A web-based protein interaction network visualizer.

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

doi:10.1186/1471-2105-15-129

Gustavo A Salazar, Richard O Akinola + Show 4 more

Open Access

https://doi.org/10.1186/1471-2105-15-129

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Journal: BMC bioinformatics	Publication Date: May 6, 2014
Citations: 36	License type: cc-by

Affiliation: University of Cape Town

Abstract

BackgroundInteraction 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.ResultsGiven 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.ConclusionsThe 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.

Highlights

Interaction between proteins is one of the most important mechanisms in the execution of cellular functions
Due to recent developments, this is possible: the data can be acquired using a request via Asynchronous JavaScript and XML (AJAX); it can be processed and injected into the current document with JavaScript; the document can contain structured graphics in Scalable Vector Graphics (SVG) format; the styles defined with CSS3; and all within reasonable response time thanks to the most recent generation of browsers
Two more filters were applied to this example, the combined use of the filters results in a 103 interaction subnetwork, which is small enough to allow Protein interaction network visualizer (PINV) to run smoothly and generates a graphic like that in Figure 1 (Right)

Summary

Introduction

Interaction between proteins is one of the most important mechanisms in the execution of cellular functions. 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. There are several tools that allow the exploration of this data, providing different methods to visualize protein network interactions. There are several software tools that allow the visualization of protein interactions, including Cytoscape [2,3], Networkx [4] and NAVIGaTOR [5,6] Each of these tools provide different methods to visualize protein networks, and their strengths and weaknesses have been discussed in several earlier reviews [7,8,9,10]. Due to recent developments (such as the set of technologies grouped under the term HTML5), this is possible: the data can be acquired using a request via AJAX; it can be processed and injected into the current document with JavaScript; the document can contain structured graphics in SVG format; the styles defined with CSS3; and all within reasonable response time thanks to the most recent generation of browsers

Results

Discussion

Conclusion