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An analysis pipeline for the inference of protein-protein interaction networks...

Publication Type
Journal
Journal Name
International Journal of Data Mining and Bioinformatics
Publication Date
Page Numbers
409 to 430
Volume
3
Issue
4
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.