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Recognition of transcription factor binding sites by the SiteGA method

  • Molecular Biophysics
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Abstract

A new method, SiteGA, is proposed to recognize transcription factor binding sites. The method is based on the determination of locally positioned dinucleotides using a genetic algorithm and discriminant analysis. The method was used to develop programs for recognizing sites involved in the regulation of immune response and the cell growth (AP-1, IRF1, ISGF3, NFκB, STAT1) and the regulation of lipid metabolism (HNF4, PPAR, SREBP) and expression of steroidogenesis genes (SF-1). It was shown that the SiteGA method is far superior in accuracy to the widely used position weight matrix method. The web interface of the SiteGA recognition program is available at the address: http://wwwmgs2.bionet.nsc.ru/mgs/programs/sitega.

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Abbreviations

TFBS:

transcription factor binding sites

PWM:

position weight matrix

TF:

transcription factor

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Authors and Affiliations

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

    V. G. Levitskii, E. V. Ignat’eva, E. A. Anan’ko, T. I. Merkulova & N. A. Kolchanov

  2. Novosibirsk State University, Novosibirsk, 630090, Russia

    V. G. Levitskii, E. V. Ignat’eva & N. A. Kolchanov

  3. Multidisciplinary Centre for Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK

    C. Hodgman

Authors
  1. V. G. Levitskii
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  2. E. V. Ignat’eva
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  3. E. A. Anan’ko
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  4. T. I. Merkulova
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  5. N. A. Kolchanov
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  6. C. Hodgman
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Additional information

Original Russian Text © V.G. Levitskii, E.V. Ignat’eva, E.A. Anan’ko, T.I. Merkulova, N.A. Kolchanov, C.Hodgman, 2006, published in Biofizika, 2006, Vol. 51, No. 4, pp. 633–639.

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Levitskii, V.G., Ignat’eva, E.V., Anan’ko, E.A. et al. Recognition of transcription factor binding sites by the SiteGA method. BIOPHYSICS 51, 565–570 (2006). https://doi.org/10.1134/S0006350906040087

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  • DOI: https://doi.org/10.1134/S0006350906040087

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