Discover Protein Complexes in Protein-Protein Interaction Networks Using Parametric Local Modularity

Background: Recent advances in proteomic technologies have enabled us to create detailed protein-protein interaction maps in multiple species and in both normal and diseased cells. As the size of the interaction dataset increases, powerful computational methods are required in order to effectively distil network models from largescale interactome data. Results: We present an algorithm, miPALM (Module Inference by Parametric Local Modularity), to infer protein complexes in a protein-protein interaction network. The algorithm uses a novel graph theoretic measure, parametric local modularity, to identify highly connected sub-networks as candidate protein complexes. Using gold standard sets of protein complexes and protein function and localization annotations, we show our algorithm achieved an overall improvement over previous algorithms in terms of precision, recall, and biological relevance of the predicted complexes. We applied our algorithm to predict and characterize a set of 138 no...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Jongkwang Kim, Kai Tan
• Keywords: BMCBI 2010, Parametric Local Modularity, Protein Complexes, Protein-protein Interactions