Title: An analysis pipeline for the inference of protein-protein interaction networks

Authors: Ronald C. Taylor, Mudita Singhal, Don S. Daly, Jason Gilmore, William R. Cannon, Kelly Domico, Amanda M. White, Deanna L. Auberry, Kenneth J. Auberry, Brian S. Hooker, Greg Hurst, Jason E. McDermott, W. Hayes McDonald, Dale A. Pelletier, Denise Schmoyer, H. Steven Wiley

Addresses: Computational Biology and Bioinformatics Group, Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory (US Department of Energy), P.O. Box 999, MS K7-90, Richland, WA 99352, USA. ' Computational Biology and Bioinformatics Group, Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory (US Department of Energy), P.O. Box 999, MS K7-90, Richland, WA 99352, USA. ' Pacific Northwest National Laboratory (US Department of Energy), SIGMA2/room 313B, Mail Stop K6-08, P.O. Box 999, Richland, WA 99352, USA. ' HB 7560, One Medical Center Drive, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA. ' Computational Biology and Bioinformatics Group, Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory (US Department of Energy), P.O. Box 999, MS K7-90, Richland, WA 99352, USA. ' Pacific Northwest National Laboratory, Battelle Seattle Research Center, 1100 Dexter Avenue North, Suite 400, Seattle, 98109 Washington, USA. ' Pacific Northwest National Laboratory (US Department of Energy), SIGMA2/room 521, Mail Stop K6-08, P.O. Box 999, Richland, WA 99352, USA. ' Pacific Northwest National Laboratory (US Department of Energy), BSEL/room 121, Mail Stop P8-60, P.O. Box 999, Richland, WA 99352, USA. ' Pacific Northwest National Laboratory (US Department of Energy), EMSL/room 2172, Mail Stop K8-91, P.O. Box 999, Richland, WA 99352, USA. ' Pacific Northwest National Laboratory (US Department of Energy), LSL2/room 1515, Mail Stop K4-12, P.O. Box 999, Richland, WA 99352, USA. ' Oak Ridge National Laboratory, Mail Stop 6131, P.O. Box 2008, Oak Ridge, TN 37831-6131, USA. ' Computational Biology and Bioinformatics Group, Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory (US Department of Energy), P.O. Box 999, MS K7-90, Richland, WA 99352, USA. ' Mass Spectrometry Research Center, Vanderbilt University, School of Medicine, 465 21St. Ave. South, Nashville, TN 37232, USA. ' Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA. ' Oak Ridge National Laboratory, Mail Stop 6164, P.O. Box 2008, Oak Ridge, TN 37831, USA. ' Pacific Northwest National Laboratory (US Department of Energy), P.O. Box 999, MS K7-90, Richland, WA 99352, USA

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.

Keywords: network inference pipeline; protein-protein interactions; biological networks; mass spectrometry; Bayesian estimator; bait-prey data; bioinformatics; protein-protein associations; structured workflow.

DOI: 10.1504/IJDMB.2009.029204

International Journal of Data Mining and Bioinformatics, 2009 Vol.3 No.4, pp.409 - 430

Published online: 09 Nov 2009 *

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