title: Systems-level analyses identify extensive coupling among gene expression machines.
abstract: Here, we develop computational methods to assess and consolidate large, diverse protein interaction data sets, with the objective of identifying proteins involved in the coupling of multicomponent complexes within the yeast gene expression pathway. From among approximately 43 000 total interactions and 2100 proteins, our methods identify known structural complexes, such as the spliceosome and SAGA, and functional modules, such as the DEAD-box helicases, within the interaction network of proteins involved in gene expression. Our process identifies and ranks instances of three distinct, biologically motivated motifs, or patterns of coupling among distinct machineries involved in different subprocesses of gene expression. Our results confirm known coupling among transcription, RNA processing, and export, and predict further coupling with translation and nonsense-mediated decay. We systematically corroborate our analysis with two independent, comprehensive experimental data sets. The methods presented here may be generalized to other biological processes and organisms to generate principled, systems-level network models that provide experimentally testable hypotheses for coupling among biological machines.
authors.affiliation: Bauer Center for Genomics Research, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Karolina
authors.initials: K
authors.lastname: Maciag
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Altschuler
authors.forename: Michael D
authors.initials: MD
authors.lastname: Slack
authors.forename: Nevan J
authors.initials: NJ
authors.lastname: Krogan
authors.forename: Andrew
authors.initials: A
authors.lastname: Emili
authors.forename: Jack F
authors.initials: JF
authors.lastname: Greenblatt
authors.forename: Tom
authors.initials: T
authors.lastname: Maniatis
authors.forename: Lani F
authors.initials: LF
authors.lastname: Wu
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D005656:Fungal Proteins / Q000235:genetics / Q000502:physiology; D015870:Gene Expression; D015966:Gene Expression Regulation, Fungal; D046912:Multiprotein Complexes; D015003:Yeasts / Q000235:genetics*
chemical_list: D005656:Fungal Proteins; D046912:Multiprotein Complexes