I ran module preservation analysis between two condition and on the basis of preservation z summary i would to go for downstream analysis.So I m interested in looking for hub-genes of those modules which have lowest z summary. But so far in the tutorial i didn't find a section in the WGCNA tutorial where how to find hubgenes after module preservation analysis was mentioned.

Any suggestion would be really appreciated


Simply select the module(s) you are interested in and look for hub genes using the standard calculations. Having done a module preservation analysis does not change the procedure in the slightest.

  • $\begingroup$ but so far what i used to do i run network analysis on individual condition and find hub genes but in module preservation i haven;t found the step or the output from which I can look for hub-genes it would be really helpful ,if you can cite me "using the standard calculations. " in your site $\endgroup$ – krushnach Chandra Jan 10 '20 at 20:12
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    $\begingroup$ Well, if you ran module preservation, you must have already previoulsy done a network analysis of at least the reference data. Go back to that network analysis and focus on the modules flagged by the preservation analysis. Use kME in those modules to select the top hubs. Section 3d of Tutorial I shows you how to create a table of kMEs. $\endgroup$ – Peter Langfelder Jan 13 '20 at 21:46
  • $\begingroup$ thank you for the reference $\endgroup$ – krushnach Chandra Jan 14 '20 at 6:50

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