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

Hakes, L., Robertson, D. L. and Oliver, S. G. (2005) Effect of dataset selection on the topological interpretation of protein interaction networks. BMC Genomics, 6, 131. (doi:10.1186/1471-2164-6-131) (PMID:16174296) (PMCID:PMC1249571)

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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 highthroughput or small-scale studies, and different modelling methodologies for the derivation pairwise 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 be taken into account when interpreting the topologies of the networks generated. Consideration must be given to the type of data included and appropriate controls that take into account the idiosyncrasies of the data must be selected.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Robertson, Professor David
Authors: Hakes, L., Robertson, D. L., and Oliver, S. G.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:BMC Genomics
Publisher:Biomed Central
ISSN:1471-2164
ISSN (Online):1471-2164
Copyright Holders:Copyright © 2005 Hakes et al.
First Published:First published in BMC Genomics 6: 131
Publisher Policy:Reproduced under a Creative Commons License

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