Figure 1

Network alignment overview. Similar shapes represent similar proteins that should be aligned. Dotted lines and shapes represent parts that are missing from the respective networks. Arrows represent identified correspondences. The figure on the left shows a network, checkered in the center, which is used to optimally align the other two networks on the left and right. Missing nodes and interactions can be inferred. The figure in the center shows an alignment between only the two outer networks without a central PPIN serving as a scaffold. The alignment will either have to ignore the middle node or accept a suboptimal node alignment. No information about missing nodes and their potential location can be inferred from these two networks alone. Finally, the figure on the right shows an alignment of three networks. The two topmost proteins (diamond and square) are aligned across all three networks and they each interact in their respective PPIN. The interaction diamond-squareis thus conserved in all three species. Since the pentagon has only an aligned protein that also forms an interaction in the two leftmost PPINs, square-pentagonis conserved in two species only. Pentagon and circle are aligned but since the interaction pentagon-circleis missing from the middle PPIN, the edge is not considered conserved.