Compare two networks with the same nodes but from two different species.

[Charles]

Hi,

I have two networks loaded onto Cytoscape and I was hoping to compare these networks. I created the networks using STRING. The networks are from honey bees and their orthologous genes from house fly. I was hoping to use Gasoline but I have no idea on how to calculate the prob_interaction values. I was hoping to compare the networks and find common modules of genes between the two. I am also open to new ideas on how to compare the networks. I could not find any publications about network comparisons being done between species using Cytoscape and I would be grateful if some links could be provided. I know that topological comparisons can be drawn. However, I could not find any publications for this too to use as a reference. 

Is there apps beside Gasoline I can use for network comparison. Kindly advice.

[Alex Pico]

Good question. Other than an example file, I couldn’t find anything in their manual, tutorial or paper about HOW to get this input file. My guess would be to perform a protein-protein Blast yourself and then make sure the output conforms to their example format and the identifiers match the ones you are using to define your network nodes.

Here’s a link to the Blast tool:

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

 - Alex

On Nov 16, 2018, at 11:45 AM, Charles <potter...@gmail.com> wrote:

Hi,

I have two networks loaded onto Cytoscape and I was hoping to compare these networks. I created the networks using STRING. The primary network is from honey bees and its orthologous genes from house fly. I was hoping to use Gasoline but I have no idea on how to calculate the prob_interaction values. I was hoping to compare the networks and find common modules of genes between the two. Iam also open to new ideas on how to compare the networks. I could not find any publications about network comparisons being done between species using Cytoscape and I would be grateful if some links could be provided. I know that topological comparisons can be drawn. However, I could not find any publications to use as a reference. 

Is there apps beside Gasoline I can use for network comparison. Kindly advice.

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[ugurdogrusoz]

In case you'd like to make use of network visualization through synchronous layout, you might want to check this tool out (based on Cytoscape.js): https://github.com/iVis-at-Bilkent/even.

Best,

UD