1Department of Mathematics and Computer Science, Ernst-Moritz-Arndt-University, Greifswald, Germany.
BMC Bioinformatics. 2009 Oct 12;10:327. doi: 10.1186/1471-2105-10-327.
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.
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.
蛋白质-蛋白质相互作用（PPI）是许多生物过程的基础。在进化过程中，出现了蛋白质-蛋白质相互作用网络等生物网络。通过在进化过程中寻找具有相同共同祖先的实例（例如蛋白质），可以对齐不同物种的生物网络，这些实例被称为同源物。为了更好地理解生物网络的进化，需要探索这些对齐的网络。可视化可以在揭示各种关系方面发挥关键作用。
我们提出了一种新颖的 3D 空间中对齐生物网络的可视化系统，该系统自然地嵌入了现有的 2D 布局。除了显示网络内的连接性外，我们还通过将对齐的实体放置在单独的层上彼此重叠，提供了关于各个网络如何相互关联的深入了解。我们以全局方式优化整个对齐图的布局，同时考虑到网络内和网络间的关系。布局算法包括将对齐网络合并为一个图的步骤，根据特定于应用程序的要求布置图，再次将合并的图拆分为各个网络，并以层的形式显示网络对齐。除了以静态方式表示数据外，我们还提供了不同的交互技术，以针对特定于应用程序的任务探索数据。
我们的系统提供了对齐 PPI 网络的直观全局理解，并允许针对关键生物学问题进行调查。我们通过将其应用于记录如何使用我们的系统针对这些关键问题调查数据的真实示例来评估我们的系统。我们的工具 VANLO（具有布局优化的对齐网络可视化）可在 http://www.math-inf.uni-greifswald.de/VANLO 上访问。
