title: VANLO--interactive visual exploration of aligned biological networks.
abstract: BACKGROUND
  Protein-protein interaction (PPI) is fundamental to many biological processes. In the course of evolution, biological networks such as protein-protein interaction networks have developed. Biological networks of different species can be aligned by finding instances (e.g. proteins) with the same common ancestor in the evolutionary 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 relationships transparent.
  
  
  RESULTS
  We present a novel visualization system for aligned biological networks in 3D space that naturally embeds existing 2D layouts. In addition to displaying the intra-network connectivities, we also provide insight into how the individual networks relate to each other by placing aligned entities on top of each other in separate layers. We optimize the layout of the entire alignment graph in a global fashion that takes into account inter- as well as intra-network relationships. The layout algorithm includes a step of merging aligned networks into one graph, laying out the graph with respect to application-specific requirements, splitting the merged graph again into individual networks, and displaying the network alignment in layers. In addition to representing the data in a static way, we also provide different interaction techniques to explore the data with respect to application-specific tasks.
  
  
  CONCLUSIONS
  Our system provides an intuitive global understanding of aligned PPI networks and it allows the investigation of key biological questions. We evaluate our system by applying it to real-world examples documenting how our system can be used to investigate the data with respect to these key questions. Our tool VANLO (Visualization of Aligned Networks with Layout Optimization) can be accessed at http://www.math-inf.uni-greifswald.de/VANLO.
authors.affiliation: 1Department of Mathematics and Computer Science, Ernst-Moritz-Arndt-University, Greifswald, Germany. sbrasch@uni-greifswald.de
authors.forename: Steffen
authors.initials: S
authors.lastname: Brasch
authors.forename: Lars
authors.initials: L
authors.lastname: Linsen
authors.forename: Georg
authors.initials: G
authors.lastname: Fuellen
mesh_terms: D030562:Databases, Protein; D025941:Protein Interaction Mapping / Q000379:methods; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins