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Bioinformatics Advance Access originally published online on September 17, 2004
Bioinformatics 2005 21(2):227-238; doi:10.1093/bioinformatics/bth484
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Bioinformatics vol. 21 issue 2 © Oxford University Press 2005; all rights reserved.

Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution

S. Ott 1,*, A. Hansen 2, S.-Y. Kim 1 and S. Miyano 1

1 Human Genome Center, Institute of Medical Science, University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
2 Wolfson Institute for Biomedical Research, University College London The Cruciform Building, Gower Street, London, WC1E 6AU, UK

*To whom correspondence should be addressed at Wolfson Institute for Biomedical Research, University College London, The Cruciform Building, Gower Street, London WC1E 6AU, UK.

Motivation: Estimating the network of regulative interactions between genes from gene expression measurements is a major challenge. Recently, we have shown that for gene networks of up to around 35 genes, optimal network models can be computed. However, even optimal gene network models will in general contain false edges, since the expression data will not unambiguously point to a single network.

Results: In order to overcome this problem, we present a computational method to enumerate the most likely m networks and to extract a widely common subgraph (denoted as gene network motif) from these. We apply the method to bacterial gene expression data and extensively compare estimation results to knowledge. Our results reveal that gene network motifs are in significantly better agreement to biological knowledge than optimal network models. We also confirm this observation in a series of estimations using synthetic microarray data and compare estimations by our method with previous estimations for yeast. Furthermore, we use our method to estimate similarities and differences of the gene networks that regulate tryptophan metabolism in two related species and thereby demonstrate the analysis of gene network evolution.

Availability: Commercial license negotiable with Gene Networks Inc. (cherkis{at}gene-networks.com)

Contact: sascha-ott{at}gmx.net


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