%0 Journal Article
%T Partitioning a PPI Network into Overlapping Modules Constrained by High-Density and Periphery Tracking
%A Md. Altaf-Ul-Amin
%A Masayoshi Wada
%A Shigehiko Kanaya
%J ISRN Biomathematics
%D 2012
%R 10.5402/2012/726429
%X This paper presents an algorithm called DPClusO for partitioning simple graphs into overlapping modules, that is, clusters constrained by density and periphery tracking. The major advantages of DPClusO over the related and previously published algorithm DPClus are shorter running time and ensuring coverage, that is, each node goes to at least one module. DPClusO is a general-purpose clustering algorithm and useful for finding overlapping cohesive groups in a simple graph for any type of application. This work shows that the modules generated by DPClusO from several PPI networks of yeast with high-density constraint match with more known complexes compared to some other recently published complex generating algorithms. Furthermore, the biological significance of the high density modules has been demonstrated by comparing their P values in the context of Gene Ontology (GO) terms with those of the randomly generated modules having the same size, distribution, and zero density. As a consequence, it was also learnt that a PPI network is a combination of mainly high-density and star-like modules. 1. Introduction The ability to generate comprehensive datasets incorporating all biological molecules and their interactions at different omics levels has led to the emergence of system biology. Cellular functions rely on the coordinated actions of multiple genes, RNAs, proteins, and metabolites. Therefore, organizing biological information in the context of networks is important for holistic understanding of biological systems. Some characteristics of the biological networks are that they are complex, autonomous, robust, function to execute physicochemical processes, and are conserved but can adjust [1]. Constructing biological networks by integrating information piece by piece has led to the discovery of emergent topological properties in terms of degree distribution, average path length, clustering coefficient, robustness, and so forth. These emergent properties of biological networks are quite distinct compared to those of the randomized networks of the same size and could not be understood by analyzing an individual or a small group of components. On the other hand networks having the same global topological property for example, degree distributionn may have different local topologies [2]. Analyzing these local topologies is useful to understand the design principles of biological networks and the functions of the individual components. A feature for many networks including biological networks is their modular organization. Modularity is a property that allows
%U http://www.hindawi.com/journals/isrn.biomathematics/2012/726429/