Bayesian infinite mixture model based clustering of gene expression profiles

Bioinformatics

Volumn 18, Issue 9, 2002, Pages 1194-1206

  Medvedovic, Mario ^a   Sivaganesan, Siva ^b  

^a UNIVERSITY OF CINCINNATI MEDICAL CENTER   (United States)

^b UNIVERSITY OF CINCINNATI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ACCURACY; ARTICLE; AUTOMATION; BAYES THEOREM; CALCULATION; CELL CYCLE; CLUSTER ANALYSIS; COMPUTER SIMULATION; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION PROFILING; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; QUALITATIVE ANALYSIS; STATISTICAL MODEL; STOCHASTIC MODEL; YEAST CELL;

EID: 0036739286     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.9.1194     Document Type: Article

References (44)

1. Baggerly,K.A., Coombes,K.R., Hess,K.R., Stivers,D.N., Abruzzo,L.V. and Zhang,W. (2001) Identifying differentially expressed genes in cDNA microarray experiments. J. Comput. Biol., 8, 639-659.
2. Baldi,P. and Brunak,S. (1998) Bioinformatics: The Machine Learning Approach. The MIT Press, Cambridge, MA.
3. Baldi,P. and Long,A.D. (2001) A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics, 17, 509-519.
4. Biernacki,C. and Govaert,G. (1999) Choosing models in model-based clustering and discriminant analysis. J. Statis. Comput. Simul., 64, 49-71.
5. Cho,R.J., Campbell,M.J., Winzeler,E.A., Steinmetz,L., Conway,A., Wodicka,L., Wolfsberg,T.G., Gabrielian,A.E., Landsman,D., Lockhart,D.J. and Davis,R.W. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2, 65-73.
6. Cowell,R.G, Dawid,PA., Lauritzen,S.L. and Spiegelhalter,D.J. (1999) Probabilistic Networks and Expert Systems. Springer, New York.
7. D'haeseleer,P., Liang,S. and Somogyi,R. (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics, 16, 707-726.
8. Efron,B. and Tibshirani,R.J. (1998) An Introduction to the Bootstrap. Chapman & Hall/CRC, Boca Raton.
9. Eisen,M.B., Spellman,P.T., Brown,P.O. and Botstein,D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
10. Escobar,M.D. (1994) Estimating normal means with a Dirichlet process prior. J. Amer. Stat. Assoc., 89, 268-277.
11. Escobar,M.D. and West,M. (1995) Bayesian density estimation and inference using mixtures. J. Amer. Stat. Assoc., 90, 577-588.
12. Everitt,B.S. (1993) Cluster Analysis. Edward Arnold, London.
13. Ferguson,T.S. (1973) A Bayesian analysis of some nonparametric problems. Ann. Stat., 1, 209-230.
14. Fraley,C. and Raftery,A.E. (1999) Mclust: Software for Modelbased Cluster Analysis. Journal of Classification, 16, 297-306.
15. Gelfand,E.A. and Smith,F.M.A. (1990) Sampling-based approaches to calculating marginal densities. J. Amer. Stat. Assoc., 85, 398-409.
16. Herrero,J., Valencia,A. and Dopazo,J. (2001) A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics, 17, 126-136.
17. Holmes,I. and Bruno,W.J. (2000) Finding regulatory elements using joint likelihoods for sequence and expression profile data. Proc. Int. Conf. Intell. Syst. Mol. Biol., 8, 202-210.
18. 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., Kidd,M.J., King,A.M., Meyer,M.R., Slade,D., Lum,P.Y., Stepaniants,S.B., Shoemaker,D.D., Gachotte,D., Chakraburtty,K., Simon,J., Bard,M. and Friend,S.H. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109-126.
19. Ideker,T., Thorsson,V., Siegel,A.F. and Hood,L.E. (2000) Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data. J. Comput. Biol., 7, 805-817.
20. Jain,S. and Neal,R. (2000) A split-merge Markov chain Monte Carlo procedure for the Dirichlet process mixture model. Technical Report No. 2003, Department of Statistics, University of Toronto.
21. Keff,K.M. and Churchill,G.A. (2001) Experimental design for gene expression microarrays. Biostatistics, 2, 183-201.
22. Kerr,K.M., Martin,M. and Churchill,G.A. (2000) Analysis of variance for gene expression microarray data. J. Comput. Biol., 7, 819-837.
23. Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F. and Wootton,J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
24. Liu,J.S. and Lawrence,C.E. (1999) Bayesian inference on biopolymer models. Bioinformatics, 15, 38-52.
25. Long,A.D., Mangalam,H.J., Chan,B.Y., Tolleri,L., Hatfield,G.W. and Baldi,P. (2001) Improved statistical inference from dna microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J. Biol. Chem., 276, 19937-19944.
26. Lonnstedt,I. and Speed,T.P. (2001) Replicated microarray data. Statistical Sinica, 12, 31-46.
27. Lukashin,A.V. and Fuchs,R. (2001) Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the, optimal number of clusters. Bioinformatics, 17, 405-414.
28. MacEachern,S.N. (1994) Estimating normal means with a conjugate style Dirichlet process prior. Communications in Statistics: Simulation and Computation, 23, 727-741.
29. McLachlan,J.G. and Basford,E.K. (1987) Mixture Models: Inference and Applications to Clustering. Marcel Dekker, New York.
30. Medvedovic,M. (2000) clustering multinomial observations via finite and infinite mixture models and MCMC Algorithms. Proceedings of the Joint Statistical Meeting 2000: Statistical Computing Section. pp. 48-51.
31. Mewes,H.W., Heumann,K., Kaps,A., Mayer,K., Pfeiffer,F., Stocker,S. and Frishman,D. (1999) MIPS: a database for protein sequences and complete genomes. Nucleic Acids Res., 27, 44-48.
32. Neal,R.M. (2000) Markov chain sampling methods for Dirichlet process mixture models. Journal of Computational and Graphical Statistics, 9, 249-265.
33. Newton,M.A., Kendziorski,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.
34. Rasmussen,C.A. (2000) The infinite gaussian mixture model. Advances in Neural Information Processing Systems, 12, 554-560.
35. Rocke,D.M. and Dubin,B. (2001) A Model for Measurement Error for Gene Expression Arrays. J. Comput Biol., 8, 557-569.
36. SAS/STAT User's Guide, (1999) SAS Institute, Cary, NC.
37. Schmidler,S.C., Liu,J.S. and Brutlag,D.L. (2000) Bayesian segmentation of protein secondary structure. J, Comput. Biol., 7, 233-248.
38. Tamayo,P., Slonim,D., Mesirov,J., Zhu,Q., Kitareewan,S., Dmitrovsky,E., Lander,E.S. and Golub,T.R. (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA, 96, 2907-2912.
39. Tavazoie,S., Hughes,J.D., Campbell,M.J., Cho,R.J. and Church,G.M. (1999) Systematic determination of genetic network architecture. Nature Genet., 22, 281-285.
40. Wolfinger,R.D., Gibson,G., Wolfinger,E.D., Bennett,L., Hamadeh,H., Bushel,P., Afshari,C. and Paules,R.S. (2001) Assessing Gene Significance From CDNA Microarry Expression Data Via Mixed Models. J. Comput. Biol., 8, 625-637.
41. Yang,YH., Dudoit,S., Luu,P. and Speed,T. (2001) Normalization for cDNA microarray data. SPIE BiOS 2001. San Jose, California.
42. Yeung,K.Y, Fraley,C., Murua,A., Raftery,A.E. and Ruzzo,W.L. (2001a) Model-based clustering and data transformations for gene expression data. Bioinformatics, 17, 977-987.
43. Yeung,K.Y, Haynor,D.R. and Ruzzo,W.L. (2001b) Validating clustering for gene expression data. Bioinformatics, 17, 309-318.
44. Zhu,J., Liu,J.S. and Lawrence,C.E. (1998) Bayesian adaptive sequence alignment algorithms. Bioinformatics, 14, 25-39.