An example to illustrate the idea of modules in a multi-layer network. The co-association networks of species A and B are linked together to form a multi-layer network via orthologous relationship between genes. There are three modules. The middle one is a conserved module with genes from both species, corresponding to fundamental biological functions across different species. The left and right ones are specific modules consisting of genes from species A and B, respectively. They correspond to novel functions that emerged in each of the two species.