BIOLOGY GETS COMPLEX. “Approaches that come closer to a systems driven analysis of differential expression have used gene network data to guide the multivariate analysis under the assumption that genes for which an interaction exist are correlated in their differential expression states or have taken an Empirical Bayes approach by modeling networks as a Markov random field (MRF) to identify genes and sub-networks that are related to diseases.”
https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1