Answers.Body: <p>I believe the clustering is based on connectivity, not your fold change values, so it would matter exactly how you got your network.</p>
  
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Answers.CreationDate: 2024-12-12T01:55:17.800Z
Answers.LastActivityDate: 2024-12-12T01:55:17.800Z
Answers.UserDisplayName: Scooter Morris
Body: <p>I'm a bit stuck trying to figure out how Cytoscape ReactomeFIViz decides how nodes are colored in my Cytoscape functional interaction network generated from my input RNAseq dataset (table).</p>
  <p>Can you please clarify?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-11-23T01:30:07.543Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
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Comments.CreationDate: 2024-11-25T14:00:16.833Z
Comments.Text: Could you show us an image of what you are seeing, perhaps? That could help. Have you looked at any of the tool's [documentation](https://reactome.org/tools/reactome-fiviz)?
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2024-12-02T21:29:33.773Z
Comments.Text: Thank you terdon! I am unable to find the share/upload image option. However, what I am seeing looks something like the image under the 'Cluster FI network' paragraph on reactome.org/tools/reactome-fiviz#Gene_Set.2FMutation_Analysis . I looked through this documentation & under 4.1 Gene Set/Mutation Analysis 
  it says
  Cluster FI network: run a network clustering algorithm (spectral partition based network clustering by Newman 2006) on the displayed FI network. Nodes in different network modules
Comments.UserDisplayName: Stanislav Luban
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Comments.CreationDate: 2024-12-02T21:29:44.623Z
Comments.Text: will be shown in different colors (different colors used only for first 15 modules based on sizes).
  What does this mean exactly?
  Does the same apply to my analysis which uses 
  4.3 Microarray Data Analysis (even though the data I am analyzing is RNAseq)
  ?
Comments.UserDisplayName: Stanislav Luban
Tags: <rna-seq><differential-expression><gene-expression><cytoscape>
Title: What do the different node colors mean in the Cytoscape ReactomeFIViz functional interaction network?
ThreadText: # What do the different node colors mean in the Cytoscape ReactomeFIViz functional interaction network?
  
  (Asked by: username_0 on 2024-11-22)
  
  I'm a bit stuck trying to figure out how Cytoscape ReactomeFIViz decides how nodes are colored in my Cytoscape functional interaction network generated from my input RNAseq dataset (table).
  
  Can you please clarify?
  
  **Tags:** rna-seq, differential-expression, gene-expression, cytoscape
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: Could you show us an image of what you are seeing, perhaps? That could help. Have you looked at any of the tool's [documentation](https://reactome.org/tools/reactome-fiviz)?  
  > **username_0**: Thank you username_2! I am unable to find the share/upload image option. However, what I am seeing looks something like the image under the 'Cluster FI network' paragraph on reactome.org/tools/reactome-fiviz#Gene_Set.2FMutation_Analysis . I looked through this documentation & under 4.1 Gene Set/Mutation Analysis  it says Cluster FI network: run a network clustering algorithm (spectral partition based network clustering by Newman 2006) on the displayed FI network. Nodes in different network modules  
  > **username_0**: will be shown in different colors (different colors used only for first 15 modules based on sizes). What does this mean exactly? Does the same apply to my analysis which uses  4.3 Microarray Data Analysis (even though the data I am analyzing is RNAseq) ?  
  
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  ## 1 answers
  
  ### Answer by username_3 on 2024-12-12. Score: 0
  
  I believe the clustering is based on connectivity, not your fold change values, so it would matter exactly how you got your network.
  
  
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