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Bioinformatics. 2003 May 22;19(8):973-80.

Fuzzy C-means method for clustering microarray data.

Author information

1
Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS-IMSERM-ULP, BP 10142, 67404 Illkirch Cedex, France. doulaye@titus.u-strasbg.fr

Abstract

MOTIVATION:

Clustering analysis of data from DNA microarray hybridization studies is essential for identifying biologically relevant groups of genes. Partitional clustering methods 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 partitioning 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 at http://www-igbmc.u-strasbg.fr/fcm/

PMID:
12761060
[Indexed for MEDLINE]

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