Visualizing multifunctional PPI network with Gene Ontology annotation

Abstract

Protein-protein interaction (PPI) network data contain interactions between two proteins in organisms. Some proteins are involved in more than one biological process. Those multifunctional proteins are important in the biological system because they connect various biological pathways. However, the multifunctionality of proteins increases the complexity of the PPI network and makes visualizing a challenging problem. In this research, we suggest a new method to visualize the multifunctional PPI network by integrating interaction data and Gene Ontology (GO) terms of each protein. By matching GO annotations of two proteins, we annotate edges between those two proteins with common GO terms. Also, we suggest a novel algorithm for color mapping specialized to express hierarchical relationships among GO terms based on the multidimensional scaling algorithm. Annotated edges are divided corresponding to their GO terms, and visualized by selected color, width, and opacity to represent semantic relationships among edges clearly. Those visual features are assigned to represent semantic distance among GO terms and their concreteness. This visualization method is available through the web.