Answers.Body: <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.sstatic.net/8BhSw.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/8BhSw.png" alt="enter image description here"></a></p>
  
  <p>Then go to the style tab:</p>
  
  <p><a href="https://i.sstatic.net/poiDr.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/poiDr.png" alt="enter image description here"></a></p>
  
  <p>... and make sure edge is selected.</p>
  
  <p><a href="https://i.sstatic.net/S7eT2.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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.sstatic.net/vRD48.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/vRD48.png" alt="enter image description here"></a>:</p>
  
  <p>... and transparency panels as examples.</p>
  
  <p><a href="https://i.sstatic.net/Ci0Ap.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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.sstatic.net/RucPs.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/RucPs.png" alt="enter image description here"></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-19T21:07:14.327Z
Answers.LastActivityDate: 2018-12-19T21:07:14.327Z
Answers.UserDisplayName: conchoecia
Answers.Body: <p>I think what you're looking for, as I suggested in this <a href="https://bioinformatics.stackexchange.com/questions/5436/compare-two-networks-of-the-same-genes-between-two-species/5451#5451">old question</a> (quite similar to this one, I believe), is the <a href="http://apps.cytoscape.org/apps/gasoline" rel="nofollow noreferrer">GASOLINE app</a> 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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-20T11:23:55.540Z
Answers.LastActivityDate: 2018-12-20T11:23:55.540Z
Answers.UserDisplayName: gbt
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-19T21:12:06.993Z
Comments.Text: Do you hope to perform any more analyses on these networks aside from visualization?
Comments.UserDisplayName: conchoecia
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-19T21:38:25.900Z
Comments.Text: @conchoecia I have edited the question. Please check.
Comments.UserDisplayName: The Last Word
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-20T00:14:17.877Z
Comments.Text: 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.
Comments.UserDisplayName: conchoecia
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-20T11:25:47.397Z
Comments.Text: Possible duplicate of [Compare two networks of the same genes between two species](https://bioinformatics.stackexchange.com/questions/5436/compare-two-networks-of-the-same-genes-between-two-species)
Comments.UserDisplayName: gbt
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-20T17:02:52.377Z
Comments.Text: @gabrielet I did ask that previous question as well. That was about inferences that can be drawn from topological comparisons.
Comments.UserDisplayName: The Last Word
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-20T17:04:22.153Z
Comments.Text: @conchoecia The edges have no weights but I would say consider those homologues with similar edges would more than suffice.
Comments.UserDisplayName: The Last Word
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-21T08:07:39.097Z
Comments.Text: @TheLastWord, I see the difference but I believe that the goal is the same in both questions since what you want to achieve is the comparison of networks to find similarities.
Comments.UserDisplayName: gbt
Tags: <visualization><networks>
Title: Visualize similar interactions in two homologous networks
ThreadText: # Visualize similar interactions in two homologous networks
  
  (Asked by: username_0 on 2018-12-19)
  
  ## 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.
  
  **Tags:** visualization, networks
  
  > **Comments:**
  > **username_1**: Do you hope to perform any more analyses on these networks aside from visualization?  
  > **username_0**: @username_1 I have edited the question. Please check.  
  > **username_1**: 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.  
  > **username_2**: Possible duplicate of [Compare two networks of the same genes between two species](https://bioinformatics.stackexchange.com/questions/5436/compare-two-networks-of-the-same-genes-between-two-species)  
  > **username_0**: @gabrielet I did ask that previous question as well. That was about inferences that can be drawn from topological comparisons.  
  > **username_0**: @username_1 The edges have no weights but I would say consider those homologues with similar edges would more than suffice.  
  > **username_2**: @username_0, I see the difference but I believe that the goal is the same in both questions since what you want to achieve is the comparison of networks to find similarities.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2018-12-19. Score: 4
  
  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:
  
  [![enter image description here](https://i.sstatic.net/8BhSw.png)](https://i.sstatic.net/8BhSw.png)
  
  Then go to the style tab:
  
  [![enter image description here](https://i.sstatic.net/poiDr.png)](https://i.sstatic.net/poiDr.png)
  
  ... and make sure edge is selected.
  
  [![enter image description here](https://i.sstatic.net/S7eT2.png)](https://i.sstatic.net/S7eT2.png)
  
  Then you can adjust the transparency, edge color, and edge stroke settings, like so using edge stroke color:
  
  [![enter image description here](https://i.sstatic.net/vRD48.png)](https://i.sstatic.net/vRD48.png):
  
  ... and transparency panels as examples.
  
  [![enter image description here](https://i.sstatic.net/Ci0Ap.png)](https://i.sstatic.net/Ci0Ap.png)
  
  **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](https://i.sstatic.net/RucPs.png)](https://i.sstatic.net/RucPs.png)
  
  
  ---
  
  ### Answer by username_2 on 2018-12-20. Score: 0
  
  I think what you're looking for, as I suggested in this [old question](https://bioinformatics.stackexchange.com/questions/5436/compare-two-networks-of-the-same-genes-between-two-species/5451#5451) (quite similar to this one, I believe), is the [GASOLINE app](http://apps.cytoscape.org/apps/gasoline) 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.
  
  
  ---
  
  