title: Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins.
abstract: BACKGROUND
  Protein-protein interactions play a key role in biological processes of proteins within a cell. Recent high-throughput techniques have generated protein-protein interaction data in a genome-scale. A wide range of computational approaches have been applied to interactome network analysis for uncovering functional organizations and pathways. However, they have been challenged because of complex connectivity. It has been investigated that protein interaction networks are typically characterized by intrinsic topological features: high modularity and hub-oriented structure. Elucidating the structural roles of modules and hubs is a critical step in complex interactome network analysis.
  
  
  RESULTS
  We propose a novel approach to convert the complex structure of an interactome network into hierarchical ordering of proteins. This algorithm measures functional similarity between proteins based on the path strength model, and reveals a hub-oriented tree structure hidden in the complex network. We score hub confidence and identify functional modules in the tree structure of proteins, retrieved by our algorithm. Our experimental results in the yeast protein interactome network demonstrate that the selected hubs are essential proteins for performing functions. In network topology, they have a role in bridging different functional modules. Furthermore, our approach has high accuracy in identifying functional modules hierarchically distributed.
  
  
  CONCLUSIONS
  Decomposing, converting, and synthesizing complex interaction networks are fundamental tasks for modeling their structural behaviors. In this study, we systematically analyzed complex interactome network structures for retrieving functional information. Unlike previous hierarchical clustering methods, this approach dynamically explores the hierarchical structure of proteins in a global view. It is well-applicable to the interactome networks in high-level organisms because of its efficiency and scalability.
authors.affiliation: Department of Computer Science Baylor University, Waco, TX 76798, USA. young-rae_cho@baylor.edu
authors.forename: Young-Rae
authors.initials: YR
authors.lastname: Cho
authors.forename: Aidong
authors.initials: A
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D005656:Fungal Proteins / Q000737:chemistry* / Q000378:metabolism; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping / Q000379:methods*; D015003:Yeasts / Q000378:metabolism
chemical_list: D005656:Fungal Proteins