Multiple networks integrated into one figure in Cytoscape

Question

[Xiaokang]

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?

[zizigolu]

NetworkAnalyzer has merge, intersect and subtract options. I hope I got you well

Answer 1

[xanderpico]

Sure. Cytoscape has a merge tool (see Tools>Merge>Networks). You could perform a UNION merge of the three networks (n1-3) to get a merged network (n4). Then using the search tool (upper right), you can paste in your lists (l1-3), one at a time to select the nodes per species.

To track the node source better, I usually create a set of Boolean columns (e.g., named after the source species). Then when you select each set of nodes via the search tool, you can simply fill in "true" for all the selected nodes (right-click>Apply to selected nodes). Then you can find them again without having to paste lists over and over using the Select tool (see Select tab). Alternatively, you can create a single column (of type list) and then do the same thing, but fill in the names of species into a single column (e.g., some nodes will have more than one source species). Then you can even use this column for discrete color mapping onto node fill color, etc.