. Biol. , vol.8 , pp. 37-52
    • Newton, M.A.1    Kendziorsky, C.M.2    Richmond, C.S.3    Blattner, F.R.4    Tsui, K.W.5
  • 23
    • 4444235995 scopus 로고    scopus 로고
    • Detecting differential gene expression with a semiparametric hierarchical mixture model
    • Newton, M., Noueriry, A., Sarkar, D. and Ahlquist, P. (2004) Detecting differential gene expression with a semiparametric hierarchical mixture model. Biostatistics, 5, 155-176.
    • (2004) Biostatistics , vol.5 , pp. 155-176
    • Newton, M.1    Noueriry, A.2    Sarkar, D.3    Ahlquist, P.4
  • 24
    • 0036372266 scopus 로고    scopus 로고
    • Model-based cluster analysis of microarray gene expression data
    • research009.1-research009.9
    • Pan, W., Lin, J. and Le, C. T. (2002) Model-based cluster analysis of microarray gene expression data. Genome Biol., 3, research009.1-research009.9.
    • (2002) Genome Biol. , vol.3
    • Pan, W.1    Lin, J.2    Le, C.T.3
  • 25
    • 0036433548 scopus 로고    scopus 로고
    • A statistical framework for expression-based molecular classification in cancer
    • Parmigiani, G., Garrett, E. S., Anbazhagan, R. and Gabrielson, E. (2002) A statistical framework for expression-based molecular classification in cancer. J. R. Statist. Soc. B, 64, 717-736.
    • (2002) J. R. Statist. Soc. B , vol.64 , pp. 717-736
    • Parmigiani, G.1    Garrett, E.S.2    Anbazhagan, R.3    Gabrielson, E.4
  • 26
    • 0038156106 scopus 로고    scopus 로고
    • Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values
    • Pounds, S. and Morris, S. (2003) Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values. Bioinformatics, 19, 1236-1242.
    • (2003) Bioinformatics , vol.19 , pp. 1236-1242
    • Pounds, S.1    Morris, S.2
  • 27
    • 0037433040 scopus 로고    scopus 로고
    • Identifying differentially expressed genes using false discovery rate controlling procedures
    • Reiner, A., Yekutieli, D. and Benjamini, Y. (2003) Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics, 19, 368-375.
    • (2003) Bioinformatics , vol.19 , pp. 368-375
    • Reiner, A.1    Yekutieli, D.2    Benjamini, Y.3
  • 28
    • 0035684378 scopus 로고    scopus 로고
    • A model for measurement error for gene expression arrays
    • Rocke, D. M. and Durbin, B. (2001) A model for measurement error for gene expression arrays. J. Comput. Biol., 8, 557-569.
    • (2001) J. Comput. Biol. , vol.8 , pp. 557-569
    • Rocke, D.M.1    Durbin, B.2
  • 29
    • 14644410246 scopus 로고    scopus 로고
    • An exploration of aspects of bayesian multiple testing
    • Institute of Statistics and Decision Sciences, Duke University, Durham
    • Scott, J. and Berger, J. (2003) An exploration of aspects of bayesian multiple testing. Technical Report. Institute of Statistics and Decision Sciences, Duke University, Durham.
    • (2003) Technical Report
    • Scott, J.1    Berger, J.2
  • 30
    • 0000720609 scopus 로고
    • A constructive definition of dirichlet priors
    • Sethurman, J. (1994) A constructive definition of dirichlet priors. Statist. Sin., 4, 639-650.
    • (1994) Statist. Sin. , vol.4 , pp. 639-650
    • Sethurman, J.1
  • 31
    • 0038048164 scopus 로고    scopus 로고
    • Statistical issues in cDNA microarray data analysis
    • (eds M. J. Brownstein and A. B. Khodursky). Totowa: Humana
    • Smyth, G. K., Yang, Y. H. and Speed, T. (2002) Statistical issues in cDNA microarray data analysis. In Functional Genomics: Methods and Protocols (eds M. J. Brownstein and A. B. Khodursky). Totowa: Humana.
    • (2002) Functional Genomics: Methods and Protocols
    • Smyth, G.K.1    Yang, Y.H.2    Speed, T.3
  • 32
    • 0036020892 scopus 로고    scopus 로고
    • A direct approach to false discovery rates
    • Storey, J. D. (2002) A direct approach to false discovery rates. J. R. Statist. Soc. B, 64, 479-498.
    • (2002) J. R. Statist. Soc. B , vol.64 , pp. 479-498
    • Storey, J.D.1
  • 33
    • 0041423883 scopus 로고    scopus 로고
    • Sam thresholding and false discovery rates for detecting differential gene expression in DNA microarrays
    • New York: Springer
    • Storey, J. S. and Tibshirani, R. (2003) Sam thresholding and false discovery rates for detecting differential gene expression in DNA microarrays. In The Analysis of Gene Expression Data: Methods and Software. New York: Springer.
    • (2003) The Analysis of Gene Expression Data: Methods and Software
    • Storey, J.S.1    Tibshirani, R.2
  • 34
    • 0000576595 scopus 로고
    • Markov chains for exploring posterior distributions
    • Tierney, L. (1994) Markov chains for exploring posterior distributions. Ann. Statist., 22, 1701-1762.
    • (1994) Ann. Statist. , vol.22 , pp. 1701-1762
    • Tierney, L.1
  • 35
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher, V. G., Tibshirani, R. and Chu, G. (2002) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natn. Acad. Sci. USA, 98, 5116-5121.
    • (2002) Proc. Natn. Acad. Sci. USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 36
    • 0001541832 scopus 로고    scopus 로고
    • Bayesian nonparametric inference for random distributions and related functions
    • Walker, S. G., Damien, P., Laud, P. W. and Smith, A. F. M. (1999) Bayesian nonparametric inference for random distributions and related functions (with discussion). J. R. Statist. Soc. B, 61, 485-527.
    • (1999) J. R. Statist. Soc. B , vol.61 , pp. 485-527
    • Walker, S.G.1    Damien, P.2    Laud, P.W.3    Smith, A.F.M.4
  • 37
    • 0034807713 scopus 로고    scopus 로고
    • Analyzing gene expression data from DNA microarrays to identify candidate genes
    • Wu, T. D. (2001) Analyzing gene expression data from DNA microarrays to identify candidate genes. J. Pathol., 195, 53-65.
    • (2001) J. Pathol. , vol.195 , pp. 53-65
    • Wu, T.D.1
  • 38
    • 0034869983 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data
    • Yang, Y. H., Dudoit, S., Luu, P. and Speed, T. P. (2001) Normalization for cDNA microarray data. Proc. SPIE, 4266, 141-152.
    • (2001) Proc. SPIE , vol.4266 , pp. 141-152
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3    Speed, T.P.4


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