VANLO - Interactive visual exploration of aligned biologicalnetworks
Protein-protein interaction (PPI) is fundamental to many biological processes. In the course ofevolution, biological networks such as protein-protein interaction networks have developed.
Biological networksof different species can be aligned by finding instances (e.g. proteins) with the same common ancestor in theevolutionary process, so-called orthologs.
For a better understanding of the evolution of biological networks,such aligned networks have to be explored. Visualization can play a key role in making the various relationshipstransparent.
Results: We present a novel visualization system for aligned biological networks in 3D space that naturallyembeds existing 2D layouts.
In addition to displaying the intra-network connectivities, we also provide insightinto how the individual networks relate to each other by placing aligned entities on top of each other in separatelayers. We optimize the layout of the entire alignment graph in a global fashion that takes into account inter- aswell as intra-network relationships.
The layout algorithm includes a step of merging aligned networks into onegraph, laying out the graph with respect to application-specific requirements, splitting the merged graph againinto individual networks, and displaying the network alignment in layers. In addition to representing the data ina static way, we also provide different interaction techniques to explore the data with respect toapplication-specific tasks.
Conclusions: Our system provides an intuitive global understanding of aligned PPI networks and it allows theinvestigation of key biological questions.
We evaluate our system by applying it to real-world examplesdocumenting how our system can be used to investigate the data with respect to these key questions. Our toolVANLO (Visualization of Aligned Networks with Layout Optimization) can be accessed athttp://www.math-inf.uni-greifswald.de/VANLO.
Author: Steffen BraschLars LinsenGeorg Fuellen
Credits/Source: BMC Bioinformatics 2009, 10:327
Published on: 2009-10-12
Copyright by the authors listed above - made available via BioMedCentral (Open Access). Please
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