title: An experimentally derived confidence score for binary protein-protein interactions.
abstract: Information on protein-protein interactions is of central importance for many areas of biomedical research. At present no method exists to systematically and experimentally assess the quality of individual interactions reported in interaction mapping experiments. To provide a standardized confidence-scoring method that can be applied to tens of thousands of protein interactions, we have developed an interaction tool kit consisting of four complementary, high-throughput protein interaction assays. We benchmarked these assays against positive and random reference sets consisting of well documented pairs of interacting human proteins and randomly chosen protein pairs, respectively. A logistic regression model was trained using the data from these reference sets to combine the assay outputs and calculate the probability that any newly identified interaction pair is a true biophysical interaction once it has been tested in the tool kit. This general approach will allow a systematic and empirical assignment of confidence scores to all individual protein-protein interactions in interactome networks.
authors.affiliation: Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA.
authors.forename: Pascal
authors.initials: P
authors.lastname: Braun
authors.forename: Murat
authors.initials: M
authors.lastname: Tasan
authors.forename: Matija
authors.initials: M
authors.lastname: Dreze
authors.forename: Miriam
authors.initials: M
authors.lastname: Barrios-Rodiles
authors.forename: Irma
authors.initials: I
authors.lastname: Lemmens
authors.forename: Haiyuan
authors.initials: H
authors.lastname: Yu
authors.forename: Julie M
authors.initials: JM
authors.lastname: Sahalie
authors.forename: Ryan R
authors.initials: RR
authors.lastname: Murray
authors.forename: Luba
authors.initials: L
authors.lastname: Roncari
authors.forename: Anne-Sophie
authors.initials: AS
authors.lastname: de Smet
authors.forename: Kavitha
authors.initials: K
authors.lastname: Venkatesan
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Rual
authors.forename: Jean
authors.initials: J
authors.lastname: Vandenhaute
authors.forename: Michael E
authors.initials: ME
authors.lastname: Cusick
authors.forename: Tony
authors.initials: T
authors.lastname: Pawson
authors.forename: David E
authors.initials: DE
authors.lastname: Hill
authors.forename: Jan
authors.initials: J
authors.lastname: Tavernier
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Wrana
authors.forename: Frederick P
authors.initials: FP
authors.lastname: Roth
authors.forename: Marc
authors.initials: M
authors.lastname: Vidal
mesh_terms: D000818:Animals; D006801:Humans; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000032:analysis* / Q000378:metabolism*; D012680:Sensitivity and Specificity
chemical_list: D011506:Proteins