Body: <p>I am working on network analysis of differentially expressed genes, but the problem I am facing is that the gene set is very small (around 16 genes only), so when I'm trying to build an interaction network with these genes using STRING, the nodes starts to dissociate from the interaction when I set the confidence score to 0.400 or above (as the genes are related to <em>Homo sapiens</em>).</p>
  <p>DE gene network has to be made in cytoscape, for that STRING ppi interactions are needed, that interaction network will tell us co-expression, homology etc and provide us a combined score.</p>
  <p>So, to build an interaction network between these genes, I have to decrease the confidence score to 0.150 since it is only with this score that I am finding interactors.</p>
  <p>So, I want to ask <em><strong>whether this low confidence score is valid for this short gene set related to Homo sapiens</strong></em> or, if not, what should I do in this case?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-06-08T11:03:32.487Z
Comments.Text: Why do you think there _should be_ a connection between these genes or proteins? Are you working with genes and trying to build a _gene regulatory network_ or are you working with proteins and trying to build a _protein-protein interaction network_?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-06-11T13:36:55.213Z
Comments.Text: We really can't help unless you explain why you think there should be connections between these genes and why that connection would be detectable from PPI networks as opposed to gene regulatory networks.
Comments.UserDisplayName: terdon
Tags: <networks><stringdb>
Title: Network analysis: confidence score (STRING database) validation
ThreadText: # Network analysis: confidence score (STRING database) validation
  
  (Asked by: username_0 on 2021-06-08)
  
  I am working on network analysis of differentially expressed genes, but the problem I am facing is that the gene set is very small (around 16 genes only), so when I'm trying to build an interaction network with these genes using STRING, the nodes starts to dissociate from the interaction when I set the confidence score to 0.400 or above (as the genes are related to *Homo sapiens*).
  
  DE gene network has to be made in cytoscape, for that STRING ppi interactions are needed, that interaction network will tell us co-expression, homology etc and provide us a combined score.
  
  So, to build an interaction network between these genes, I have to decrease the confidence score to 0.150 since it is only with this score that I am finding interactors.
  
  So, I want to ask ***whether this low confidence score is valid for this short gene set related to Homo sapiens*** or, if not, what should I do in this case?
  
  **Tags:** networks, stringdb
  
  > **Comments:**
  > **username_1**: Why do you think there _should be_ a connection between these genes or proteins? Are you working with genes and trying to build a _gene regulatory network_ or are you working with proteins and trying to build a _protein-protein interaction network_?  
  > **username_1**: We really can't help unless you explain why you think there should be connections between these genes and why that connection would be detectable from PPI networks as opposed to gene regulatory networks.  
  
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  ## 0 answers
  
  