During the last years, high throughput experiments have become very popular. During the analysis of such data the need for a functional grouping of genes arises. In this paper, we propose grouping genes according to their biological function by means of kernel functions, which are similarity measures having special mathematical properties and play a crucial role e.g. in SVM classification. Thereby our kernel functions rely on functional information on the genes provided by Gene Ontology

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... on. We investigate and compare several provably symmetric, positive semidefinite kernel functions in combination with spectral clustering, dual kmeans and average linkage and demonstrate that our approach leads to good clustering results.