After a systematically reviewing recently-published literatures, we refined family assignment rules in v2.0. Families that do not meet the criteria ('Transcription factors are proteins that show sequence-specific DNA binding and are capable of activating or/and repressing transcription') were excluded in the updated version, such as transcription cofactors (e.g. AUX/IAA, GIF and chromatin related proteins like chromatin remodeling factors (e.g. ARID), histone demethylases (e.g. JUMONJI), histone acetyltransferase (e.g. PcG ). Moreover, questionable families (e.g. TUBBY-like, Alfin-like, FHA, and ZIM) were also removed in the updated PlantTFDB. On the other side, five newly identified TF families (DBB, FAR1, LSD, NF-X1, STAT) were added. Considering differences in domain composition, DNA binding specificity and function, AP2/ERF and HB families in previous PlantTFDB were divided to sub-families. Especially, because it has been reported that some M type MADS could be potential pseudogenes or a new class of transposable elements, we also subdivided those M type MADS to a new subfamily.

In new rules, there were three types of domain to determine which family a TF belongs to, including DNA-binding domain, auxiliary domain and forbidden domain. In most cases, DNA-binding domain self can assign a TF to one certain family correctly. But In some cases, an auxiliary domain was needed to classify TF into corresponding family. For example, if a protein only contains a DNA-binding domain - B3, we can assign it to B3 superfamily. However, B3 superfamily can be divided into two subfamilies (ARF and B3), and so auxiliary domain need be used to distinguish these two families: if the protein contains Auxin_resp domain, it was assigned to ARF family, else it will be assigned to B3 family. Different from previous version, forbidden domains were used to distinguish proteins containing DNA-binding domain but having no transcription activity. If a protein contains the forbidden domain, then we think it was not TF, and should not be collected by PlantTFDB.