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Open Access Highly Accessed Research article

The yeast kinome displays scale free topology with functional hub clusters

Robin EC Lee12 and Lynn A Megeney12*

Author Affiliations

1 Ottawa Health Research Institute, Molecular Medicine Program, Ottawa, Canada

2 University of Ottawa, Department of Cellular and Molecular Medicine, Ottawa, Canada

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BMC Bioinformatics 2005, 6:271  doi:10.1186/1471-2105-6-271

Published: 9 November 2005

Abstract

Background

The availability of interaction databases provides an opportunity for researchers to utilize immense amounts of data exclusively in silico. Recently there has been an emphasis on studying the global properties of biological interactions using network analysis. While this type of analysis offers a wide variety of global insights it has surprisingly not been used to examine more localized interactions based on mechanism. In as such we have particular interest in the role of key topological components in signal transduction cascades as they are vital regulators of healthy and diseased cell states.

Results

We have used publicly available databases and a novel software tool termed Hubview to model the interactions of a subset of the yeast interactome, specifically protein kinases and their interaction partners. Analysis of the connectivity distribution has inferred a fat-tailed degree distribution with parameters consistent with those found in other biological networks. In addition, Hubview identified a functional clustering of a large group of kinases, distributed between three separate groupings. The complexity and average degree for each of these clusters is indicative of a specialized function (cell cycle propagation, DNA repair and pheromone response) and relative age for each cluster.

Conclusion

Using connectivity analysis on a functional subset of proteins we have evidence that reinforces the scale free topology as a model for protein network evolution. We have identified the hub components of the kinase network and observed a tendency for these kinases to cluster together on a functional basis. As such, these results suggest an inherent trend to preserve scale free characteristics at a domain based modular level within large evolvable networks.