title: Unveiling protein functions through the dynamics of the interaction network.
abstract: Protein interaction networks have become a tool to study biological processes, either for predicting molecular functions or for designing proper new drugs to regulate the main biological interactions. Furthermore, such networks are known to be organized in sub-networks of proteins contributing to the same cellular function. However, the protein function prediction is not accurate and each protein has traditionally been assigned to only one function by the network formalism. By considering the network of the physical interactions between proteins of the yeast together with a manual and single functional classification scheme, we introduce a method able to reveal important information on protein function, at both micro- and macro-scale. In particular, the inspection of the properties of oscillatory dynamics on top of the protein interaction network leads to the identification of misclassification problems in protein function assignments, as well as to unveil correct identification of protein functions. We also demonstrate that our approach can give a network representation of the meta-organization of biological processes by unraveling the interactions between different functional classes.
authors.affiliation: Complex Systems Group, Universidad Rey Juan Carlos, Madrid, Spain. irene.sendina@urjc.es
authors.forename: Irene
authors.initials: I
authors.lastname: Sendiña-Nadal
authors.forename: Yanay
authors.initials: Y
authors.lastname: Ofran
authors.forename: Juan A
authors.initials: JA
authors.lastname: Almendral
authors.forename: Javier M
authors.initials: JM
authors.lastname: Buldú
authors.forename: Inmaculada
authors.initials: I
authors.lastname: Leyva
authors.forename: Daqing
authors.initials: D
authors.lastname: Li
authors.forename: Shlomo
authors.initials: S
authors.lastname: Havlin
authors.forename: Stefano
authors.initials: S
authors.lastname: Boccaletti
mesh_terms: D000465:Algorithms; D011485:Protein Binding; D025941:Protein Interaction Mapping; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000145:classification / Q000378:metabolism*
chemical_list: D029701:Saccharomyces cerevisiae Proteins