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Nucleic Acids Research, 2003, Vol. 31, No. 21 6283-6289
© 2003 Oxford University Press

Functional modules by relating protein interaction networks and gene expression

Sabine Tornow*,1 and H. W. Mewes1,2

1 Institute for Bioinformatics, German National Center for Health and Environment, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany and 2 Technische Universität München, Wissenschaftszentrum Weihenstephan, Lehrstuhl fur Genomorientierte Bioinformatik, Am Forum 1, 85435 Freising-Weihenstephan, Germany

*To whom correspondence should be addressed. Tel: + 49 89 31873578; Fax: + 49 89 31873585; Email: sabine.tornow{at}t-online.de

Genes and proteins are organized on the basis of their particular mutual relations or according to their interactions in cellular and genetic networks. These include metabolic or signaling pathways and protein interaction, regulatory or co-expression networks. Integrating the information from the different types of networks may lead to the notion of a functional network and functional modules. To find these modules, we propose a new technique which is based on collective, multi-body correlations in a genetic network. We calculated the correlation strength of a group of genes (e.g. in the co-expression network) which were identified as members of a module in a different network (e.g. in the protein interaction network) and estimated the probability that this correlation strength was found by chance. Groups of genes with a significant correlation strength in different networks have a high probability that they perform the same function. Here, we propose evaluating the multi-body correlations by applying the superparamagnetic approach. We compare our method to the presently applied mean Pearson correlations and show that our method is more sensitive in revealing functional relationships.


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