A generalized clustering problem, with application to DNA microarrays

Statistical Applications in Genetics and Molecular Biology

Volumn 5, Issue 1, 2006, Pages

  Belitskaya Levy, Ilana ^a  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Cluster analysis; Clustering algorithm; Clustering on subsets of variables; Dissimilarity measures; dna microarrays; Multiple clustering; Nearest neighbor graphs

Indexed keywords

ALGORITHM; ANALYTICAL PARAMETERS; ARTICLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; CORRELATION ANALYSIS; DNA MICROARRAY; EXPERIMENT; GENE CLUSTER; GENE EXPRESSION; GENE MAPPING; HUMAN; COLON TUMOR; EVALUATION; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; METHODOLOGY;

ALGORITHMS; CLUSTER ANALYSIS; COLONIC NEOPLASMS; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 30344471882     PISSN: 15446115     EISSN: 15446115     Source Type: Journal    
DOI: 10.2202/1544-6115.1197     Document Type: Article

References (15)

1. Alon, U., Barkai, N., Notterman, D., Gish, K., Ybarra, S., Mack, D. & Levine, A. (1999), 'Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays', Proc. Natl. Acad. Sci. 96, 6745-6750.
2. Belitskaya, I. (2003), Finding Multiple Clustering Structures in Data, With Applications to DNA Microarrays, PhD thesis, Stanford University.
3. Dudoit, S. & Fridlyand, J. (2002), 'A prediction-based resampling method for estimating the number of clusters in a dataset', Genome Biology 3(7), 0036.1-0036.21.
4. Eisen, M., Spellman, P., Brown, P. & Botstein, D. (1998), 'Cluster analysis and display of genome-wide expression patterns', Proc. Natl. Acad. Sci., USA. 95, 14863-14868.
5. Fellenberg, K., Hauser, N., Brors, B., Neutzner, A., Hoheisel, J. & Vingron, M. (2001), 'Correspondence analysis applied to microarray data', Proceedings of the National Academy of Science 98(19), 10781-10786.
6. Friedman, J. & Meulman, J. (2002), Clustering objects on subsets of attributes, Technical report, Stanford University. URL: http://www-stat. stanford.edu/∼jhf
7. Friedman, J. & Rafsky, L. (1983), 'Graph-theoretic measures of multivariate association and prediction', Annals of Statistics 11, 377-391.
8. Getz, G., Levine, E. & Domany, E. (2000), 'Coupled two-way clustering analysis of gene microarray data', Proc. Natl. Acad. Sci 97, 12079-12084.
9. Hartigan, J. & Wong, M. (1979), 'A k-means clustering algorithm', Applied Statistics 28, 100-108.
10. Hastie, T., Tibshirani, R., Eisen, M., Alizadeh, A., Levy, R., Staudt, L., Botstein, D. & Brown, P. (2000), 'Identifying distinct sets of genes with similar expression patterns via "gene shaving"', Genome Biology 1(2), 1-21.
11. Kaufman, L. & Rousseeuw, P. (1990), Finding Groups in Data: An Introduction to Cluster Analysis, Wiley, New York.
12. MacQueen, J. (1967), Some methods for classi.cation and analysis of multivariate observations, in 'Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability', Vol. 1, pp. 281-296.
13. Pollard, K. & van der Laan, M. (2002), 'Statistical inference for simultaneous clustering of gene expression data', Mathematical Biosciences 176(1), 99-121.
14. Ross, D., Scherf, U., Eisen, M., Perou, C., Spellman, P., Iyer, V., Rees, C., Jeffrey, S., Van de Rijn, M., Waltham, M., Pergamenschikov, A., Lee, J., Lashkari, D., Shalon, D., Myers, T., Weinstein, J., Botstein, D. & Brown, P. (2000), 'Systematic variation in gene expression patterns in human cancer cell lines', Nature Genetics 24, 227-235.
15. Tibshirani, R., Hastie, T., Eisen, M., Ross, D., Botstein, D. & Brown, P. (1999), Clustering methods for the analysis of DNA microarray data, Technical report, Department of Statistics, Stanford Univ.