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Transcription Regulation of Eukaryotic Genes: Description in the TRRDatabase

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Abstract

The structure of the Transcription Regulatory Regions Database (TRRD) and the principles of describing transcription regulation of eukaryotic genes in TRRD are considered. Formalized description of the structural and functional organization of the regulatory gene regions is illustrated with examples. By now, TRRD is based on 3500 original works and contains data on transcription regulation of more than 1100 genes known to possess more than 5000 transcription factor binding sites and about 1600 regulatory elements (promoters, enhancers, silencers). TRRD is available at http://www.bionet.nsc.ru/trrd/

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References

  1. Stoesser, G., Baker, W., van den Broek, A., et al., Nucleic Acids Res., 2001, vol. 29, pp. 17–21.

    PubMed  Google Scholar 

  2. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., et al., Nucleic Acids Res., 2000, vol. 28, pp. 15–18.

    PubMed  Google Scholar 

  3. Bairoch, A. and Apweiler, R., Nucleic Acids Res., 2000, vol. 28, pp. 45–48.

    PubMed  Google Scholar 

  4. Barker, W.C., Garavelli, J.S., Hou, Z., et al., Nucleic Acids Res., 2001, vol. 29, pp. 29–32.

    PubMed  Google Scholar 

  5. Bhat, T.N., Bourne, P., Feng, Z., et al., Nucleic Acids Res., 2001, vol. 29, pp. 214–218.

    PubMed  Google Scholar 

  6. Wingender, E., Chen, X., Fricke, E., et al., Nucleic Acids Res., 2001, vol. 29, pp. 281–283.

    PubMed  Google Scholar 

  7. Kel-Margoulis, O.V., Romashchenko, A.G., Kolchanov, N.A., et al., Nucleic Acids Res., 2000, vol. 28, pp. 311–315.

    PubMed  Google Scholar 

  8. Perier, R.C., Praz, V., Junier, T., et al., Nucleic Acids Res., 2000, vol. 28, pp. 302–303.

    PubMed  Google Scholar 

  9. Kolchanov, N.A., Podkolodnaya, O.A., Ananko, E.A., et al., Nucleic Acids Res., 2000, vol. 28, pp. 298–301.

    PubMed  Google Scholar 

  10. Kolchanov, N.A., Ananko, E.A., Podkolodnaya, O.A., et al., Nucleic Acids Res., 1999, vol. 27, pp. 303–306.

    PubMed  Google Scholar 

  11. Kolchanov, N.A., Ponomarenko, M.P., Kel, A.E., et al., Proc. Int. Conf. Intell. Syst. Mol. Biol., 1998, pp. 95–104.

  12. Kolchanov, N.A., Ponomarenko, M.P., Frolov, A.S., et al., Bioinformatics, 1999, vol. 15, pp. 669–686.

    PubMed  Google Scholar 

  13. Kel', A.E., Kolchanov, N.A., Kel', O.V., et al., Mol. Biol., 1997, vol. 31, pp. 626–636.

    Google Scholar 

  14. Carey, M. and Smale, S.T., Transcriptional Regulation in Eukaryotes, Cold Spring Harbor, N.Y.: Cold Spring Harbor Lab. Press, 1999.

    Google Scholar 

  15. Vorobiev, D.G., Ponomarenko, J.V., and Podkolodnaya, O.A., '98, Novosibirsk, 1998, pp. 58–61.

  16. Darnell, J.E., Jr., Kerr, I.M., and Stark, G.R., Science, 1994, vol. 264, pp. 1415–1421.

    Google Scholar 

  17. Harada, H., Takahashi, E.-I., Itoh, S., et al., Mol. Cell. Biol., 1998, vol. 14, pp. 1500–1509.

    Google Scholar 

  18. Pitha, P.M., Au, W.C., Lowther, W., et al., Biochimie, 1998, vol. 80, pp. 651–658.

    PubMed  Google Scholar 

  19. Jesse, T.L., LaChance, R., Iademarco, M.F., and Dean, D.C., J. Cell Biol., 1998, vol. 140, pp. 1265–1276.

    PubMed  Google Scholar 

  20. Eklund, E.A., Jalava, A., and Kakar, R., J. Biol. Chem., 1998, vol. 273, pp. 13957–13965.

    PubMed  Google Scholar 

  21. Peters, B., Merezhinskaya, N., Diffley, J.F.X., and Noguchi, C.T., J. Biol. Chem., 1993, vol. 268, pp. 3430–3437.

    PubMed  Google Scholar 

  22. Raich, N., Clegg, C.H., Grofti, J., et al., EMBO J., 1995, vol. 14, pp. 801–809.

    PubMed  Google Scholar 

  23. Garlatti, M., Daheshia, M., Slater, E., et al., Mol. Cell. Biol., 1994, vol. 14, pp. 8007–8017.

    PubMed  Google Scholar 

  24. Kel, O.V., Romaschenko, A.G., Kel, A.E., et al., Nucleic Acids Res., 1995, vol. 23, pp. 4097–4103.

    PubMed  Google Scholar 

  25. Harnish, D.C., Malik, S., and Karathanasis, S.K., J. Biol. Chem., 1994, vol. 269, pp. 28220–28226.

    PubMed  Google Scholar 

  26. Grosveld, F., van Assendelft, G.B., Greaves, D.R., and Kollias, G., Cell, 1987, vol. 51, pp. 975–985.

    Article  PubMed  Google Scholar 

  27. Jackson, J.D., Petrykowska, H., Philipsen, S., et al., J. Biol. Chem., 1996, vol. 271, pp. 11871–11888.

    PubMed  Google Scholar 

  28. Lowrey, C.H., Bodine, D.M., and Neinhuis, A.W., Proc. Natl. Acad. Sci. USA, 1992, vol. 89, pp. 1143–1147.

    PubMed  Google Scholar 

  29. Podkolodnaya, O.A., Levitsky, V.G., and Podkolodnyi, N.L., Mol. Biol., 2001, vol. 35, pp. 943–951.

    Google Scholar 

  30. Johnson, D.G., Ohtani, K., and Nevis, J.R., Genes Dev., 1994, vol. 8, pp. 1514–1525.

    PubMed  Google Scholar 

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Kolchanov, N.A., Podkolodnaya, O.A., Ananko, E.A. et al. Transcription Regulation of Eukaryotic Genes: Description in the TRRDatabase. Molecular Biology 35, 794–801 (2001). https://doi.org/10.1023/A:1013269831147

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