Open Access Highly Accessed Software

A web-based protein interaction network visualizer

Gustavo A Salazar*, Ayton Meintjes, Gaston K Mazandu, Holifidy A Rapanoël, Richard O Akinola and Nicola J Mulder

Author Affiliations

Computational Biology Group, IDM, Faculty of Health Sciences, University of Cape Town, Anzio Road, Cape Town, South Africa

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BMC Bioinformatics 2014, 15:129  doi:10.1186/1471-2105-15-129

Published: 6 May 2014

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 webcite). 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 webcite.

Keywords:
Visualization; Protein-Protein Interactions; PPI; Web development