Characterisation of protein-protein interaction network base on ℓ1-norm optimisation

Knowledge of interactions between proteins is an importance piece of information on the understanding of cellular mechanism. One of the challenges is to quantify how similar the two protein-protein interaction (PPI) networks. To provide a candidate solution of this problem, a distance measure for PPI networks is proposed. This distance measure involves solving an optimisation problem with which the objective function being a weighted sum of topological and biological measure of an alignment respectively. To solve this problem, the projected subgradient method is employed. To illustrate the performance and usage of this distance measure, it is applied to the PPI networks of herpesvirus family. Five herpesviruses: EpsteinBarr virus (EBV), Herpes simplex virus (HSV), Mouse Cytomegalovirus (mCMV), Kaposi´s sarcoma-associated herpesvirus (KSHV) and Varicella zoster virus (VZV) are considered in this paper. PPI network distances of the five her-pesviruses are computed and visualized using multidimensional scaling (MDS). Results show that the distance measure can reflect the dissimilarity among organisms. In addition our algorithm can also separate herpesvirus subfamilies given only topological information of the PPI network.