A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings

Bioinformatics

Volumn 21, Issue 21, 2005, Pages 3993-3999

  Torrente, Aurora ^a,b   Kapushesky, Misha ^a   Brazma, Alvis ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSIDAD CARLOS III DE MADRID   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLUSTER ANALYSIS; COMPUTER SIMULATION; GENE CLUSTER; GENE EXPRESSION; GENETIC ALGORITHM; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; METHODOLOGY; ONLINE SYSTEM; PRIORITY JOURNAL; PROCESS OPTIMIZATION;

EID: 27744459345     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti644     Document Type: Article

References (16)

1. Quackenbush,J. (2001) Computational analysis of microarray data. Nat. Rev. Genet., 2, 418-427.
2. Rand,W.M. (1971) Objective criteria for the evaluation of clustering methods. J. Am. Stat. Assoc., 66, 846-850.
3. Fowlkes,E.B. and Mallows,C.L. (1983) A method for comparing two hierarchical clusterings. J. Am. Stat. Assoc., 78, 553-584.
4. Kaufman,L. and Rousseeuw,P.J. (1990) Finding Groups in Data: An Introduction to Cluster Analysis, (1990) Wiley, New York, 2, 418-427.
5. Eisen,M.B. et al. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
6. Tibshirani,R., Hastie,T., Eisen,M., Ross,D., Botstein,D. and Brown,P. (1999) Clustering methods for the analysis of DNA microarray data. Technical Report. Department of Statistics, Stanford University.
7. Rissanen,J. Modelling by shortest data description. Automatica, 14, 465-471.
8. Chen,D. et al. (2001) Global transcriptional responses of fission yeast to environmental stress. Mol. Biol. Cell, 14, 214-229.
9. Kapushesky,M. et al. (2003) Expression Profiler: Next generation an online platform for analysis of microarray data. Nucleic Acids Res. Web Server issue, W465-470.
10. Eades,P., McKay,B. and Wormald,N. (1986) On an edge crossing problem. In Proceedings of the 9th Australian Computer Science Conference, Australian National University, Canberra, January 29-31, pp. 327-334.
11. Gansner,E.R. et al. (1993) A technique for drawing directed graphs. IEEE Trans. Software eng., 19, 214 230.
12. Sharan,R. and Shamir,R. (2000) CLICK: A clustering algorithm with applications to gene expression analysis. Proc. Int. Conf. Intell. Syst. Mol. Biol., 8, 307-316.
13. Hartuv,E., Schmitt,A., Lange,J., Meier-Ewert,S., Lehrach,H. and Shamir,R. (1999) An algorithm for clustering cDNA for gene expression analysis using short oligonucleotide fingerprints. In Proceedings of the Third International Symposium on Computational Molecular Biology RECOMB'99, Lyon, France, August 11-14, 1999, ACM Press, New York, pp. 188-197.
14. Shannon,C.E. (1948) A mathematical theory of communication. Bell Syst. Tech. J., 27, 379-423, 623-656.
15. Jonnalagadda,S. and Srinivasan,R. (2004) An information theory approach for validating clusters in microarray data. In Proceedings of the 12th Intelligent Systems for Molecular Biology, Glasgow, UK, July 31-August 4, 2004. http://www.iscb.org/ismbeccb2004/short%20papers/39.pdf.
16. Harper,D.A.T. (1999) Numerical Palaeobiology. John Wiley & Sons, New York.