ProViz - interactive visualisation of protein interactions
The understanding of a cell's machinery that regulates its development and function as well as the discovery of new drug targets can be greatly enhanced by studying protein-protein interactions. In the past few years, high-throughput methods such as affinity purification have been used to characterise protein-protein interactions and have produced a wealth of data in the form of networks. Aiming to address the needs of biologists exploring local and distant databases of protein-protein interactions, researchers at the Université Bordeaux 1 have integrated analysis and visualisation tools within ProViz. This software platform can be used to identify protein interactions of interest either through keyword search or through analysis of networks' structure. It has been designed for drawing graphs, but more importantly for the interactive exploration of large graphs. Based on the Tulip platform and the molecular interaction extensible markup language (XML) format, ProViz provides a rich set of basic and advanced operations on graphs. Subgraphs produced either by selection or clustering related proteins interactions are automatically organised into views that can be manipulated independently as well as used to produce further views. When building views, users can employ external controlled vocabularies such as the Gene Ontology vocabularies that describe gene products in terms of their associated biological processes and cellular components. ProViz is freely available from http://cbi.labri.fr/eng/proviz.htm as a stand-alone application. At the software download site, links to interactive tutorials have also been added for biologists who wish to explore the possibilities offered to handle large datasets of interacting proteins networks.
