signed kME(MM) for finding hub genes in modules of interest
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chiayi • 0
@chiayi-13269
Last seen 6.1 years ago
New York University

I found a related but not quite the same quesiton in this post (Using WGCNA egiengenes for modules in correlated networks) as mine is specific about findind the hub genes in modules of interest. The hub gene I refer to in this post follows the definition in 7d of this turorial (https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/Simulated-07-Membership.pdf): abs(GS) and abs(MM) above a certain threshold.

Following this criteria I found some of the hubs turned out coming from modules outside the module of interest. For example, if I want to find hub genes in module brown by requesting hub=abs(GS) > .75 & abs(datKME$MM.brown)> .75, a few hubs that met the requirement belong to non-brown module. This is due to the fact that their MMbrown was smaller than -0.75. 

My understanding for MM is the corelation of  the gene expression and the module eigengene. Finding hubs with negative corelation with eigengene seems counter-intuitive to me. Maybe I miss some part about this concept. Any input/clarification would be greatly appreciated.

wgcna • 1.8k views
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Why did you not restrict the selection of hub genes to the subset of genes assigned to the brown module? You are interested in hub genes of that module, aren't you? So don't subset all the genes,

As you can see in the linked question I personally don't like to select hub genes by the absolute value of their correlations. The cor(MM, GS) of a module can be quite different from cor(abs(MM), abs(GS)).

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