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Proc Natl Acad Sci U S A. 2006 Jul 18;103(29):10967-72. Epub 2006 Jul 11.

Cross-species analysis of biological networks by Bayesian alignment.

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  • 1Institut für Theoretische Physik, Universität zu Köln, Zülpicherstrasse 77, 50937 Cologne, Germany.


Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction networks by alignment, which maps bona fide functional relationships between genes in different organisms. Network alignment is based on a scoring function measuring mutual similarities between networks, taking into account their interaction patterns as well as sequence similarities between their nodes. High-scoring alignments and optimal alignment parameters are inferred by a systematic Bayesian analysis. We apply this method to analyze the evolution of coexpression networks between humans and mice. We find evidence for significant conservation of gene expression clusters and give network-based predictions of gene function. We discuss examples where cross-species functional relationships between genes do not concur with sequence similarity.

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