VANLO - Interactive visual exploration of aligned biological networks

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.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 webcite.In many biological processes proteins play a key role. They are involved in biological regulation, development, growth, locomotion, metabolism, and reproduction. Therefore, the study and analysis of proteins is of high importance in the fields of biology and medicine. Due to their chemical structure proteins are able to interact with each other. These interactions trigger many biological processes. For example, signals from the exterior of a cell are mediated to the interior of the cell by protein-protein interaction (PPI) of the signaling proteins. Such processes are also involved in diseases such as cancer. PPIs are fundamental to life, an