title: Pepper: cytoscape app for protein complex expansion using protein-protein interaction networks.
abstract: We introduce Pepper (Protein complex Expansion using Protein-Protein intERactions), a Cytoscape app designed to identify protein complexes as densely connected subnetworks from seed lists of proteins derived from proteomic studies. Pepper identifies connected subgraph by using multi-objective optimization involving two functions: (i) the coverage, a solution must contain as many proteins from the seed as possible, (ii) the density, the proteins of a solution must be as connected as possible, using only interactions from a proteome-wide interaction network. Comparisons based on gold standard yeast and human datasets showed Pepper's integrative approach as superior to standard protein complex discovery methods. The visualization and interpretation of the results are facilitated by an automated post-processing pipeline based on topological analysis and data integration about the predicted complex proteins. Pepper is a user-friendly tool that can be used to analyse any list of proteins.
  
  
  BACKGROUND
  Pepper is available from the Cytoscape plug-in manager or online (http://apps.cytoscape.org/apps/pepper) and released under GNU General Public License version 3.
authors.affiliation: iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbruères, 91030 Evry Cedex, France, School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and UMR 144 CNRS/Institut Curie, 26 rue d'Ulm, Paris, 75248 cedex 05, France iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbruères, 91030 Evry Cedex, France, School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and UMR 144 CNRS/Institut Curie, 26 rue d'Ulm, Paris, 75248 cedex 05, France.
authors.forename: C
authors.initials: C
authors.lastname: Winterhalter
authors.affiliation: iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbruères, 91030 Evry Cedex, France, School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and UMR 144 CNRS/Institut Curie, 26 rue d'Ulm, Paris, 75248 cedex 05, France iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbruères, 91030 Evry Cedex, France, School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and UMR 144 CNRS/Institut Curie, 26 rue d'Ulm, Paris, 75248 cedex 05, France.
authors.forename: R
authors.initials: R
authors.lastname: Nicolle
authors.affiliation: iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbruères, 91030 Evry Cedex, France, School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and UMR 144 CNRS/Institut Curie, 26 rue d'Ulm, Paris, 75248 cedex 05, France.
authors.forename: A
authors.initials: A
authors.lastname: Louis
authors.affiliation: iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbruères, 91030 Evry Cedex, France, School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and UMR 144 CNRS/Institut Curie, 26 rue d'Ulm, Paris, 75248 cedex 05, France.
authors.forename: C
authors.initials: C
authors.lastname: To
authors.affiliation: iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbruères, 91030 Evry Cedex, France, School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and UMR 144 CNRS/Institut Curie, 26 rue d'Ulm, Paris, 75248 cedex 05, France.
authors.forename: F
authors.initials: F
authors.lastname: Radvanyi
authors.affiliation: iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbruères, 91030 Evry Cedex, France, School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and UMR 144 CNRS/Institut Curie, 26 rue d'Ulm, Paris, 75248 cedex 05, France.
authors.forename: M
authors.initials: M
authors.lastname: Elati
mesh_terms: D000465:Algorithms; D006801:Humans; D025941:Protein Interaction Mapping / Q000379:methods*; D040901:Proteomics; D012984:Software