A web-based protein interaction network visualizer

 

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dc.contributor.author Salazar, Gustavo A
dc.contributor.author Meintjes, Ayton
dc.contributor.author Mazandu, Gaston K
dc.contributor.author Rapanoël, Holifidy A
dc.contributor.author Akinola, Richard O
dc.contributor.author Mulder, Nicola J
dc.date.accessioned 2015-01-19T11:37:45Z
dc.date.available 2015-01-19T11:37:45Z
dc.date.issued 2014-05-06
dc.identifier.citation Salazar et al.: A web-based protein interaction network visualizer. BMC Bioinformatics 2014 15:129 en_ZA
dc.identifier.issn 1471-2334 en_ZA
dc.identifier.uri http://dx.doi.org/10.1186/1471-2105-15-129
dc.identifier.uri http://hdl.handle.net/11427/12265
dc.identifier.uri http://hdl.handle.net/11427/12265
dc.identifier.uri http://dx.doi.org/10.1186/1471-2105-15-129
dc.description.abstract 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 . en_ZA
dc.language eng en_ZA
dc.publisher BioMed Central en_ZA
dc.rights Creative Commons Attribution 4.0 International (CC BY 4.0) *
dc.rights.uri http://creativecommons.org/licenses/by/4.0/ en_ZA
dc.source BMC Bioinformatics en_ZA
dc.source.uri http://www.biomedcentral.com/1471-2105 en_ZA
dc.subject.other Visualization en_ZA
dc.subject.other Protein-Protein Interactions en_ZA
dc.subject.other Web development en_ZA
dc.title A web-based protein interaction network visualizer en_ZA
dc.type Journal Article en_ZA
dc.date.updated 2015-01-15T17:52:30Z
dc.language.rfc3066 en
dc.rights.holder Salazar et al.; licensee BioMed Central Ltd.
uct.type.publication Research en_ZA
uct.type.resource Article en_ZA
dc.publisher.institution University of Cape Town
dc.publisher.faculty Faculty of Health Sciences en_ZA
dc.publisher.department Institute of Infectious Disease and Molecular Medicine en_ZA
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uct.type.filetype Text
uct.type.filetype Image


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