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 |
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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 > School of Infection & Immunity College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research |
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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