The core of TRANSFAC® comprises contents of two domains: One documents TF binding sites, usually in promoters or enhancers. The other describes the binding proteins (TFs).
Binding sites referring to the same TF are merged into a positional weight matrix. Such a matrix reflects the frequency with which each nucleotide is found in each position of this TF’s binding sites and, thus, the base preference in each position.
Transcription factors are subsumed to classes, based on the general properties of their DNA-binding domains. This early attempt has been expanded to a comprehensive TF classification, the latest version of which can be found here.