Repositori URV

Author, as appears in the article.: Li, GuiPeng; Li, Ming; Zhang, YiWei; Wang, Dong; Li, Rong; Guimera, Roger; Gao, Juntao Tony; Zhang, Michael Q

Department: Enginyeria Química

URV's Author/s: Guimera Manrique, Roger

Keywords: Yeast Software Saccharomycetales Protein interaction maps Protein interaction mapping Prostatic neoplasms Platform Mice Male Identification Humans Hippo pathway Growth Gene regulatory networks Computational biology Complexes Cell polarity Animals Algorithm

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.

Thematic Areas: Zootecnia / recursos pesqueiros Sociology Sociología Serviço social Saúde coletiva Química Psychology Psicología Planejamento urbano e regional / demografia Odontología Nutrição Multidisciplinary sciences Multidisciplinary Medicine (miscellaneous) Medicina veterinaria Medicina iii Medicina ii Medicina i Materiais Matemática / probabilidade e estatística Linguística e literatura Letras / linguística Interdisciplinary research in the social sciences Interdisciplinar Human geography and urban studies History & philosophy of science Historia Geografía Geociências General medicine General biochemistry,genetics and molecular biology General agricultural and biological sciences Farmacia Environmental studies Ensino Engenharias iv Engenharias iii Engenharias ii Engenharias i Enfermagem Educação física Educação Economia Direito Demography Comunicação e informação Ciências sociais aplicadas i Ciências biológicas iii Ciências biológicas ii Ciências biológicas i Ciências ambientais Ciências agrárias i Ciência política e relações internacionais Ciência de alimentos Ciência da computação Biotecnología Biology Biodiversidade Biochemistry, genetics and molecular biology (miscellaneous) Astronomia / física Arquitetura, urbanismo e design Archaeology Antropologia / arqueologia Anthropology Agricultural and biological sciences (miscellaneous) Administração, ciências contábeis e turismo Administração pública e de empresas, ciências contábeis e turismo

licence for use: https://creativecommons.org/licenses/by/3.0/es/

Author's mail: roger.guimera@urv.cat

Author identifier: 0000-0002-3597-4310

Record's date: 2024-10-26

Papper version: info:eu-repo/semantics/publishedVersion

Link to the original source: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094608

Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/

Papper original source: Plos One. 9 (5): e94608-

APA: Li, GuiPeng; Li, Ming; Zhang, YiWei; Wang, Dong; Li, Rong; Guimera, Roger; Gao, Juntao Tony; Zhang, Michael Q (2014). ModuleRole: A Tool for Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks. Plos One, 9(5), e94608-. DOI: 10.1371/journal.pone.0094608

Article's DOI: 10.1371/journal.pone.0094608

Entity: Universitat Rovira i Virgili

Journal publication year: 2014

Publication Type: Journal Publications