Os factores de transcrición clasifícanse con frecuencia baseándose na similaridadesemellanza das súas secuencias e, por tanto, na [[estrutura terciaria]] dos seus dominios de unión ao ADN. Distínguense os seguintes grupos:<ref name="pmid15706513">{{Cita publicación periódica | author = Stegmaier P, Kel AE, Wingender E | title = Systematic DNA-binding domain classification of transcription factors | journal = Genome informatics. International Conference on Genome Informatics | volume = 15 | issue = 2 | pages = 276–86 | year = 2004 | pmid = 15706513 | doi = | url = http://www.jsbi.org/journal/GIW04/GIW04F028.html}}</ref><ref name="pmid16381825">{{Cita publicación periódica | author = Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E | title = TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes | journal = Nucleic Acids Res. | volume = 34 | issue = Database issue | pages = D108–10 | year = 2006 | pmid = 16381825 | pmc = 1347505 | doi = 10.1093/nar/gkj143}}</ref><ref>{{cite web|title=TRANSFAC database|url=http://www.gene-regulation.com/pub/databases/transfac/cl.html|accessdate = 2007-08-05}}</ref>
