Fuzzy C-means method for clustering microarray data

Motivation: Clustering analysis of data from DNA microar-ray hybridization studies is essential for identifying biologi-cally relevant groups of genes. Partitional clustering meth-ods such as K-means or self-organizing maps assign each gene to a single cluster. However, these methods do not provide information about the influence of a given gene for the overall shape of clusters. Here we apply a fuzzy parti-tioning method, Fuzzy C-means (FCM), to attribute cluster membership values to genes. Results: A major problem in applying the FCM method for clustering microarray data is the choice of the fuzziness parameter m. We show that the commonly used value m = 2 is not appropriate for some data sets, and that optimal values for m vary widely from one data set to another. We propose an empirical method, based on the distribution of distances between genes in a given data set, to determine an adequate value for m. By setting threshold levels for the membership values, genes which are tigthly associated to a given cluster can be selected. Using a yeast cell cycle data set as an example, we show that this selection increases the overall biological significance of the genes within the cluster. Availability: Supplementary text and Matlab functions are available a