Bayesian clustering and feature selection for cancer tissue samples

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Marttinen, Pekka ^a   Myllykangas, Samuel ^b,c   Corander, Jukka ^d  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

^c HELSINKI UNIVERSITY CENTRAL HOSPITAL   (Finland)

^d ÅBO AKADEMI UNIVERSITY   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMIC TECHNIQUES; HIER-ARCHICAL CLUSTERING; MEASUREMENT TECHNIQUES; MODEL-BASED CLUSTERING; SIMULTANEOUS IDENTIFICATION; SOFTWARE IMPLEMENTATION; STATISTICAL LITERATURE; SUB-OPTIMAL PERFORMANCE;

ALGORITHMS; BAYESIAN NETWORKS; MAXIMUM LIKELIHOOD ESTIMATION; PRINCIPAL COMPONENT ANALYSIS;

TISSUE;

ALGORITHM; ARTICLE; BAYES THEOREM; BAYESIAN LEARNING; CANCER TISSUE; CHROMOSOME ANALYSIS; CLUSTER ANALYSIS; COMPUTER PROGRAM; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; SIMULATION; VALIDATION PROCESS; BIOLOGY; CLASSIFICATION; GENE DOSAGE; GENETIC DATABASE; GENETICS; HUMAN; METABOLISM; METHODOLOGY; NEOPLASM;

DNA;

ALGORITHMS; BAYES THEOREM; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA, NEOPLASM; GENE DOSAGE; GENE EXPRESSION PROFILING; HUMANS; NEOPLASMS; SOFTWARE;

EID: 65549143555     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-90     Document Type: Article

References (31)

1. Myllykangas S Himberg J Böhling T Nagy B Hollmén J Knuutila S DNA copy number amplification profiling of human neoplasms Oncogene 2006, 25:7324-7332. 10.1038/sj.onc.1209717 16751803
2. Myllykangas S Tikka J Böhling T Knuutila S Hollmén J Classification of human cancers based on DNA copy number amplification modeling BMC Medical Genomics 2008, 1:15. 2397431 18477412 10.1186/ 1755-8794-1-15
3. Mitelman F Johansson B Mertens F Catalog of Chromosome Aberrations in Cancer New York: Wiley-Liss 1994.
4. Myllykangas S Böhling T Knuutila S Specificity, selection and significance of gene amplifications in cancer Seminars in Cancer Biology 2007, 17:42-55. 10.1016/j.semcancer.2006.10.005 17161620
5. Bock K Language production: Methods and methodologies Psychonomic Bulletin & Review 1996, 3:395-421.
6. Jain AK Duin RPW Mao J Statistical Pattern Recognition: A Review IEEE Transactions on Pattern Analysis and Machine Intelligence 2000, 22:4-37. 10.1109/34.824819
7. Tikka J Hollmén J Myllykangas S Mixture modeling of DNA copy number amplification patterns in cancer Proceedings of the 9th International Work-Conference on Artificial Neural Networks Heidelberg: Springer-Verlag Sandoval F, Prieto A, Cabestany J, Graña M 2007, 972-979.
8. Robert C Casella Monte Carlo Statistical Methods New York: Springer second 2005.
9. Geyer CJ Thompson EA Annealing Markov Chain Monte Carlo with Applications to Ancestral Inference Journal of American Statistical Association 1995, 90:909-920. 10.2307/2291325
10. Jensen ST Liu XS Zhou Q Liu JS Computational Discovery of Gene Regulatory Binding Motifs: A Bayesian Perspective Statistical Science 2004, 19:188-204. 10.1214/088342304000000107
11. Marttinen P Corander J Törönen P Holm L Bayesian search of functionally divergent protein subgroups and their function specific residues Bioinformatics 2006, 22:2466-2474. 10.1093/bioinformatics/ btl411 16870932
12. Corander J Gyllenberg M Koski T Random partition models and exchangeability for Bayesian identification of population structure Bulletin of Mathematical Biology 2007, 69:797-815. 10.1007/ s11538-006-9161-1 17086368
13. Bernardo JS Smith AFM Bayesian Theory Chichester: Wiley 1994.
14. Corander J Gyllenberg M Koski T Bayesian model learning based on a parallel MCMC strategy Statistics and Computing 2006, 16:355-362. 10.1007/s11222-006-9391-y
15. Corander J Marttinen P Mäntyniemi S Bayesian identification of stock mixtures from molecular marker data Fishery Bulletin 2006, 104:550-558.
16. Ripley BD Pattern Recognition and Neural Networks Cambridge: Cambridge University Press 1996.
17. Kass R Raftery AE Bayes factors Journal of American Statistical Association 1995, 90:773-795. 10.2307/2291091
18. Dy JG Brodley CE Feature selection for unsupervised learning Journal of Machine Learning Research 2004, 5:845-889.
19. Law MHC Figueiredo MAT Jain AK Simultaneous feature selection and clustering using mixture models IEEE Transactions on Pattern Analysis and Machine Intelligence 2004, 26:1154-1166. 10.1109/TPAMI.2004.71
20. Cheeseman P Stutz J Bayesian classification (AutoClass): Theory and results Advances in Knowledge Discovery and Data Mining Cambridge (Mass.): MIT Press Fayyad U, Piatetsky-Shapiro G, Smyth P, Uthurusamy R 1996, 153-180.
21. Gyllenberg M Koski T Verlaan M Classification of binary vectors by stochastic complexity Journal of Multivariate Analysis 1997, 63:47-72. 10.1006/jmva.1997.1687
22. Peña JM Lozano JA Larrañaga P Learning recursive Bayesian multinets for data clustering by means of constructive induction Machine Learning 2002, 47:63-89. 10.1023/A:1013683712412
23. Zhang NL Hierarchical latent class models for cluster analysis Journal of Machine Learning Research 2004, 5::697-723.
24. Santafé G Lozano JA Larrañaga P Bayesian model averaging of naive Bayes for clustering IEEE Transactions on Systems, Man, and Cybernetics-Part B:CYbernetics 2006, 36:1149-1161. 10.1109/ TSMCB.2006.874132
25. Corander J Marttinen P Bayesian identification of admixture events using multi-locus molecular markers Molecular ecology 2006, 15:2833-2843. 16911204
26. Gelman A Carlin JB Stern HS Rubin DB Bayesian Data Analysis Boca Raton: Chapman & Hall/CRC 2 2004.
27. Neal RM Markov Chain Sampling Methods for Dirichlet Process Mixture Models Journal of Computational and Graphical Statistics 2000, 9:249-265. 10.2307/1390653
28. Hubert L Arabie P Comparing partitions Journal of Classification 1985, 2:193-218. 10.1007/BF01908075
29. Gschwind A Fischer OM Ullrich A The discovery of receptor tyrosine kinases: Targets for cancer therapy Nature Reviews Cancer 2004, 4:361-370. 10.1038/nrc1360 15122207
30. Imai K Takaoka A Comparing antibody and small-molecule therapies for cancer Nature Reviews Cancer 2006, 6:714-727. 10.1038/nrc1913 16929325
31. Baselga J Targeting tyrosine kinases in cancer: The second wave Science 2006, 312:1175-1178. 10.1126/science.1125951 16728632