title: Large-scale identification of yeast integral membrane protein interactions.
abstract: We carried out a large-scale screen to identify interactions between integral membrane proteins of Saccharomyces cerevisiae by using a modified split-ubiquitin technique. Among 705 proteins annotated as integral membrane, we identified 1,985 putative interactions involving 536 proteins. To ascribe confidence levels to the interactions, we used a support vector machine algorithm to classify interactions based on the assay results and protein data derived from the literature. Previously identified and computationally supported interactions were used to train the support vector machine, which identified 131 interactions of highest confidence, 209 of the next highest confidence, 468 of the next highest, and the remaining 1,085 of low confidence. This study provides numerous putative interactions among a class of proteins that have been difficult to analyze on a high-throughput basis by other approaches. The results identify potential previously undescribed components of established biological processes and roles for integral membrane proteins of ascribed functions.
authors.affiliation: Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
authors.forename: John P
authors.initials: JP
authors.lastname: Miller
authors.forename: Russell S
authors.initials: RS
authors.lastname: Lo
authors.forename: Asa
authors.initials: A
authors.lastname: Ben-Hur
authors.forename: Cynthia
authors.initials: C
authors.lastname: Desmarais
authors.forename: Igor
authors.initials: I
authors.lastname: Stagljar
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
authors.forename: Stanley
authors.initials: S
authors.lastname: Fields
mesh_terms: D000465:Algorithms; D008565:Membrane Proteins / Q000235:genetics*; D025941:Protein Interaction Mapping / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D025801:Ubiquitin
chemical_list: D008565:Membrane Proteins; D029701:Saccharomyces cerevisiae Proteins; D025801:Ubiquitin