Based on the analysis of the published literature, we have defined two groups of direct targets: confirmed and unconfirmed. A confirmed direct target has been defined as a gene that responds to a given TF according to the following criteria. (1) The TF binds directly to the regulatory region of the target gene, as shown by electrophoretic mobility shift assay, yeast one-hybrid analysis, and/or ChIP; or (2) the TF directly regulates the target gene, based on use of transgenic plants expressing an inducible TF-GR fusion protein, and the effect of CHX on the DEX activated/repressed genes; and (3) in vivo evidence of regulation showing expression of the target gene is affected by either loss-of-function mutations in the TF or ectopic expression of that TF in the plant.

An unconfirmed direct target is one that has been suggested to be a direct target of a given TF by one of the approaches described above.