Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Research article

FragViz: visualization of fragmented networks

Miha Štajdohar1, Minca Mramor1, Blaž Zupan12 and Janez Demšar1*

Author Affiliations

1 Faculty of Computer and Information Science, University of Ljubljana, Slovenia

2 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, USA

For all author emails, please log on.

BMC Bioinformatics 2010, 11:475  doi:10.1186/1471-2105-11-475

Published: 22 September 2010

Abstract

Background

Researchers in systems biology use network visualization to summarize the results of their analysis. Such networks often include unconnected components, which popular network alignment algorithms place arbitrarily with respect to the rest of the network. This can lead to misinterpretations due to the proximity of otherwise unrelated elements.

Results

We propose a new network layout optimization technique called FragViz which can incorporate additional information on relations between unconnected network components. It uses a two-step approach by first arranging the nodes within each of the components and then placing the components so that their proximity in the network corresponds to their relatedness. In the experimental study with the leukemia gene networks we demonstrate that FragViz can obtain network layouts which are more interpretable and hold additional information that could not be exposed using classical network layout optimization algorithms.

Conclusions

Network visualization relies on computational techniques for proper placement of objects under consideration. These algorithms need to be fast so that they can be incorporated in responsive interfaces required by the explorative data analysis environments. Our layout optimization technique FragViz meets these requirements and specifically addresses the visualization of fragmented networks, for which standard algorithms do not consider similarities between unconnected components. The experiments confirmed the claims on speed and accuracy of the proposed solution.