title: Context-based retrieval of functional modules in protein-protein interaction networks.
abstract: Various techniques have been developed for identifying the most probable interactants of a protein under a given biological context. In this article, we dissect the effects of the choice of the protein-protein interaction network (PPI) and the manipulation of PPI settings on the network neighborhood of the influenza A virus (IAV) network, as well as hits in genome-wide small interfering RNA screen results for IAV host factors. We investigate the potential of context filtering, which uses text mining evidence linked to PPI edges, as a complement to the edge confidence scores typically provided in PPIs for filtering, for obtaining more biologically relevant network neighborhoods. Here, we estimate the maximum performance of context filtering to isolate a Kyoto Encyclopedia of Genes and Genomes (KEGG) network Ki from a union of KEGG networks and its network neighborhood. The work gives insights on the use of human PPIs in network neighborhood approaches for functional inference.
authors.affiliation: Swiss Institute of Bioinformatics, Quartier Sorge, bâtiment Génopode - Lausanne.
authors.forename: Maria Pamela
authors.initials: MP
authors.lastname: Dobay
authors.affiliation: University of Zurich.
authors.forename: Silke
authors.initials: S
authors.lastname: Stertz
authors.affiliation: Bioinformatics Core Facility at the Swiss Institute of Bioinformatics (SIB).
authors.forename: Mauro
authors.initials: M
authors.lastname: Delorenzi
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D057225:Data Mining; D053263:Gene Regulatory Networks; D055106:Genome-Wide Association Study / Q000706:statistics & numerical data; D000076662:Host Microbial Interactions / Q000235:genetics / Q000502:physiology; D006801:Humans; D009980:Influenza A virus / Q000235:genetics / Q000472:pathogenicity / Q000502:physiology; D025941:Protein Interaction Mapping / Q000706:statistics & numerical data; D060066:Protein Interaction Maps / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics
chemical_list: D034741:RNA, Small Interfering