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Partitioned 3,000 genes into 30 clusters with the K-means algorithm [78]. For each cluster, 600 base pairs upstream sequences of the genes were searched for potential motifs. 18 motifs were found from 12 clusters in their experiments and 7 of them can be verified according to previous empirical results. Figure 2 (a) and (b) illustrate the application of hierarchical clustering and SOFM for the small round blue-cell tumors (SRBCTs) data set, which consists of the measurement of the expression levels of 2,308 genes across 83 samples [47].

The last step combines the subtours back into one complete tour. Tours with good quality for up to 25 million cities were obtained within 13,500 seconds on a 2GHz AMD Athlon MP processor with 512M of DDR RAM. 40 R. Xu, D. 2 Bioinformatics - Gene Expression Data Analysis Genome sequencing projects have achieved great advance in recent years. However, these successes can only be seen as the first step towards understanding the functions of genes and proteins and the interactions among cellular molecules.

Ramakrishnan, and U. Shaft: When is nearest neighbor meaningful. In: Proceedings of 7th International Conference on Database Theory, 1999, 217–235. 8. J. Bezdek: Pattern Recognition with Fuzzy Objective Function Algorithms. Plenum Press, New York, 1981. 9. C. Bishop: Neural networks for pattern recognition. Oxford University Press, 1995. Computational Intelligence in Clustering Algorithms 47 10. J. Burke, D. Davison, and W. Hide: d2 Cluster: a validated method for clustering EST and full-length cDNA sequences.

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