A web-based protein interaction network visualizer

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dc.contributor.authorSalazar, Gustavo A
dc.contributor.authorMeintjes, Ayton
dc.contributor.authorMazandu, Gaston K
dc.contributor.authorRapanoël, Holifidy A
dc.contributor.authorAkinola, Richard O
dc.contributor.authorMulder, Nicola J
dc.date.accessioned2015-01-19T11:37:45Z
dc.date.available2015-01-19T11:37:45Z
dc.date.issued2014-05-06
dc.date.updated2015-01-15T17:52:30Z
dc.description.abstractAbstract Background Interaction between proteins is one of the most important mechanisms in the execution of cellular functions. The study of these interactions has provided insight into the functioning of an organism’s processes. As of October 2013, Homo sapiens had over 170000 Protein-Protein interactions (PPI) registered in the Interologous Interaction Database, which is only one of the many public resources where protein interactions can be accessed. These numbers exemplify the volume of data that research on the topic has generated. Visualization of large data sets is a well known strategy to make sense of information, and protein interaction data is no exception. There are several tools that allow the exploration of this data, providing different methods to visualize protein network interactions. However, there is still no native web tool that allows this data to be explored interactively online. Results Given the advances that web technologies have made recently it is time to bring these interactive views to the web to provide an easily accessible forum to visualize PPI. We have created a Web-based Protein Interaction Network Visualizer: PINV, an open source, native web application that facilitates the visualization of protein interactions ( http://biosual.cbio.uct.ac.za/pinv.html ). We developed PINV as a set of components that follow the protocol defined in BioJS and use the D3 library to create the graphic layouts. We demonstrate the use of PINV with multi-organism interaction networks for a predicted target from Mycobacterium tuberculosis, its interacting partners and its orthologs. Conclusions The resultant tool provides an attractive view of complex, fully interactive networks with components that allow the querying, filtering and manipulation of the visible subset. Moreover, as a web resource, PINV simplifies sharing and publishing, activities which are vital in today’s research collaborative environments. The source code is freely available for download at https://github.com/4ndr01d3/biosual .en_ZA
dc.identifier.apacitationSalazar, G. A., Meintjes, A., Mazandu, G. K., Rapanoël, H. A., Akinola, R. O., & Mulder, N. J. (2014). A web-based protein interaction network visualizer. <i>BMC Bioinformatics</i>, http://hdl.handle.net/11427/12265en_ZA
dc.identifier.chicagocitationSalazar, Gustavo A, Ayton Meintjes, Gaston K Mazandu, Holifidy A Rapanoël, Richard O Akinola, and Nicola J Mulder "A web-based protein interaction network visualizer." <i>BMC Bioinformatics</i> (2014) http://hdl.handle.net/11427/12265en_ZA
dc.identifier.citationSalazar et al.: A web-based protein interaction network visualizer. BMC Bioinformatics 2014 15:129en_ZA
dc.identifier.issn1471-2334en_ZA
dc.identifier.ris TY - Journal Article AU - Salazar, Gustavo A AU - Meintjes, Ayton AU - Mazandu, Gaston K AU - Rapanoël, Holifidy A AU - Akinola, Richard O AU - Mulder, Nicola J AB - Abstract Background Interaction between proteins is one of the most important mechanisms in the execution of cellular functions. The study of these interactions has provided insight into the functioning of an organism’s processes. As of October 2013, Homo sapiens had over 170000 Protein-Protein interactions (PPI) registered in the Interologous Interaction Database, which is only one of the many public resources where protein interactions can be accessed. These numbers exemplify the volume of data that research on the topic has generated. Visualization of large data sets is a well known strategy to make sense of information, and protein interaction data is no exception. There are several tools that allow the exploration of this data, providing different methods to visualize protein network interactions. However, there is still no native web tool that allows this data to be explored interactively online. Results Given the advances that web technologies have made recently it is time to bring these interactive views to the web to provide an easily accessible forum to visualize PPI. We have created a Web-based Protein Interaction Network Visualizer: PINV, an open source, native web application that facilitates the visualization of protein interactions ( http://biosual.cbio.uct.ac.za/pinv.html ). We developed PINV as a set of components that follow the protocol defined in BioJS and use the D3 library to create the graphic layouts. We demonstrate the use of PINV with multi-organism interaction networks for a predicted target from Mycobacterium tuberculosis, its interacting partners and its orthologs. Conclusions The resultant tool provides an attractive view of complex, fully interactive networks with components that allow the querying, filtering and manipulation of the visible subset. Moreover, as a web resource, PINV simplifies sharing and publishing, activities which are vital in today’s research collaborative environments. The source code is freely available for download at https://github.com/4ndr01d3/biosual . DA - 2014-05-06 DB - OpenUCT DO - 10.1186/1471-2105-15-129 DP - University of Cape Town J1 - BMC Bioinformatics LK - https://open.uct.ac.za PB - University of Cape Town PY - 2014 SM - 1471-2334 T1 - A web-based protein interaction network visualizer TI - A web-based protein interaction network visualizer UR - http://hdl.handle.net/11427/12265 ER - en_ZA
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2105-15-129
dc.identifier.urihttp://hdl.handle.net/11427/12265
dc.identifier.urihttp://hdl.handle.net/11427/12265
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2105-15-129
dc.identifier.vancouvercitationSalazar GA, Meintjes A, Mazandu GK, Rapanoël HA, Akinola RO, Mulder NJ. A web-based protein interaction network visualizer. BMC Bioinformatics. 2014; http://hdl.handle.net/11427/12265.en_ZA
dc.languageengen_ZA
dc.language.rfc3066en
dc.publisherBioMed Centralen_ZA
dc.publisher.departmentInstitute of Infectious Disease and Molecular Medicineen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsCreative Commons Attribution 4.0 International (CC BY 4.0)*
dc.rights.holderSalazar et al.; licensee BioMed Central Ltd.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_ZA
dc.sourceBMC Bioinformaticsen_ZA
dc.source.urihttp://www.biomedcentral.com/1471-2105en_ZA
dc.subject.otherVisualizationen_ZA
dc.subject.otherProtein-Protein Interactionsen_ZA
dc.subject.otherWeb developmenten_ZA
dc.titleA web-based protein interaction network visualizeren_ZA
dc.typeJournal Articleen_ZA
uct.type.filetype
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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