I recently finished a WGCNA analysis with much success!
We found a module whose eigengene is highly associated with disease status and whose GO results indicate the module genes are associated with inflammatory processes that have been recurrently associated with the disease previously.
My question revolves around module hub gene selection methods. I know selecting a hub gene with a high gene significance value is important, but what about intramodular connectivity vs. kME values?
I have seen papers where folks select a hub gene based on it having a high intramodular k (connectivity) value within the module itself, and I have also seen people select a hub gene based on it having a high kME value (its expression values are highly correlated with that module's eigengene values across samples).
Does anyone understand the merits of using intramodular connectivity (k) vs. high modular membership (kME) values to pick a hub gene?
Discussion of these merits or pointing me to a paper would be most appreciated as I am having trouble finding evidence for one being a superior selection method over another.