A Method to Identify Significant Clusters in Gene Expression Data
Download the Paper Forward to a colleague
Article comments:
Published 2002 in Proceedings, SCI (World Multiconference on Systemics, Cybernetics and Informatics), V. II, 318-325.
Abstract:
Clustering algorithms have been widely applied to gene expression data. For both hierarchical and partitioning clustering algorithms, selecting the number of significant clusters is an important problem and many methods have been proposed. Existing methods for selecting the number of clusters tend to find only the global patterns in the data (e.g.: the over and under expressed genes). We have noted the need for a better method in the gene expression context, where small, biologically meaningful clusters can be difficult to identify. In this paper, we define a new criteria, Mean Split Silhouette (MSS), which is a measure of cluster heterogeneity. We propose to choose the number of clusters as the minimizer of MSS. In this way, the number of significant clusters is defined as that which produces the most homogeneous clusters. The power of this method compared to existing methods is demonstrated on simulated microarray data. The minimum MSS method is an example of a general approach that can be applied to any clustering routine with any global criteria.
Subject Area:
Microarrays, Multivariate Analysis, Statistical Theory and Methods
Suggested Citation:
Katherine S. Pollard and Mark J. van der Laan, "A Method to Identify Significant Clusters in Gene Expression Data" (April 2002). U.C. Berkeley Division of Biostatistics Working Paper Series. Working Paper 107.
http://www.bepress.com/ucbbiostat/paper107