Fuzzy Types Clustering for Microarray Data
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Fuzzy Types Clustering for Microarray Data

Authors: Seo Young Kim, Tai Myong Choi

Abstract:

The main goal of microarray experiments is to quantify the expression of every object on a slide as precisely as possible, with a further goal of clustering the objects. Recently, many studies have discussed clustering issues involving similar patterns of gene expression. This paper presents an application of fuzzy-type methods for clustering DNA microarray data that can be applied to typical comparisons. Clustering and analyses were performed on microarray and simulated data. The results show that fuzzy-possibility c-means clustering substantially improves the findings obtained by others.

Keywords: Clustering, microarray data, Fuzzy-type clustering, Validation

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1059829

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References:


[1] N. Belacel, M. Cuperlovic-Culf, M.R. Boulassel, "The variable neighvorhood search metaheuristic for fuzzy clustering cDNA microarray gene expression data", Proceedings of IASTED-AIA-04 Conference. Innsbruck, Austria. February 16-18, 2004. 6 pages.
[2] P. Tamayo, D. Slonim, J. Mesirov, Q. Zhu, S. Kitareewan, E. Dmitrovsky, E. Lander, and T. Golub, "Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation", Proc. Natl Acad. Sci., vol. 96, 1999, pp. 2907-2912.
[3] P.T. Spellman, G. Sherlock, M.Q. Zhang, V.R. Iyer, K. Anders, M.B. Eisen, P.O. Brown, D. Botstein, and B. Futcher, "Comprehensive identification of cell cycle-regulated genes of the yest Saccharomyces cerevisiae by microarray hydridization", Mol. Biol. Cell, vol. 9, pp. 3273-3279.
[4] M.B. Eisen, P.T. Spellman, P.O. Brown, and D. Botstein, "Cluster analysis and display of genome-wide expression patterns", Proceeding of the National Academy of Sciences, vol. 95, 1998, pp. 14863-14868.
[5] S. Tavazoie, J. Hughes, M. Campbell, R. Cho, and G. Church, "Systematic determination of genetic network architecture", Nat. Genet., vol.22, 1999, pp. 281-285.
[6] R. Guthke, W. Schmidt-Heck, D. Hahn, and M. Pfaff, "Gene expression data mining for functional genomics", Proceedings of European Symposium on Intelligent Techniques (EIST 2000), Aachen, Germany, 2000, pp. 170-177.
[7] S. Carla, K.H. Cho, and W. Olaf, "DNA microarray data clustering based on temporal variation: FCV with TSD preclustering", submitted 2003.
[8] B.J.T. Morgan, A.P.G. Ray, "Non-uniqueness and inversions in clusters analysis", Applied Statistics, vol.44, 1985, pp. 117-134.
[9] S. Chu et al., "The transcriptional program of sporulation in budding yeast", Science, vol.282, 1998, pp. 699-705.
[10] S. Raychaudhui, J.M. Stuart, and R.M. Altman, "Principal components analysis to summarize microarray experiments: application to sporulation time series", In Pacific Symposium on Biocomputing, Hawaii, 2000, pp. 452-463.
[11] J. Yu, "General c-means clustering model and it application", Proceedings of the 2003 IEEE Computer Society Conference on Computer Vision and Pattern Recognition 9CVPR-03), 2003.
[12] J.C. Bezdek, "Pattern recognition with fuzzy objective function algorithms (New York: Plenum Press, 1981).
[13] M. Halkidi, Y. Batistakis, M. Vazirgiannis, "On clustering validation techniques", Journal of intelligenet information system, vol.17, 2001, pp. 107-145.
[14] R. Krishnapuram and J. Keller, "A possibilisitic approach to clustering", IEEE Trans, Fuzzy syst., vol. 1, 1993, pp. 98-110.
[15] N.R. Pal, K. Pal, and J.C. Bezdek, "A mixed c-means clustering model", Fuzzy- IEEE-97, 1997, 0-7803-3796-4.
[16] T.R. Golub, D.K. Slonim, P. Tamayo et al., "Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring", Science, vol.286, 1999, pp. 531-537.
[17] http://www.genome.wi.mit.edu/MPR.
[18] M. Bittner, P. Meltzer, Y. Chen et al., "Molecular classification of cutaneous malignant melanoma by gene expression profiling", Nature, vol.406, 2000, pp. 536-540.
[19] http://www.nhgri.nih.gov/DIR/Microarray/Melanoma_Supplement/index .html.
[20] S. Dudoit and J. Fridlyand, " A prediction-based resampling method for estimating the number of clusters in a dataset", Genome biology
[21] V.G. Tusher, R. Tibshirani, G. Chu, "Significance analysis of microarrays applied to the ionizing radiation response", Proceedings of the Natonal Academy of Science, vol.98, 2001, pp. 5116-5121.
[22] P. Broberg, "Ranking genes with respect to differential expression", Genome Biology, vol.3, 2002, preprint0007.1-0007.23.
[23] L. Kaufman, P.J. Rousseeuw, "Finding groups in data: An introduction to custer analysis", New York: John Wiley, 1990.
[24] K.Y. Yeung, and W.L. Ruzzo, "An empirical study on principal component analysis for clustering gene expression data", Technical Report 2000 UW-CSE-00-11-01, Department of Computer Science and Engineering, University of Washington.