title: Determining the Significance of Protein Network Features and Attributes Using Permutation Testing.
abstract: Network analysis methods are increasing in popularity. An approach commonly applied to analyze proteomics data involves the use of protein-protein interaction (PPI) networks to explore the systems-level cooperation between proteins identified in a study. In this context, protein interaction networks can be used alongside the statistical analysis of proteomics data and traditional functional enrichment or pathway enrichment analyses. In network analysis it is possible to adjust for some of the complexities that arise due to the known, explicit interdependence between the measured quantities, in particular, differences in the number of interactions between proteins. Here we describe a method for calculating robust empirical p-values for protein interaction networks. We also provide a worked example with python code demonstrating the implementation of this methodology.
authors.affiliation: Systems Biology Laboratory, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC, 3010, Australia.|ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC, 3010, Australia.|Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
authors.forename: Joseph
authors.initials: J
authors.lastname: Cursons
authors.affiliation: Systems Biology Laboratory, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC, 3010, Australia.|Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.|Faculty of Medicine, Dentistry and Health Science, Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Davis
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012984:Software; D049490:Systems Biology; D064878:Web Browser; D057188:Workflow
chemical_list: D011506:Proteins
keywords: Computational systems biology; Network structure; PPI; PROSPERITI; Permutation testing; Protein interaction; Proteomics