P053 - GCB 2004 - German Conference on Bioinformatics

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Konferenzbeitrag
Probabilistic methods for predicting protein functions in protein-protein interaction networks
(German Conference on Bioinformatics 2004, GCB 2004, 2004) Best, Christoph; Zimmer, Ralf; Apostolakis, Joannis
We discuss probabilistic methods for predicting protein functions from protein-protein interaction networks. Previous work based on Markov Randon Fields is extended and compared to a general machine-learning theoretic approach. Using actual protein interaction networks for yeast from the MIPS database and GO-SLIM function assignments, we compare the predictions of the different probabilistic methods and of a standard support vector machine. It turns out that, with the currently available networks, the simple methods based on counting frequencies perform as well as the more sophisticated approaches.