Dynamical differential expression (DyDE) reveals the period control mechanisms of the Arabidopsis circadian oscillator
Fig 1
Treatments effects in transcriptional networks.
Treatment effects can be perceived as perturbations in molecular networks [18,19]. In transcriptional networks, such perturbations usually only affect a very small number of regulatory links directly. For example, only the red links have been directly affected by the treatment. All other links are unchanged, although all nodes (concentrations) in the Figure have been (indirectly) affected due to cascading and feedback effects. Hence, Differential Expression (DE) might not distinguish between direct and indirect effects of a treatment. Dynamical Differential Expression (DyDE), therefore, investigates how and why changes occur, instead of simply measuring what and how much is produced by those changes.