NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families.

Hyun-Myung Woo,Hyundoo Jeong,Byung-Jun Yoon,Yang Zhang

doi:10.1371/journal.pone.0227598

Abstract

Comparative network analysis provides effective computational means for gaining novel insights into the structural and functional compositions of biological networks. In recent years, various methods have been developed for biological network alignment, whose main goal is to identify important similarities and critical differences between networks in terms of their topology and composition. A major impediment to advancing network alignment techniques has been the lack of gold-standard benchmarks that can be used for accurate and comprehensive performance assessment of such algorithms. The original NAPAbench (network alignment performance assessment benchmark) was developed to address this problem, and it has been widely utilized by many researchers for the development, evaluation, and comparison of novel network alignment techniques. In this work, we introduce NAPAbench 2—a major update of the original NAPAbench that was introduced in 2012. NAPAbench 2 includes a completely redesigned network synthesis algorithm that can generate protein-protein interaction (PPI) network families whose characteristics closely match those of the latest real PPI networks. Furthermore, the network synthesis algorithm comes with an intuitive GUI that allows users to easily generate PPI network families with an arbitrary number of networks of any size, according to a flexible user-defined phylogeny. In addition, NAPAbench 2 provides updated benchmark datasets—created using the redesigned network synthesis algorithm—which can be used for comprehensive performance assessment of network alignment algorithms and their scalability.

Highlights

Comparative network analysis through local or global network alignment provides effective computational means to identify orthologous proteins and conserved functional modules across biological networks of different species
NAPAbench 2 consists of benchmarks that consist of families of networks generated by new and/or updated network synthesis models, whose characteristics closely resemble those of the latest real protein-protein interaction (PPI) networks
NAPAbench performs a bifurcation process along a given phylogenetic tree in order to synthesize a set of realistic PPI network families that are biologically related to each other

Summary

Introduction

Comparative network analysis through local or global network alignment provides effective computational means to identify orthologous proteins and conserved functional modules (e.g., molecular complexes or pathways) across biological networks of different species. One of the major barriers slowing down further advances in comparative network analysis research has been the lack of a gold standard benchmark that allows a fair and comprehensive performance assessment of comparative network analysis algorithms. To overcome this barrier, NAPAbench (Network Alignment Performance Assessment benchmark)—probably the first comprehensive synthetic benchmark for network alignment—was released in 2012 [2]. NAPAbench 2 consists of benchmarks that consist of families of networks generated by new and/or updated network synthesis models, whose characteristics closely resemble those of the latest real PPI networks. The new release of NAPAbench is accompanied by a network synthesis tool with an intuitive and user-friendly interface, which allows users to create additional benchmarks that consist of network families with an arbitrary number of networks of any size, according to a user-specified phylogeny

Materials and methods

Results

Concluding remarks