Open Access Highly Accessed Open Badges Methodology article

An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network

Brian J Holden1, John W Pinney1*, Simon C Lovell1, Grigoris D Amoutzias12 and David L Robertson1*

Author Affiliations

1 Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK

2 Bioinformatics & Evolutionary Genomics, VIB/Ghent University, Technologiepark 927, B-9052 Ghent, Belgium

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BMC Bioinformatics 2007, 8:289  doi:10.1186/1471-2105-8-289

Published: 6 August 2007



Alternative representations of biochemical networks emphasise different aspects of the data and contribute to the understanding of complex biological systems. In this study we present a variety of automated methods for visualisation of a protein-protein interaction network, using the basic helix-loop-helix (bHLH) family of transcription factors as an example.


Network representations that arrange nodes (proteins) according to either continuous or discrete information are investigated, revealing the existence of protein sub-families and the retention of interactions following gene duplication events. Methods of network visualisation in conjunction with a phylogenetic tree are presented, highlighting the evolutionary relationships between proteins, and clarifying the context of network hubs and interaction clusters. Finally, an optimisation technique is used to create a three-dimensional layout of the phylogenetic tree upon which the protein-protein interactions may be projected.


We show that by incorporating secondary genomic, functional or phylogenetic information into network visualisation, it is possible to move beyond simple layout algorithms based on network topology towards more biologically meaningful representations. These new visualisations can give structure to complex networks and will greatly help in interpreting their evolutionary origins and functional implications. Three open source software packages (InterView, TVi and OptiMage) implementing our methods are available.