Fuellen G: Visualization of Aligned Biological Networks: A Survey

Abstract—In modern biology, major efforts are undertaken to understand diseases, aging, evolution, and many other aspects of life. Biological networks play a key role in this research. Examples of such networks are protein-protein interaction (PPI) networks, gene regulatory networks, and metabolic pathways. Intuitive and comprehensible visualizations can significantly support the understanding and the analysis of such biological networks. Therefore, much research is conducted in the areas of bio-informatics and information visualization dealing with the problem of visualizing networks. In the course of evolution biological networks changed grad-ually. Therefore, the conserved core parts of the networks of different species can be aligned by matching the corresponding instances in the species, such as orthologous proteins or genes. Analyzing these alignments is of high relevance, as they con-vey significant information on protein function and organismal phenotype. For analysis purposes, the alignments have to be made transparent. Visualization methods are needed to display alignments in conjunction with the individual network structures. This is no standard network visualization problem, as we have to deal with more than one network and inter-network relationships. Several approaches to visualize aligned networks exist. In this survey we present and discuss these different approaches and report on their advantages and drawbacks. We draw conclusions on the applicability of the various approaches. I