After performing gene co-expression network analysis in a case-control study, I am ending up with a bunch of genes whose expression, along with its partners, is dysregulated in two conditions. These highly connected genes are considered as putative "hub" biomarkers. Since, it is not possible for us to consider all of them for experimental validation (for inhibition), what other analysis/tests can be performed to choose one or few of them? I know there is no so caller "master regulator", but somehow if I need to pick only "interesting" genes, what other statistical analysis can be performed?
All suggestions and comments are appreciated.