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

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dc.contributor.ISNI0000 0001 1707 1372 (Zhang, MQ)
dc.contributor.LCNA99086074‏ ‎(Zhang, MQ)
dc.contributor.authorLi, GuiPengen_US
dc.contributor.authorLi, Mingen_US
dc.contributor.authorZhang, YiWeien_US
dc.contributor.authorWang, Dongen_US
dc.contributor.authorLi, Rongen_US
dc.contributor.authorGuimera, Rogeren_US
dc.contributor.authorGao, Juntao Tonyen_US
dc.contributor.authorZhang, Michael Q.en_US
dc.contributor.utdAuthorZhang, Michael Q.en_US
dc.date.accessioned2014-08-22T17:11:04Z
dc.date.available2014-08-22T17:11:04Z
dc.date.created2014-05-01en_US
dc.date.issued2014-05-01en_US
dc.description.abstractRapidly 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.en_US
dc.description.sponsorship"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)."en_US
dc.identifier.bibliographicCitationLi, 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.en_US
dc.identifier.issn1932-6203en_US
dc.identifier.issue5en_US
dc.identifier.urihttp://hdl.handle.net/10735.1/3915
dc.identifier.volume9en_US
dc.language.isoenen_US
dc.publisherPublic Library of Scienceen_US
dc.relation.urihttp://dx.doi.org/10.1371/journal.pone.0094608
dc.rightsCC BY 4.0 Attributionen_US
dc.rights©2014 The Authorsen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.sourcePLOS One
dc.subjectCell Polarityen_US
dc.subjectGene expressionen_US
dc.subjectProstate--Canceren_US
dc.subjectProtein interactionsen_US
dc.subjectTopologyen_US
dc.titleModuleRole: A Tool for Modulization, Role Determination and Visualization in Protein-Protein Interaction Networksen_US
dc.type.genreArticleen_US

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Zhang, Michael Q.