Answers.Body: <p>The easiest way to do what you want would be to use the stringApp in Cytoscape to select your 10 genes.  That will give you the same PPI that you got from the web site.  Then, run enrichment on that set of genes, and only select KEGG, Reactome, and WikiPathways.  This will give you a set of pathways that your 10 genes are enriched in.  An alternative would be to use the stringApp to download the Alzheimer's disease network, extend that to add your 10 genes (if they aren't already there) and color by your fold change.  That will give you an idea of the relationship between your genes and known alzheimer's genes.</p>
  
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Answers.CreationDate: 2024-05-16T13:35:54.513Z
Answers.LastActivityDate: 2024-05-16T13:35:54.513Z
Answers.UserDisplayName: Scooter Morris
Body: <p>I'm using for first time Cytoscape. I am working with 10 selected genes with fold-change values in 3 different groups. I am not fishing, I am evaluating gene expression.
  We are trying to relate these genes with Alzheimer.</p>
  <p>The thing is  I have already send my network to Cytoscape from String but now I don't know how to search for disease/pathways related and overlay them to my nodes (=genes), to see how they are related</p>
  <p>I am pretty new for that but seems to me that I just can add multiple nodes but without a neural point as diseases or functional processs</p>
  <p>Thank you!</p>
  <p><a href="https://i.sstatic.net/xFOtk7Zi.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/xFOtk7Zi.png" alt="enter image description here" /></a></p>
  
Tags: <pathway><cytoscape>
Title: Overlay pathway over a set of genes in Cytoscape
ThreadText: # Overlay pathway over a set of genes in Cytoscape
  
  (Asked by: username_0 on 2024-05-14)
  
  I'm using for first time Cytoscape. I am working with 10 selected genes with fold-change values in 3 different groups. I am not fishing, I am evaluating gene expression.
  We are trying to relate these genes with Alzheimer.
  
  The thing is I have already send my network to Cytoscape from String but now I don't know how to search for disease/pathways related and overlay them to my nodes (=genes), to see how they are related
  
  I am pretty new for that but seems to me that I just can add multiple nodes but without a neural point as diseases or functional processs
  
  Thank you!
  
  [![enter image description here](https://i.sstatic.net/xFOtk7Zi.png)](https://i.sstatic.net/xFOtk7Zi.png)
  
  **Tags:** pathway, cytoscape
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2024-05-16. Score: 0
  
  The easiest way to do what you want would be to use the stringApp in Cytoscape to select your 10 genes. That will give you the same PPI that you got from the web site. Then, run enrichment on that set of genes, and only select KEGG, Reactome, and WikiPathways. This will give you a set of pathways that your 10 genes are enriched in. An alternative would be to use the stringApp to download the Alzheimer's disease network, extend that to add your 10 genes (if they aren't already there) and color by your fold change. That will give you an idea of the relationship between your genes and known alzheimer's genes.
  
  
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