I have a set of biologically relevant transcriptional regulatory networks which are bipartite with a set of transcription factors and the genes that they regulate. However, when I put my network on Cytoscape to get the centrality measures, average path length etc and treat the network as directed, I get a value of either 1 or zero for each node. When I treat the network as un-directed, I get a range of different values for centrality measures etc. I need to compare this network with another one which I have. Does it make sense that I treat the network as un-directed to get the values for comparison because with just 1 and 0 I cant get much. Could you refer to any published papers in which networks have been treated as un-directed for a comparison of topological features.

  • $\begingroup$ Some sidenotes: 1) Have you ensured that your software is properly working for directed networks? 2) Don’t use an approach or measure because somebody else has used it before you (probably for a different application); use it because it makes sense for your question. Don’t just slap measures and transformations onto your network until you get some data (that is not obviously nonsensical); think about what you want to find out! $\endgroup$ – Wrzlprmft Oct 5 '17 at 16:03
  • $\begingroup$ @Wrzlprmft price.systemsbiology.org/research/… On this page, there is an excel sheet with the network on it. Could you please take a look at it and let me know what you think. I don't think I am using Cytoscape wrong. I split that network into 8 clusters using the community clustering algorithm and what I want to do is basically compare the toplogical features of the different clusters. $\endgroup$ – Charles Oct 6 '17 at 12:24

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