Decomposing PPI networks for complex discovery

Abstract--Protein complexes are important for understanding principles of cellular organization and functions. With the availability of large amounts of high-throughput proteinprotein interactions (PPI), many algorithms have been proposed to discover protein complexes from PPI networks. However, none of existing algorithms takes into consideration the fact that not all the interactions in a PPI network take place at the same time. As a result, predicted complexes often contain many spuriously included proteins, precluding them from matching true complexes. We propose two methods to tackle this problem: (1) We utilize cellular component Gene Ontology (GO) terms to decompose PPI networks into several smaller networks such that the proteins in each decomposed network are annotated with the same cellular component GO term. (2) Hub proteins are more likely to fuse clusters that correspond to different complexes. To avoid this, we remove hub proteins from PPI networks, and then apply a compl...

• Type: Journal
• Year: 2010
• Where: BIBM
• Authors: Guimei Liu, Chern Han Yong, Limsoon Wong, Hon Nian Chua
• Keywords: BIBM 2010, Bioinformatics, Hub Proteins, Ppi Network, Proteins