TRANSFAC® Release 7.0 - Documentation
The FACTOR table contains 6133 entries, but this figure does not reflect the number of independent transcription factors. First of all, homologous factors from different species such as human and mouse SRF are given in different entries since they may differ in some molecular aspects. Moreover, factors which have originally been described by different research groups to bind to different genes may turn out to be identical as soon as they have been cloned. On the other hand, more and more factors are recognized to be representatives of whole transcription factor families comprising products of distinct but very similar genes or alternative splice products. In many cases, a more general term originally defining just a specific DNA-binding activity such as AP-1 appears as one entry. In most cases, this activity has not been analyzed for its subunit composition by members of the Jun and Fos families. Nevertheless, all known fos- and jun-related proteins are included as separate entries.
All factors that are mentioned in the SITE table appear in the FACTOR table as well. However, it includes also polypeptides which do not bind to DNA by themselves. One well-known example is c-Fos which is forced to contact DNA not until being complexed with, e. g., c-Jun. Information about non-DNA binding subunits of transcription factor complexes such as the TAFs is given by FACTOR as well. There are also proteins that act as inhibitors for a particular DNA-binding activity and which are of regulatory importance. Therefore, proteins such as Id, IkappaB or hsp90 have been included in TRANSFAC® FACTOR.
On the other hand, we have in general not yet entered proteins just because of the presence of a putative DNA-binding motif. Thus, there are much more zinc finger or homeo domain proteins known than are included in FACTOR, but for many of them, no data about DNA-binding specificity or about other gene important regulatory features are available.