Kernel hierarchical gene clustering from microarray expression data

Bioinformatics

Volumn 19, Issue 16, 2003, Pages 2097-2104

  Qin, Jie ^a   Lewis, Darrin P ^b   Noble, William Stafford ^c  

^a Columbia University ^*  (United States)

^b University of Washington ^*  (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; DNA MICROARRAY; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE MAPPING; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC IDENTIFICATION; PRIORITY JOURNAL; VALIDATION PROCESS;

EID: 0242475337     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg288     Document Type: Article

References (24)

1. 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. PNAS, 96, 6745-6750.
2. Alpaydin,E. (1999) Combined 5 × 2 cv f test for comparing supervised classification learning algorithms. Neural Comput., 11, 1885-1892.
3. Brown,M.P.S., Grundy,W.N., Lin,D., Cristianini,N., Sugnet,C., Furey,T.S., Ares,J.M. and Haussler,D. (2000) Knowledge-based analysis of microarray gene expression data using support vector machines. PNAS, 97, 262-267.
4. Chu,S., DeRisi,J., Eisen,M., Mulholland,J., Botstein,D., Brown,P. and Herskowitz,I. (1998) The transcriptional program of sporulation in budding yeast. Science, 282, 699-705.
5. Cristianini,N. and Shawe-Taylor,J. (2000) An Introduction to Support Vector Machines. Cambridge University Press, Cambridge.
6. DeRisi,J., Iyer,V and Brown,P. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680-686.
7. Dietterich,T. (1998) Approximate statistical tests for comparing supervised classification learning algorithms. Neural Comput., 10, 1885-1923.
8. Duda,R.O. and Hart,P.E. (1973) Pattern Classification and Scene Analysis. Wiley, New York.
9. Eisen,M., Spellman,P., Brown,P. and Botstein,D. (1998) Cluster analysis and display of genome-wide expression patterns. PNAS, 95, 14863-14868.
10. Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25-9.
11. Golub,T.R., Slonim,D.K., Tamayo,P., Huard,C., Gaasenbeek,M., Mesirov,J.P., Coller,H., Loh,M.L., Downing,J.R., Caligiuri,M.A. et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286, 531-537.
12. Jaakkola,T. and Haussler,D. (1998) Exploiting generative models in discriminative classifiers. In Advances in Neural Information Processing Systems 11. Morgan Kauffmann, San Mateo, CA.
13. Jain,A. and Dubes,R. (1988) Algorithms for Clustering Data. Prentice Hall, New Jersey.
14. Mewes,H.W., Frishman,D., Gruber,C., Geier,B., Haase,D., Kaps,A., Lemcke,K., Mannhaupt,G., Pfeiffer,F., Schüller,C. et al. (2000) MIPS: a database for genomes and protein sequences. Nucleic Acids Res., 28, 37-40.
15. Mika,S., Rätsch,G., Weston,J., Schölkopf,B. and Müller,K.-R. (1999) Fisher discriminant analysis with kernels. In Proceedings of the IEEE Neural Networks for Signal Processing Workshop 1999.
16. Sandberg,R., Yasuda,R., Pankratz,D., Carter,T., Rio,J.D., Wodicka,L., Mayford,M., Lockhart,D. and Barlow,C. (2000) Regional and strain-specific gene expression mapping in the adult mouse brain. PNAS, 97, 11038-11043.
17. Schölkopf, B., Smola, A. and Müller, K.-R. (1997) Kernel principal component analysis. In Proceedings ICANN97. Springer Lecture Notes in Computer Science, p. 583.
18. Sharan, R. and Shamir, R. (2000) CLICK: A clustering algorithm for gene expression analysis. In Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology. AAAI Press, pp. 307-316.
19. Slonim, D.K. (2002) From patterns to pathways: gene expression data analysis comes of age. Nat. Genet. (Suppl. 2), 502-508.
20. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
21. Troyanskaya, O., Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D. and Altman, R. (2001) Missing value estimation methods for DNA microarrays. Bioinformatics, 17, 520-525.
22. Tsuda, K., Kawanabe, M. and Müller, K.-R. (2003) Clustering with the Fisher score. In Advances in Neural Information Processing Systems. Morgan Kauffman (to appear).
23. Vapnik, V.N. (1998) Statistical Learning Theory. Adaptive and learning systems for signal processing, communications, and control. Wiley, New York.
24. Yeung, K.Y., Haynor ,D.R. and Ruzzo, W.L. (2000) Validating clustering for gene expression data. Technical Report UW-CSE-00-01-01, University of Washington.