Figure 1.

An illustration of the concept of the gene ensemble (vertical oval) and the gene ensemble instance (horizontal oval), representing the essence of the MED method for deriving principles of transcription regulation. A gene ensemble is defined as a collection of genes containing a motif set of interest, whereas one of its instances comprises a subset of this collection containing the motif set with specified constraints such as motif geometry. Other constraints can also encompass motif exact sequence (a specific instance motif consensus sequence), multiplicity, cooccurrence with other motif sets, or any combination. Each horizontal oval object's color represents a gene expression pattern pertaining to such gene ensemble instance.