Analysis of temporal gene expression profiles: Clustering by simulated annealing and determining the optimal number of clusters

Bioinformatics

Volumn 17, Issue 5, 2001, Pages 405-414

  Lukashin, Alexander V ^a   Fuchs, Rainer ^a  

^a BIOGEN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CELL CYCLE; CLUSTER ANALYSIS; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA MICROARRAY; GENE CLUSTER; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC CODE; GENETIC ENGINEERING; GENOME; NONHUMAN; PRIORITY JOURNAL; SAMPLE; SIMULATION; STANDARD; STATISTICAL ANALYSIS; YEAST;

EID: 0035014159     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.5.405     Document Type: Article

References (21)

1. Aart, E.H.L. and van Laarhoven, P.J.M. (1987) Simulated Annealing: a Review of the Theory and Applications. Kluwer, Dordrecht.
2. 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. Proc. Natl Acad. Sci. USA, 96, 6745-6750.
3. Brown, M.P.S., Grundy, W.N., Lin, D., Cristianini, N., Sugnet, C.W., Furey, T.S., Ares, M. and Haussler, D. (2000) Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl Acad. Sci. USA, 97, 262-267.
4. Chen, T., He, H.L. and Church, G.M. (1999) Modeling gene expression with differential equations. Pacific Symposium on Biocomputing '99. World Scientific, Singapore, pp. 29-40.
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. 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.
7. Hartigan, J. (1975) Clustering Algorithms. Wiley, New York.
8. Jain, A. and Dubes, R. (1988) Algorithms for Clustering Data. Prentice-Hall, Englewood Cliffs, NJ.
9. Kirkpatrick, S., Gelatt, C.D. and Vecchi, M.P. (1983) Optimization by simulated annealing. Science, 220, 671-680.
10. Lockhart, D.J. and Winzeler, E.A. (2000) Genomics, gene expression and DNA arrays. Nature, 405, 827-846.
11. Perou, C.M., Jeffrey, S.S., van de Rijn, M., Rees, C.A., Eisen, M.B., Ross, D.T., Pergamenschikov, A., Williams, C.F., Zhu, S.X., Lee, J.C.F., Lashkari, D., Shalon, D., Brown, P.O. and Botstein, D. (1999) Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc. Natl Acad. Sci. USA, 96, 9212-9217.
12. Roberts, C.J., Nelson, B., Marton, M.J., Stoughton, R., Meyer, M.R., Bennett, H.A., He, Y.D., Dai, H., Walker, W.L., Hughes, T.R., Tyers, M., Boone, C. and Friend, S.H. (2000) Signaling and circuitry of multiple MAPK pathways revealed by matrix and global gene expression profiles. Science, 287, 873-880.
13. Ross, D.T., Scherf, U., Eisen, M.B., Perou, C.M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S.S., van de Rijn, M., Waltham, M., Pergamenschikov, A., Lee, J.C.F., Lashkari, D., Shalon, D., Myers, T.G., Weinstein, J.N., Botstein, D. and Brown, P.O. (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nature Genet., 24, 227-235.
14. Spellman, P.T., Sherlock, G., Zhang, M.O., 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.
15. 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.
16. 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.
17. Weaver, D.C., Workman, C.T. and Stormo, G.D. (1999) Modeling regulatory networks with weight matrices. Pacific Symposium on Biocomputing'99. World Scientific, Singapore, pp. 112-123.
18. Wen, X., Fuhrman, S., Michaels, G.S., Carr, D.B., Smith, S., Barker, J.L. and Somogayi, R. (1998) Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl Acad. Sci. USA, 95, 334-339.
19. White, K.P., Rifkin, S.A., Hurban, P. and Hogness, D.S. (1999) Microarray analysis of Drosophila development during metamorphosis. Science, 286, 2179-2184.
20. Young, R.A. (2000) Biomedical discovery with DNA arrays. Cell, 102, 9-15.
21. Zweiger, G. (1999) Knowledge discovery in gene-expression-microarray data: mining the information output of the genome. Trends Biotechnol., 17, 429-436.