title: Protein complex identification by supervised graph local clustering.
abstract: BACKGROUND
  Protein complexes integrate multiple gene products to coordinate many biological functions. Given a graph representing pairwise protein interaction data one can search for subgraphs representing protein complexes. Previous methods for performing such search relied on the assumption that complexes form a clique in that graph. While this assumption is true for some complexes, it does not hold for many others. New algorithms are required in order to recover complexes with other types of topological structure.
  
  
  RESULTS
  We present an algorithm for inferring protein complexes from weighted interaction graphs. By using graph topological patterns and biological properties as features, we model each complex subgraph by a probabilistic Bayesian network (BN). We use a training set of known complexes to learn the parameters of this BN model. The log-likelihood ratio derived from the BN is then used to score subgraphs in the protein interaction graph and identify new complexes. We applied our method to protein interaction data in yeast. As we show our algorithm achieved a considerable improvement over clique based algorithms in terms of its ability to recover known complexes. We discuss some of the new complexes predicted by our algorithm and determine that they likely represent true complexes.
  
  
  BACKGROUND
  Matlab implementation is available on the supporting website: www.cs.cmu.edu/~qyj/SuperComplex.
authors.affiliation: School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
authors.forename: Yanjun
authors.initials: Y
authors.lastname: Qi
authors.forename: Fernanda
authors.initials: F
authors.lastname: Balem
authors.forename: Christos
authors.initials: C
authors.lastname: Faloutsos
authors.forename: Judith
authors.initials: J
authors.lastname: Klein-Seetharaman
authors.forename: Ziv
authors.initials: Z
authors.lastname: Bar-Joseph
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D003198:Computer Simulation; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D020543:Proteome