[4] In 1997, TRANSFAC was transferred to a newly established company, BIOBASE, in order to secure long-term financing of the database.

[7] The content of the database is organized in a way that it is centered around the interaction between transcription factors (TFs) and their DNA binding sites (TFBS).

[12] The TF classification enables to analyze such data sets with regard to the properties of the DNA-binding domains.

In the context of systems-biological studies, the TF-target gene relations documented in TRANSFAC were used to construct and analyze transcription regulatory networks.

A number of algorithms exist which either use the individual binding sites or the matrix library for this purpose: Comparison of matrices with the matrix library of TRANSFAC and other sources: A number of servers provide genomic annotations computed with the aid of TRANSFAC.