ExportingWGCNA data for Ingenutity IPA
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Last seen 5.3 years ago
University of Illinois, Urbana-Champaign

I have RNASeq data for which I performed differential expression analysis (using the R package edgeR) and gene coexpression analysis using the R package WGCNA in order to separate my genes into gene modules.

I see that wgcna has functions to export its data to cytoscape and visant for network visualization.

My question is:

  • Is IPA suitable for network visualization like cytoscape does?
  • If yes, how can I export wgcna data in the right format for IPA? Is there some function in WGCNA for exporting data for IPA as well as it does for cytoscape?

Thank you!

IPA wgcna network visualization • 1.3k views
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Last seen 6 months ago
United States

I haven't worked much with IPA but it is my understanding that IPA requires a simple list of genes, and will create the network(s) from connections curated from the literature. In contrast, Cytoscape and VisANT need the network information as input, hence the need for specific network export functions.

To export genes, follow Tutorial I, section 4a, "Output gene lists for use with online software and services". Output your favorite module as Entrez IDs or gene symbols and import it into IPA.

Whether to use IPA is up to you - do you need to visualize the network WGCNA created, or connections curated from the literature?

Entering edit mode

Thank you for your response, Peter!
I think you answered my question. 
I was using cytoscape to visualize the network WGCNA created, so I guess I will just stick to that.



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