Genetic functional modules and protein complexes are being sought from combinations of gene expression and protein-protein interaction data with various clustering-type methods. As far as we know, up to now these meth- ods have used the interaction data as constraints on the clustering of expres- sion data, instead of modeling the noise in the interactions. We model the interaction links with a simple generative "topic model", which is augmented to generate also the expression data. The results outperform a represen- tative set of earlier models in the task of finding modules having enriched functional classes. Moreover, it turns out that the generative model for the links alone works very well in this task.

This work was supported in part by the Academy of Finland, decision number 207467, and in part by the IST Programme of the European Community, under the PASCAL Network of Excellence, IST-2002-506778.