ModuleRole: A tool for modulization, role determination and visualization in protein-protein interaction networks

GuiPeng Li, Ming Li, YiWei Zhang, Dong Wang, Rong Li, Roger Guimerà, Juntao Tony Gao, Michael Q. Zhang

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article numbere94608
JournalPLoS One
Volume9
Issue number5
DOIs
StatePublished - May 1 2014
Externally publishedYes

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Protein Interaction Maps
protein-protein interactions
Visualization
Proteins
biologists
world wide web
menu planning
proteins
annealing
expert opinion
Databases
Throughput
methodology
Graph theory
Complex networks
Simulated annealing
Websites

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)
  • Agricultural and Biological Sciences(all)

Cite this

ModuleRole : A tool for modulization, role determination and visualization in protein-protein interaction networks. / Li, GuiPeng; Li, Ming; Zhang, YiWei; Wang, Dong; Li, Rong; Guimerà, Roger; Gao, Juntao Tony; Zhang, Michael Q.

In: PLoS One, Vol. 9, No. 5, e94608, 01.05.2014.

Research output: Contribution to journalArticle

Li, GuiPeng ; Li, Ming ; Zhang, YiWei ; Wang, Dong ; Li, Rong ; Guimerà, Roger ; Gao, Juntao Tony ; Zhang, Michael Q. / ModuleRole : A tool for modulization, role determination and visualization in protein-protein interaction networks. In: PLoS One. 2014 ; Vol. 9, No. 5.
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