title: Predicting physical interactions between protein complexes.
abstract: Protein complexes enact most biochemical functions in the cell. Dynamic interactions between protein complexes are frequent in many cellular processes. As they are often of a transient nature, they may be difficult to detect using current genome-wide screens. Here, we describe a method to computationally predict physical interactions between protein complexes, applied to both humans and yeast. We integrated manually curated protein complexes and physical protein interaction networks, and we designed a statistical method to identify pairs of protein complexes where the number of protein interactions between a complex pair is due to an actual physical interaction between the complexes. An evaluation against manually curated physical complex-complex interactions in yeast revealed that 50% of these interactions could be predicted in this manner. A community network analysis of the highest scoring pairs revealed a biologically sensible organization of physical complex-complex interactions in the cell. Such analyses of proteomes may serve as a guide to the discovery of novel functional cellular relationships.
authors: Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital and Oslo University Hospital, Oslo, Norway. trevor.clancy@rr-research.no
authors: Trevor
authors: T
authors: Clancy
authors: Einar Andreas
authors: EA
authors: Rødland
authors: Ståle
authors: S
authors: Nygard
authors: Eivind
authors: E
authors: Hovig
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D006801:Humans; D016013:Likelihood Functions; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000706:statistics & numerical data*; D060066:Protein Interaction Maps; D055503:Protein Multimerization; D020543:Proteome / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*
chemical_list: D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins