a network synthesis model for generating protein interaction network families一个网络合成模型生成蛋白质相互作用网络的家庭.pdfVIP

A Network Synthesis Model for Generating Protein Interaction Network Families Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon* Department of Electrical and Computer Engineering, Texas AM University, College Station, Texas, United States of America Abstract In this work, we introduce a novel network synthesis model that can generate families of evolutionarily related synthetic protein–protein interaction (PPI) networks. Given an ancestral network, the proposed model generates the network family according to a hypothetical phylogenetic tree, where the descendant networks are obtained through duplication and divergence of their ancestors, followed by network growth using network evolution models. We demonstrate that this network synthesis model can effectively create synthetic networks whose internal and cross-network properties closely resemble those of real PPI networks. The proposed model can serve as an effective framework for generating comprehensive benchmark datasets that can be used for reliable performance assessment of comparative network analysis algorithms. Using this model, we constructed a large-scale network alignment benchmark, called NAPAbench, and evaluated the performance of several representative network alignment algorithms. Our analysis clearly shows the relative performance of the leading network algorithms, with their respective advantages and disadvantages. The algorithm and source code of the network synthesis model and the network alignment benchmark NAPAbench are publicly available at /bjyoon/NAPAbench/. Citation: Sahraeian SME, Yoon B-J (2012) A Network Synthesis Model for Generating Protein Interaction Network Families. PLoS ONE 7(8): e41474. doi:10.1371/ journal.pone.0041474 Editor: Franca Fraternali, King’s College London,