Abstract
BackgroundCharacterizing the structural properties of protein interaction networks will help illuminate the organizational and functional relationships among elements in biological systems.ResultsIn this paper, we present a systematic exploration of the core/periphery structures in protein interaction networks (PINs). First, the concepts of cores and peripheries in PINs are defined. Then, computational methods are proposed to identify two types of cores, k-plex cores and star cores, from PINs. Application of these methods to a yeast protein interaction network has identified 110 k-plex cores and 109 star cores. We find that the k-plex cores consist of either "party" proteins, "date" proteins, or both. We also reveal that there are two classes of 1-peripheral proteins: "party" peripheries, which are more likely to be part of protein complex, and "connector" peripheries, which are more likely connected to different proteins or protein complexes. Our results also show that, besides connectivity, other variations in structural properties are related to the variation in biological properties. Furthermore, the negative correlation between evolutionary rate and connectivity are shown toysis. Moreover, the core/periphery structures help to reveal the existence of multiple levels of protein expression dynamics.ConclusionOur results show that both the structure and connectivity can be used to characterize topological properties in protein interaction networks, illuminating the functional organization of cellular systems.
Highlights
Characterizing the structural properties of protein interaction networks will help illuminate the organizational and functional relationships among elements in biological systems
Cores/peripheries are identified from the yeast PIN (YPIN) Our KL-like algorithm has identified 110 k-plex cores with size of no less than six from the YPIN
Most of the k-plex cores are part of protein complexes according to the MIPS protein complex database [13]
Summary
Characterizing the structural properties of protein interaction networks will help illuminate the organizational and functional relationships among elements in biological systems. Studying the structure of biological networks will help elucidate the organization and functional relationships of elements in cellular systems. Guimera et al [9] classified the roles of nodes in complex networks according to their properties inside sub-network "modules". Their classification depended on dissecting the network into modules using a simulated (page number not for citation purposes). Application of the method of Guimera and Amaral [12] to separate the yeast PIN from MIPS [13] into modules showed that these structurally-defined modules did not show a significant correlation with biological functional units. We explore the role of proteins in PIN based on core/periphery structures
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