An analysis pipeline for the inferenceof protein-protein interaction networks

Journal Article · Tue Sep 01 00:00:00 EDT 2009 · International Journal of Data Mining and Bioinformatics

DOI:https://doi.org/10.1504/IJDMB.2009.029204· OSTI ID:979199

Taylor, Ronald C ^[1]; Singhal, Mudita ^[1]; Daly, Don S ^[1]; Gilmore, Jason ^[1]; Cannon, Bill ^[1]; Domico, Kelly ^[1]; White, Amanda M ^[1]; Auberry, Deanna L ^[2]; Auberry, Kenneth J ^[2]; Hooker, Brian ^[1]; McDermott, Jason ^[1]; McDonald, W Hayes ^[2]; Pelletier, Dale A ^[2]; Schmoyer, Denise D ^[2]; Wiley, Steven ^[1]

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1. Pacific Northwest National Laboratory (PNNL)
2. ORNL

We present an integrated platform that is used for the reconstruction and analysis of protein-protein interaction networks inferred from Mass Spectrometry (MS) bait-prey experiment data. At the heart of this pipeline is the Software Environment for Biological Network Inference (SEBINI), an interactive environment for the deployment and testing of network inference algorithms that use high-throughput data. 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. For integration, comparison and analysis of the inferred protein-protein interactions with interaction evidence obtained from multiple public sources, the pipeline connects to the Collective Analysis of Biological Interaction Networks (CABIN) software. Incorporating BEPro3 into SEBINI and automatically feeding the resulting inferred network into CABIN, we have created a structured workflow for protein-protein network inference and supplemental analysis from sets of MS bait-prey experiments.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 979199
• Journal Information: International Journal of Data Mining and Bioinformatics, Vol. 3, Issue 4
• Country of Publication: United States
• Language: English