text: user976: 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.
  
  user2085: 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:
  
  Then go to the style tab:
  
  ... and make sure edge is selected.
  
  Then you can adjust the transparency, edge color, and edge stroke settings, like so using edge stroke color:
  :
  ... and transparency panels as examples.
  
  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:
  
  
original_text: 976: <h2>Background</h2>
  <p>I have two networks with homologous genes from two different species.</p>
  <p>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.</p>
  <p>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.</p>
  <h2>Questions</h2>
  <p><strong>Q1:</strong> How do I check if there are overlapping patterns between both the networks on Cytoscape?</p>
  <p><strong>Q2:</strong> 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.</p>
   2085: <p>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.</p>
  
  <p>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.</p>
  
  <p>(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:</p>
  
  <pre><code>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
  </code></pre>
  
  <p>Import your network to cytoscape as a network from a file:</p>
  
  <p><a href="https://i.stack.imgur.com/8BhSw.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/8BhSw.png" alt="enter image description here"></a></p>
  
  <p>Then go to the style tab:</p>
  
  <p><a href="https://i.stack.imgur.com/poiDr.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/poiDr.png" alt="enter image description here"></a></p>
  
  <p>... and make sure edge is selected.</p>
  
  <p><a href="https://i.stack.imgur.com/S7eT2.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/S7eT2.png" alt="enter image description here"></a></p>
  
  <p>Then you can adjust the transparency, edge color, and edge stroke settings, like so using edge stroke color:</p>
  
  <p><a href="https://i.stack.imgur.com/vRD48.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/vRD48.png" alt="enter image description here"></a>:</p>
  
  <p>... and transparency panels as examples.</p>
  
  <p><a href="https://i.stack.imgur.com/Ci0Ap.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/Ci0Ap.png" alt="enter image description here"></a></p>
  
  <p><strong>Don't forget to save your style when it is complete!</strong></p>
  
  <p>When you have adjusted these settings you will have something that looks like this:</p>
  
  <p><a href="https://i.stack.imgur.com/RucPs.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/RucPs.png" alt="enter image description here"></a></p>
  