Illustration of differential coexpression scenarios. Panel A: A gene network is in a coexpressed state in condition 1 as shown by the red background. In condition 2 an important regulator of that network is now inactive and the module is no longer coexpressed. This scenario is an example of the differential coexpression type described by criterion (i). Panel B: Two pathways are coordinated in condition 1 via an important hub gene (shown in blue) whose inactivity in condition 2 means the two pathways are no longer coexpressed. This exemplifies the module-to-module differential coexpression described by criterion (ii).