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ABSTRACT: Modular architecture, which encompasses groups of genes/proteins involved in elementary biological functional units, is a basic form of the organisation of interacting proteins. Here, we propose a method that combines the Line Graph Transformation (LGT) and clique percolation-clustering algorithm to detect network modules, which may overlap each other in large sparse PPI networks. The resulting modules by the present method show a high coverage among yeast, fly, and worm PPI networks, respectively. Our analysis of the yeast PPI network suggests that most of these modules have well-biological significance in context of protein localisation, function annotation, and protein complexes.
International Journal of Data Mining and Bioinformatics 02/2009; 3(1):68-84. · 0.43 Impact Factor
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IJDMB. 01/2009; 3:68-84.
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ABSTRACT: With ever increasing amount of available data on protein-protein interaction (PPI) networks, understanding the topology of the networks and then biochemical processes in cells has become a key problem. Modular architecture which encompasses groups of genes/proteins involved in elementary biological functional units is a basic form of the organization of interacting proteins. Here we propose a method that combines the line graph transformation and clique percolation clustering algorithm to detect network modules which may overlap each other in large sparse protein-protein interaction (PPI) networks. The resulting modules by the present method show a high coverage among yeast, fly, and worm PPI networks respectively. Our analysis of the yeast PPI network suggests that most of these modules have well biological significance in context of protein localization, function annotation, and protein complexes
Data Mining Workshops, 2006. ICDM Workshops 2006. Sixth IEEE International Conference on; 01/2007
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Workshops Proceedings of the 6th IEEE International Conference on Data Mining (ICDM 2006), 18-22 December 2006, Hong Kong, China; 01/2006
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Computational Intelligence and Bioinformatics, International Conference on Intelligent Computing, ICIC 2006, Kunming, China, August 16-19, 2006. Proceedings, Part III; 01/2006
