MORO: a Cytoscape app for relationship analysis between modularity and robustness in large-scale biological networks.
BACKGROUND
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.


RESULTS
Accordingly, we developed a novel Cytoscape app called MORO, which can conveniently analyze the relationship between network modularity and robustness. We employed an existing algorithm to analyze the modularity of directed graphs and a Boolean network model for robustness calculation. 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. 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. 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. We tested the proposed app to analyze large signaling networks and showed an interesting relationship between network modularity and robustness.


CONCLUSIONS
Our app can be a promising tool which efficiently analyzes the relationship between modularity and robustness in large signaling networks.
Department of IT Convergence, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan, 680-749, Republic of Korea.
Cong-Doan
CD
Truong
Complex Network and Bioinformatics Group, Center for Research and Development, Hanoi University of Industry, Hanoi, Vietnam.
Tien-Dzung
TD
Tran
Department of IT Convergence, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan, 680-749, Republic of Korea. kwonyk@ulsan.ac.kr.
Yung-Keun
YK
Kwon
D019295:Computational Biology / Q000379:methods*; D063990:Gene Ontology; D012984:Software
Boolean network; Centrality; Cytoscape app; Gene-ontology; Modularity; Network robustness; OpenCL; Parallel computation