I have a list of genes (let’s call it L), and I want to see how they work differently in 3 different species (human, zebrafish and cod). Of course, the 3 species don’t have all the genes in the list, besides, the interactions between genes are different across 3 species. Firstly, I search the genes in this list against the genomes of 3 species, to get 3 gene lists for 3 species (let’s call them l1, l2, l3). Then I put the 3 gene lists into STRING respectively. So now I have 3 networks (let’s call them n1, n2, n3), each network for each species.
With those 3 networks and 4 lists, I come to Cytoscape. What I want to visualise is to show 3 networks together. So the background is the all the nodes from L. When I say, let’s look at human, the network n1 (including both the nodes from l1 and the edges between them) will be hi-lighted (the other genes from the other two species stay there without moving, but faded out as a background). Then you also do the same for zebrafish and cod. By doing this, one can see how the genes work differently across 3 species.
So is that possible to be done in Cytoscape?