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Gene networks

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Abstract

Gene network is a group of genes functioning in a coordinated manner to control vital processes in an organism. Each gene network includes several essential components: (1) a group of genes which form a core of a gene network, (2) proteins encoded by these genes, (3) signal transduction pathways, (4) negative and positive feedback which provide for autoregulation, and (5) low-molecular-weight compounds. To accumulate the information on gene networks, a database GeneNet has been developed (http://wwwmgs.bionet.nsc.ru/systems/mgl/genet/). At present, GeneNet contains the data on 16 gene networks which are arranged in six sections according to the subject concerned: lipid metabolism, steroidogenesis, erythropoiesis, antiviral response, plant seed development, and heat shock. Analysis of these data revealed the following principles of the gene network organization: (1) there is a great variety of molecular mechanisms which provide for a feedback regulation; (2) each gene network includes key genes which coordinate the function of the other genes of the gene network; (3) one transcription factor activates many genes via a cassette mechanism; and (4) gene networks are autoregulated via regulatory circuits with positive and negative feedback.

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References

  1. Kolpakov, F.A., Ananko, E.A., Kolesov, G.B., and Kolchanov, N.A.,Bioinformatics, 1998, vol. 14, pp. 529–537.

    Article  PubMed  CAS  Google Scholar 

  2. Kolpakov, F.A. and Ananko, E.A.,Bioinformatics, 1999, vol. 15, pp. 713–714.

    Article  PubMed  CAS  Google Scholar 

  3. Buss, W.C. and Stepanek, J.,Int. J. Immunopharmacol., 1993, vol. 15, pp. 63–76.

    Article  PubMed  CAS  Google Scholar 

  4. Pyronnet, S., Vagner, S., Bouisson, M.,et al., Cancer Res., 1996, vol. 56, pp. 1742–1745.

    Google Scholar 

  5. Nandabalan, K. and Roeder, G.S.,Mol. Cell. Biol., 1995, vol. 15, pp. 1953–1960.

    PubMed  CAS  Google Scholar 

  6. Yao, K.S., Godwin, A.K., Johnson, C., and O'Dwyer, P.J.,Cancer Res., 1996, vol. 56, pp. 1731–1736.

    Google Scholar 

  7. Hochstrasser, M.,Cell, 1996, vol. 84, pp. 813–815.

    Article  Google Scholar 

  8. Weissmuller, G. and Bisch, P.M.,Eur. Biophys. J., 1993, vol. 22, pp. 63–70.

    Article  PubMed  CAS  Google Scholar 

  9. Ratner, V.A.,Geneticheskie upravlyayushchie sistemy (Regulatory Genetic Systems), Novosibirsk: Nauka, 1966.

    Google Scholar 

  10. Kauffman, S.,J. Theor. Biol., 1969, vol. 22, pp. 437–467.

    Article  PubMed  CAS  Google Scholar 

  11. Thomas, R.,J. Theor. Biol., 1973, vol. 42, pp. 563–585.

    Article  PubMed  CAS  Google Scholar 

  12. Savageau, M.,Biomed. Biochim. Acta, 1985, vol. 44, pp. 875–880.

    PubMed  CAS  Google Scholar 

  13. McAdams, H. and Arkin, A.,Proc. Natl. Acad. Sci. USA, 1997, vol. 94, pp. 814–819.

    Article  PubMed  CAS  Google Scholar 

  14. Kolchanov, N.A., Ed.,Mol. Biol., 1997, vol. 31, pp. 581–768.

  15. Igarashi, T. and Kaminuma, T.,Pac. Symp. Biocomput., 1997, pp. 187–197.

  16. Hopkins, T., Advani, R., and Gudmunson, G.,Clin. Chem., 1995, vol. 41, pp. 1333–1337.

    PubMed  CAS  Google Scholar 

  17. Serov, V.N., Spirov, A.V., and Samsonova, M.G.,Bioinformatics, 1998, vol. 14, pp. 546–547.

    Article  PubMed  CAS  Google Scholar 

  18. Kanehisa, M. and Goto, S.,Nucleic Acids Res., 2000, vol. 28, pp. 27–30.

    Article  PubMed  CAS  Google Scholar 

  19. Karp, P.D., Riley, M., Saier, M., et al.,Nucleic Acids Res., 2000, vol. 28, pp. 56–59.

    Article  PubMed  CAS  Google Scholar 

  20. Schweigert, S., Herde, P.V., and Sibbald, P.R.,Comput. Appl. Biosci., 1995, vol. 11, pp. 339–347.

    PubMed  CAS  Google Scholar 

  21. DeGregori, J., Kowalik, T., and Nevins, J.R.,Mol. Cell. Biol., 1995, vol. 15, pp. 4215–4224.

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  23. Agarwal, M.L., Agarwal, A., Taylor, W.R., and Stark, G.R.,Proc. Natl. Acad. Sci. USA, 1995, vol. 92, pp. 8493–8497.

    Article  PubMed  CAS  Google Scholar 

  24. Kel', O.V. and Kel', A.E.,Mol. Biol., 1997, vol. 31, pp. 656–670.

    Google Scholar 

  25. Elliott, S., Lorenzini, T., Yanagihara, D.,et al., J. Biol. Chem., 1996, vol. 271, pp. 24691–24697.

    Google Scholar 

  26. Boyes, J., Byfield, P., Nakatani, Y., and Ogryzko, V.,Nature, 1998, vol. 396, pp. 594–598.

    Article  PubMed  CAS  Google Scholar 

  27. Zhang, W. and Bieker, J.J.,Proc. Natl. Acad. Sci. USA, 1998, vol. 95, pp. 9855–9860.

    Article  PubMed  CAS  Google Scholar 

  28. Dalyot, N., Fibach, E., Ronchi, A., Rachmilewitz, E.A., Ottolenghi, S., and Oppenheim, A.,Nucleic Acids Res., 1993, vol. 21, pp. 4031–4037.

    Article  PubMed  CAS  Google Scholar 

  29. Tsai, S.-F., Strauss, E., and Orkin, S.H.,Genes Dev., 1991, vol. 5, pp. 919–931.

    Article  PubMed  CAS  Google Scholar 

  30. Chin, K., Oda, N., Shen, K., and Noguchi, C.T.,Nucleic Acids Res., 1995, vol. 23, pp. 3041–3049.

    Article  PubMed  CAS  Google Scholar 

  31. Vieille-Grosjean, I. and Huber, P.,J. Biol. Chem., 1995, vol. 270, pp. 4544–4550.

    Article  PubMed  CAS  Google Scholar 

  32. Mikkonen, A., Porali, I., Cercos, M., and Ho, T.D.,Plant Mol. Biol., 1996, vol. 31, pp. 239–254.

    Article  Google Scholar 

  33. Ericsson, J., Jacson, S.M., Lee, B.C., and Edwards, P.A.,Proc. Natl. Acad. Sci. USA, 1996, vol. 93, pp. 945–950.

    Article  Google Scholar 

  34. Wang, X., Pai, J.-T., Wiedenfeld, E.A.,et al., J. Biol. Chem., 1995, vol. 270, pp. 18044–18050.

    Article  PubMed  CAS  Google Scholar 

  35. Lloyd, D.B. and Thompson, J.F.,J. Biol. Chem., 1995, vol. 270, pp. 25812–25818.

    Article  PubMed  CAS  Google Scholar 

  36. Fisher, R.F. and Long, S.R.,J. Mol. Biol., 1993, vol. 233, pp. 336–348.

    Article  PubMed  CAS  Google Scholar 

  37. Cook, D., Dreyer, D., Bonnet, D.,et al., Plant Cell, 1995, vol. 7, pp. 43–55.

    Article  PubMed  CAS  Google Scholar 

  38. Yang, W.C., de Blank, C., Meskiene, I.,et al., Plant Cell, 1994, vol. 6, pp. 1415–1426.

    Article  PubMed  CAS  Google Scholar 

  39. Minami, E., Kouchi, H., Cohn, J.R.,et al., Plant J., 1996, vol. 10, pp. 23–32.

    Article  Google Scholar 

  40. Nap, J.P. and Bisseling, T.,Science, 1990, vol. 250, pp. 948–954.

    Article  PubMed  CAS  Google Scholar 

  41. Kouchi, H. and Hata, S.,Mol. Plant-Microbe Interact., 1995, vol. 8, pp. 172–176.

    PubMed  CAS  Google Scholar 

  42. Qureshi, S.A., Salditt-Georgieff, M., and Darnell, J.E., Jr.,Proc. Natl. Acad. Sci. USA 1995, vol. 92, pp. 3829–3833.

    Article  PubMed  CAS  Google Scholar 

  43. Pine, R., Canova, A., and Schindler, C.,EMBO J., 1994, vol. 13, pp. 158–167.

    PubMed  CAS  Google Scholar 

  44. Thanos, D. and Maniatis, T.,Mol. Cell. Biol., 1995, vol. 15, pp. 152–164.

    PubMed  CAS  Google Scholar 

  45. Harada, H., Takahashi, E.-I., Itoh, S.,et al., Mol. Cell. Biol., 1994, vol. 14, pp. 1500–1509.

    PubMed  CAS  Google Scholar 

  46. Morimoto, R.,Genes Dev., 1998, vol. 12, pp. 3788–3796.

    PubMed  CAS  Google Scholar 

  47. Kim, D., Ouyang, H., and Li, G.C.,Proc. Natl. Acad. Sci. USA, 1995, vol. 92, pp. 2126–2130.

    Article  PubMed  CAS  Google Scholar 

  48. Ghoshal, K. and Jacob, S.T.,Biochem. J., 1996, vol. 317, pp. 689–695.

    Google Scholar 

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Authors and Affiliations

  1. Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, 630090, Novosibirsk, Russia

    N. A. Kolchanov, E. A. Anan’ko, F. A. Kolpakov, O. A. Podkolodnaya, E. V. Ignat’eva, T. N. Goryachkovskaya & I. L. Stepanenko

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  1. N. A. Kolchanov
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  2. E. A. Anan’ko
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  3. F. A. Kolpakov
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  5. E. V. Ignat’eva
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  6. T. N. Goryachkovskaya
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  7. I. L. Stepanenko
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Correspondence to N. A. Kolchanov.

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Kolchanov, N.A., Anan’ko, E.A., Kolpakov, F.A. et al. Gene networks. Mol Biol 34, 449–460 (2000). https://doi.org/10.1007/BF02759554

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  • DOI: https://doi.org/10.1007/BF02759554

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