![]() ![]() These plugins have a limitation, though, in that they focus only on the structural analysis of a network and its visualization, without any consideration of dynamics analysis. Another well-known plugin is NeMo, which can identify diverse network communities by means of a neighbor-sharing score based on a hierarchical agglomerative clustering method. GIANT was proposed to investigate topological or functional relationships in a metabolic network by performing a clustering analysis and a functional cartography of nodes. For example, clusterMaker implemented several clustering algorithms such as k-means, k-medoid, SCPS, and AutoSOME to visualize a structure of modules within biological networks. Many plugins based on the Cytoscape platform have been developed for modularity analysis in biological networks. A highly modularized network has dense connectivity between the nodes within each module but sparse connectivity between the nodes of different modules. Network modularity represents the degree to which a network is divided into modules of separate community structures. Our app can be a promising tool which efficiently analyzes the relationship between modularity and robustness in large signaling networks. We tested the proposed app to analyze large signaling networks and showed an interesting relationship between network modularity and robustness. The app provides various visualization modes to better elucidate topological relations between modules, and tabular results of centrality and gene ontology enrichment analyses of modules. A batch-mode simulation function was also developed to verify whether an observed relationship between modularity and robustness is conserved in a large set of randomly structured networks. In particular, to ensure the robustness algorithm’s applicability to large-scale networks, we implemented it as a parallel algorithm by using the OpenCL library. We employed an existing algorithm to analyze the modularity of directed graphs and a Boolean network model for robustness calculation. ResultsĪccordingly, we developed a novel Cytoscape app called MORO, which can conveniently analyze the relationship between network modularity and robustness. ![]() Although there have been many studies revealing that dynamic robustness of a biological network is related to its modularity characteristics, no proper tool exists to investigate the relation between network dynamics and modularity.
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