Increasing confidence of protein interactomes using network topological metrics Supplementary Materials APPENDIX A ALTERNATIVE PATHS IN PROTEIN-PROTEIN INTERACTIONS

First, we analyzed protein-protein interaction (PPI) datasets from three different species (Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans) to investigate the extent to which alternative paths are present in PPI datasets. We focus here only on interactomes that are derived by the popular high-throughput assays such as Y2H. Then, we provide some actual examples in which the presence or absence of alternative paths can be used to increase or decrease the confidence of protein-protein interactions.