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

Background: 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. Results: 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 ...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Brian J. Holden, John W. Pinney, Simon C. Lovell, Grigoris Amoutzias, David L. Robertson
• Keywords: BMCBI 2007, Network Visualisation, Phylogenetic Tree, Protein-protein Interactions