The design of "cis"-regulatory modules is such that transcription factors and epigenetic modifications serve as inputs, and the output of the module is the command given to the transcription machinery, which in turn determines the rate of gene transcription or whether it is turned on or off. There are two types of transcription factor inputs: those that determine when the target gene is to be expressed and those that serve as functional "drivers", which come into play only during specific situations during development. These inputs can come from different time points, can represent different signal ligands, or can come from different domains or lineages of cells. However, a lot still remains unknown.