title: An analysis pipeline for the inference of protein-protein interaction networks.
abstract: We present a platform for the reconstruction of protein-protein interaction networks inferred from Mass Spectrometry (MS) bait-prey data. The Software Environment for Biological Network Inference (SEBINI), an environment for the deployment of network inference algorithms that use high-throughput data, forms the platform core. Among the many algorithms available in SEBINI is the Bayesian Estimator of Probabilities of Protein-Protein Associations (BEPro3) algorithm, which is used to infer interaction networks from such MS affinity isolation data. Also, the pipeline incorporates the Collective Analysis of Biological Interaction Networks (CABIN) software. We have thus created a structured workflow for protein-protein network inference and supplemental analysis.
authors.affiliation: Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory (US Department of Energy), Richland, WA 99352, USA. ronald.taylor@pnl.gov
authors.forename: Ronald C
authors.initials: RC
authors.lastname: Taylor
authors.forename: Mudita
authors.initials: M
authors.lastname: Singhal
authors.forename: Don S
authors.initials: DS
authors.lastname: Daly
authors.forename: Jason
authors.initials: J
authors.lastname: Gilmore
authors.forename: William R
authors.initials: WR
authors.lastname: Cannon
authors.forename: Kelly
authors.initials: K
authors.lastname: Domico
authors.forename: Amanda M
authors.initials: AM
authors.lastname: White
authors.forename: Deanna L
authors.initials: DL
authors.lastname: Auberry
authors.forename: Kenneth J
authors.initials: KJ
authors.lastname: Auberry
authors.forename: Brian S
authors.initials: BS
authors.lastname: Hooker
authors.forename: Greg
authors.initials: G
authors.lastname: Hurst
authors.forename: Jason E
authors.initials: JE
authors.lastname: McDermott
authors.forename: W Hayes
authors.initials: WH
authors.lastname: McDonald
authors.forename: Dale A
authors.initials: DA
authors.lastname: Pelletier
authors.forename: Denise
authors.initials: D
authors.lastname: Schmoyer
authors.forename: H Steven
authors.initials: HS
authors.lastname: Wiley
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D013058:Mass Spectrometry; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software
chemical_list: D011506:Proteins