TF2DNA Database


Genetic regulation depends to a great extent on sequence-specific transcription factors. Transcription factors specifically recognize short DNA segments, also known as transcription factor binding sites, at promoter or enhancer regions to stimulate or repress the transcriptional process.

The TF2DNA database provides comprehensive information about transcription factor binding motifs and their regulated genes for five model organisms and humans. Binding motifs are gathered from experimental and theoretical sources. See the table below for complete statistics on the current number of binding motifs in the TF2DNA database and the corresponding references that identify the sources.

Click the Search gene tab and type or upload a list with your favorite genes to start exploring genetic networks.



  1. Pérez-Rueda, E. and Collado-Vides, J. (2000) The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res, 28, 1838-1847.
  2. Harbison, C.T., Gordon, D.B., Lee, T.I., Rinaldi, N.J., Macisaac, K.D., Danford, T.W., Hannett, N.M., Tagne, J.B., Reynolds, D.B., Yoo, J. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
  3. Reece-Hoyes, J.S., Deplancke, B., Shingles, J., Grove, C.A., Hope, I.A. and Walhout, A.J. (2005) A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol, 6, R110.
  4. Pfreundt, U., James, D.P., Tweedie, S., Wilson, D., Teichmann, S.A. and Adryan, B. (2010) FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Res, 38, D443-447.
  5. Fulton, D.L., Sundararajan, S., Badis, G., Hughes, T.R., Wasserman, W.W., Roach, J.C. and Sladek, R. (2009) TFCat: the curated catalog of mouse and human transcription factors. Genome Biol, 10, R29.
  6. Vaquerizas, J.M., Kummerfeld, S.K., Teichmann, S.A. and Luscombe, N.M. (2009) A census of human transcription factors: function, expression and evolution. Nat Rev Genet, 10, 252-263.
  7. Badis, G., Berger, M., Philippakis, A., Talukder, S., Gehrke, A., Jaeger, S., Chan, E., Metzler, G., Vedenko, A., Chen, X. et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science, 324, 1720-1723.
  8. Berger, M.F., Philippakis, A.A., Qureshi, A.M., He, F.S., Estep, P.W. and Bulyk, M.L. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol, 24, 1429-1435.
  9. Mathelier, A., Zhao, X., Zhang, A.W., Parcy, F., Worsley-Hunt, R., Arenillas, D.J., Buchman, S., Chen, C.Y., Chou, A., Ienasescu, H. et al. (2014) JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res, 42, D142-147.
  10. . Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K. et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res, 34, D108-110.
  11. Weirauch, M.T., Yang, A., Albu, M., Cote, A.G., Montenegro-Montero, A., Drewe, P., Najafabadi, H.S., Lambert, S.A., Mann, I., Cook, K. et al. (2014) Determination and inference of eukaryotic transcription factor sequence specificity. Cell, 158, 1431-1443.
  12. Zhu, C., Byers, K.J., McCord, R.P., Shi, Z., Berger, M.F., Newburger, D.E., Saulrieta, K., Smith, Z., Shah, M.V., Radhakrishnan, M. et al. (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res, 19, 556-566.
  13. Lesch, B.J., Gehrke, A.R., Bulyk, M.L. and Bargmann, C.I. (2009) Transcriptional regulation and stabilization of left-right neuronal identity in C. elegans. Genes Dev, 23, 345-358.
  14. Zhu, L.J., Christensen, R.G., Kazemian, M., Hull, C.J., Enuameh, M.S., Basciotta, M.D., Brasefield, J.A., Zhu, C., Asriyan, Y., Lapointe, D.S. et al. (2011) FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res, 39, D111-117.
  15. Berger, M.F., Badis, G., Gehrke, A.R., Talukder, S., Philippakis, A.A., Peña-Castillo, L., Alleyne, T.M., Mnaimneh, S., Botvinnik, O.B., Chan, E.T. et al. (2008) Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell, 133, 1266-1276.
  16. Chen, L., Wu, G. and Ji, H. (2011) hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. Bioinformatics, 27, 1447-1448.
  17. Jolma, A., Yan, J., Whitington, T., Toivonen, J., Nitta, K.R., Rastas, P., Morgunova, E., Enge, M., Taipale, M., Wei, G. et al. (2013) DNA-binding specificities of human transcription factors. Cell, 152, 327-339.
  18. Sebé-Pedrós, A., Ariza-Cosano, A., Weirauch, M.T., Leininger, S., Yang, A., Torruella, G., Adamski, M., Adamska, M., Hughes, T.R., Gómez-Skarmeta, J.L. et al. (2013) Early evolution of the T-box transcription factor family. Proc Natl Acad Sci U S A, 110, 16050-16055.
  19. Wei, G.H., Badis, G., Berger, M.F., Kivioja, T., Palin, K., Enge, M., Bonke, M., Jolma, A., Varjosalo, M., Gehrke, A.R. et al. (2010) Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J, 29, 2147-2160.
  20. Weirauch, M.T., Cote, A., Norel, R., Annala, M., Zhao, Y., Riley, T.R., Saez-Rodriguez, J., Cokelaer, T., Vedenko, A., Talukder, S. et al. (2013) Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol, 31, 126-134.
  21. Gerstein, M.B., Kundaje, A., Hariharan, M., Landt, S.G., Yan, K.K., Cheng, C., Mu, X.J., Khurana, E., Rozowsky, J., Alexander, R. et al. (2012) Architecture of the human regulatory network derived from ENCODE data. Nature, 489, 91-100.
  22. Kulakovskiy, I.V., Medvedeva, Y.A., Schaefer, U., Kasianov, A.S., Vorontsov, I.E., Bajic, V.B. and Makeev, V.J. (2013) HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res, 41, D195-D202.
  23. Scharer, C.D., McCabe, C.D., Ali-Seyed, M., Berger, M.F., Bulyk, M.L. and Moreno, C.S. (2009) Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer cells. Cancer Res, 69, 709-717.
  24. Pujato, M., Kieken, F., Skiles, A.A., Tapinos, N. and Fiser, A. (2014) Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes. Nucleic Acids Res, 42, 13500-13512.