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Background

I have two networks with homologous genes from two different species.

To identify homologs I performed a functional comparison. One of the species is not well studied while the other one is the house fly (D. melanogaster). I used ClueGO to predict the functions of the genes in the D. melanogaster network.

I found a function of interest influenced by a set of genes and predicted that the same genes in the other network (thus far uncharacterized) should also perform a similar function.

Questions

Q1: How do I check if there are overlapping patterns between both the networks on Cytoscape?

Q2: There are more than 100 homologs in this list and I would like to minimize the list by only considering those homologous genes that are arranged the same as well.

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  • $\begingroup$ Do you hope to perform any more analyses on these networks aside from visualization? $\endgroup$
    – conchoecia
    Commented Dec 19, 2018 at 21:12
  • $\begingroup$ @conchoecia I have edited the question. Please check. $\endgroup$
    – The Last Word
    Commented Dec 19, 2018 at 21:38
  • $\begingroup$ Thanks for your edits. The part that states, "minimize the list by only considering those homologous genes that are arranged the same as well", is still unclear. It is clear that you want to narrow the list of homologs but it is not clear what "arranged the same" means. Does this mean that they have the same synteny in the genome, the same edges and edge weights in a network, or something else? We can also provide you with a better answer if you post text examples of your data. $\endgroup$
    – conchoecia
    Commented Dec 20, 2018 at 0:14
  • $\begingroup$ Possible duplicate of Compare two networks of the same genes between two species $\endgroup$
    – gabt
    Commented Dec 20, 2018 at 11:25
  • $\begingroup$ @gabrielet I did ask that previous question as well. That was about inferences that can be drawn from topological comparisons. $\endgroup$
    – The Last Word
    Commented Dec 20, 2018 at 17:02

2 Answers 2

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An easy way to visualize this is to make a tab-delimited table that contains edge information for both species and both networks, color the edges depending on the species, and make the thickness and transparency dependent on the interaction strength.

For example, say you have a list of orthologs for the two species and just assign them a number or a name. Each edge has a "source" and a "target". The edge weight is the interaction strength.

(Note do not copy-paste the below table as the mixed tabs/spaces may make the graph topology incorrect). In my toy dataset the data look like this:

source  target  variable    value
gene1   gene2   speciesA    3
gene1   gene3   speciesA    42
gene2   gene3   speciesA    3
gene1   gene2   speciesB    9
gene2   gene3   speciesB    5
gene2   gene4   speciesB    41
gene3   gene4   speciesB    32

Import your network to cytoscape as a network from a file:

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Then go to the style tab:

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... and make sure edge is selected.

enter image description here

Then you can adjust the transparency, edge color, and edge stroke settings, like so using edge stroke color:

enter image description here:

... and transparency panels as examples.

enter image description here

Don't forget to save your style when it is complete!

When you have adjusted these settings you will have something that looks like this:

enter image description here

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I think what you're looking for, as I suggested in this old question (quite similar to this one, I believe), is the GASOLINE app for Cytoscape that allow you to perform an analysis that will tell you which parts of the two networks are conserved and which genes belong to the overlapping subnetworks.

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