• Methods Mol. Biol. · Jan 2017

    Determining the Significance of Protein Network Features and Attributes Using Permutation Testing.

    • Joseph Cursons and Melissa J Davis.
    • Systems Biology Laboratory, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC, 3010, Australia.
    • Methods Mol. Biol. 2017 Jan 1; 1549: 199-208.

    AbstractNetwork 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.

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