ModuleRole: A Tool for Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks

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ModuleRole: A Tool for Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks

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Title: ModuleRole: A Tool for Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks
Author(s):
Li, GuiPeng;
Li, Ming;
Zhang, YiWei;
Wang, Dong;
Li, Rong;
Guimera, Roger;
Gao, Juntao Tony;
Zhang, Michael Q.
Date Created: 2014-05-01
Item Type: Article
Keywords: Show Keywords
Abstract: Rapidly increasing amounts of (physical and genetic) protein-protein interaction (PPI) data are produced by various high-throughput techniques, and interpretation of these data remains a major challenge. In order to gain insight into the organization and structure of the resultant large complex networks formed by interacting molecules, using simulated annealing, a method based on the node connectivity, we developed ModuleRole, a user-friendly web server tool which finds modules in PPI network and defines the roles for every node, and produces files for visualization in Cytoscape and Pajek. For given proteins, it analyzes the PPI network from BioGRID database, finds and visualizes the modules these proteins form, and then defines the role every node plays in this network, based on two topological parameters Participation Coefficient and Z-score. This is the first program which provides interactive and very friendly interface for biologists to find and visualize modules and roles of proteins in PPI network. It can be tested online at the website http://www.bioinfo.org/modulerole/index.php, which is free and open to all users and there is no login requirement, with demo data provided by "User Guide'' in the menu Help. Non-server application of this program is considered for high-throughput data with more than 200 nodes or user's own interaction datasets. Users are able to bookmark the web link to the result page and access at a later time. As an interactive and highly customizable application, ModuleRole requires no expert knowledge in graph theory on the user side and can be used in both Linux and Windows system, thus a very useful tool for biologist to analyze and visualize PPI networks from databases such as BioGRID. Availability: ModuleRole is implemented in Java and C, and is freely available at http://www.bioinfo.org/modulerole/index.php. Supplementary information (user guide, demo data) is also available at this website. API for ModuleRole used for this program can be obtained upon request.
Publisher: Public Library of Science
ISSN: 1932-6203
Source: PLOS One
Link to Related Resource: http://dx.doi.org/10.1371/journal.pone.0094608
Persistent Link: http://hdl.handle.net/10735.1/3915
Bibliographic Citation: Li, GuiPeng, Ming Li, YiWei Zhang, Dong Wang, et al. 2014. "ModuleRole: A tool for modulization, role determination and visualization in protein-protein interaction networks." PLOS One 9(5): e94608-1 to 11.
Terms of Use: CC BY 4.0 Attribution
©2014 The Authors
Sponsors: "This work was supported by National Institute of Health (R01GM057063), the One Thousand Talents Scheme (2012CB316503, 985 QianRen program, 553303001), and Tsinghua University talents support program to J. Gao (553403003)."

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CC BY 4.0 Attribution Except where otherwise noted, this item's license is described as CC BY 4.0 Attribution