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Effect of dataset selection on the topological interpretation of protein interaction networks.doc

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Effect of dataset selection on the topological interpretation of protein interaction networks

BMC Genomics BioMedCentral Research article Open Access Effect of dataset selection on the topological interpretation of protein interaction networks Luke Hakes, David L Robertson and Stephen G Oliver* Address: Faculty of Life Sciences, The University of Manchester, Manchester, UK Email: Luke Hakes - luke.hakes@student.manchester.ac.uk; David L Robertson - robertson@bioinf.man.ac.uk; Stephen G Oliver* - steve.oliver@manchester.ac.uk * Corresponding author Published: 20 September 2005 Received: 12 July 2005 Accepted: 20 September 2005 BMC Genomics 2005, 6:131 doi:10.1186/1471-2164-6-131 This article is available from: /1471-2164/6/131 ? 2005 Hakes et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Studies of the yeast protein interaction network have revealed distinct correlations between the connectivity of individual proteins within the network and the average connectivity of their neighbours. Although a number of biological mechanisms have been proposed to account for these findings, the significance and influence of the specific datasets included in these studies has not been appreciated adequately. Results: We show how the use of different interaction data sets, such as those resulting from high- throughput or small-scale studies, and different modelling methodologies for the derivation pair- wise protein interactions, can dramatically change the topology of these networks. Furthermore, we show that some of the previously reported features identified in these networks may simply be the result of experimental or methodological errors and biases. Conclusion: When performing network-based studies, it is essential to define what is meant by the term interaction and this must b