Performance assessment of kernel density clustering for gene expression profile data

Comparative and Functional Genomics

Volumn 4, Issue 3, 2003, Pages 287-299

  Shu, Guoping ^a   Zeng, Beiyan ^a   Chen, Yiping P ^a   Smith, Oscar H ^a  

^a PIONEER HI BRED INTERNATIONAL INC   (United States)

Author keywords

Clustering analysis; Expression profile; Gene expression; Kernel density; Noisy data; Pseudo F; Pseudo t test; r2; Rand Index; Robustness; Smoothing; Unsupervised learning

Indexed keywords

ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE ISOLATION; GENETIC MODEL; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MULTIVARIATE ANALYSIS; PRIORITY JOURNAL; SIGNAL NOISE RATIO; SIMULATION;

EID: 0037712008     PISSN: 15316912     EISSN: None     Source Type: Journal    
DOI: 10.1002/cfg.290     Document Type: Article

References (40)

1. Banfield JD, Raftery AE. 1993. Model-based Gaussian and non-Gaussian clustering. Biometrics 49: 803-821.
2. Ben-Dor A, Yakhini Z. 1999. Clustering gene expression patterns. In RECOMB99: Proceedings of the Third Annual International Conference on Computational Molecular Biology, Lyon, France.
3. Brown MPS, Grundy WN, Lin D, et al. 2000. Knowledge-based analysis of microarray gene expression data using support vector machines. Proc Natl Acad Sci USA 97: 262-267.
4. Calinski T, Harabasz J. 1974. A dendrite method for cluster analysis. Commun Statist 3: 1-27.
5. Chambers JM. 1998. Programming with Data. A Guide to the S Language. Springer-Verlag: New York.
6. De Smet F, Mathys J, Marchal K, et al. 2002. Adaptive quality-based clustering of gene expression profiles. Bioinformatics 18: 735-746.
7. DeRisi JL, Vishwanath RL, Brown PO. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686.
8. Eisen MB, Spellman PT, Brown PO, Botstein D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14 863-14 868.
9. Fraley C, Raftery AE. 1999. Mclust: software for model-based cluster analysis. J Classif 16: 297-306.
10. Ghosh D, Chinnaiyan AM. 2002. Mixture modelling of gene expression data from microarray experiments. Bioinformatics 18: 275-286.
11. Gitman I. 1973. An algorithm for nonsupervised pattern classification. IEEE Trans Syst Man Cybernet SMC-3: 66-74.
12. Gordon AD. 1999. Classification, 2nd edn. Chapman & Hall/CRC: London.
13. Hartuv F, Schmitt A, Lange J, et al. 1999. An algorithm for clustering cDNAs for gene expression analysis. In RECOMB99: Proceedings of the Third Annual International Conference on Computational Molecular Biology, Lyon, France.
14. Hastie T, Tibshirani R, Friedman J. 2001. The Elements of Statistical Learning: Data Mining, Inference, and Prediction. Springer-Verlag: New York.
15. Herrero J, Valencia A, Dopazo J. 2001. A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics 17: 126-136.
16. Heyer LJ, Kruglyak S, Yooseph S. 1999. Exploring expression data: identification and analysis of co-expressed genes. Genome Res 9: 1102-1115.
17. Hubert L, Arabie P. 1985. Comparing partitions. J Classif 2: 193-218.
18. Kuiper FK, Fisher L. 1975. A Monte Carlo comparison of six clustering procedures. Biometrics 31: 777-783.
19. Huizinga DH. 1978. A Natural or Mode Seeking Cluster Analysis Algorithm. Technical Report 78-1. Behavioral Research Institute: 2305 Canyon Blvd., Boulder, CO 80 302.
20. Koontz WLG, Fukunaga K. 1972. A non-parametric valley-seeking technique for cluster analysis. IEEE Trans Comput C21: 171-178.
21. Lee J, Williams ME, Tingey SV, Rafalski JA. 2002. DNA array profiling of gene expression changes during maize embryo development. Funct Integr Genom 2: 13-27.
22. Lee M-LT, Kuo FC, Whitmore GA, Sklar J. 2000. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridization. Proc Natl Acad Sci USA 97: 9834-9839.
23. Li L, Weinberg CR, Darden TA, Pedersen LG. 2001. Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method. Bioinformatics 17: 1131-1142.
24. Lockhart DJ, Winzeler EA. 2000. Genomics, gene expression and DNA arrays. Nature 405: 827-836.
25. Milligan GW, Cooper MC. 1985. An examination of procedures for determining the number of clusters in a data set. Psychometrika 50: 159-179.
26. Milligan GW, Cooper MC. 1986. A study of the comparability of external criteria for hierarchical cluster analysis. Multivar Behav Res 21: 441-458.
27. Milliken GA, Johnson DE. 1992. Analysis of Messy Data, vol I: Designed Experiments. Chapman & Hall: London.
28. Rand WM. 1971. Objective criteria for the evaluation of clustering methods. J Am Statist Assoc 66: 846-850.
29. S-PLUS 6.0 for Windows, Professional Release 1, Copyright © 1988-2001. Insightful Corp.
30. SAS/STAT User's Guide, Version 8.0, 1999. SAS Institute Inc: Cary, NC.
31. Schena M. 2000. Microarray Biochip Technology. Eaton: Natick, MA.
32. Schwarz G. 1978. Estimating the dimension of a model. Ann Stat 6: 461-464.
33. Scott DW. 1992. Multivariate Density Estimation: Theory, Practice, and Visualization. Wiley: New York.
34. Silverman BW. 1986. Density Estimation. Chapman & Hall: New York.
35. Tamayo P, Slonim D, Mesirov J, et al. 1999. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 96: 2907-2912.
36. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. 1999. Systematic determination of genetic network architecture. Nature Genet 22: 281-285.
37. Tseng GC, Oh M-K, Rohlin L, Liao JC, Wong WH. 2001. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res 29: 2549-2557.
38. Wong MA, Schaack C. 1982. Using the Kth nearest neighbor clustering procedure to determine the number of subpopulations. Proceedings of the Statistical Computing Section. American Statistical Association: 1982; 40-48.
39. Yeung KY, Fraley C, Murua A, Raftery AE, Ruzzo WL. 2001. Model-based clustering and data transformations for gene expression data. Bioinformatics 17: 977-987.
40. Zar JH. 1999. Biostatistical Analysis, 4th edn. Prentice Hall: Upper Saddle River, NJ.