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Rough Sets in the Interpretation of Statistical Tests Outcomes for Genes Under Hypothetical Balancing Selection

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Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 4585))

Abstract

Detection of natural selection at the molecular level is one of the crucial problems in contemporary population genetics. There exists a number of statistical tests designed for it, however, the interpretation of the outcomes is often obscure, because of the existence of factors like population growth, migration and recombination. In his earlier work, the author has proposed the multi-null methodology, and he applied it for four genes implicated in human familial cancer: ATM, RECQL, WRN and BLM. Because of high computational effort required for estimating critical values under nonclassical nulls, mentioned methodology is not appropriate for selection screening. In the current paper, the author presents novel, rough set based methodology, helpful in the interpretation of tests outcomes applied versus only classical nulls. This method does not require long-lasting simulations and, as it is shown in the paper, it gives reliable results.

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References

  1. Kimura, M.: The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge (1983)

    Google Scholar 

  2. Zhang, J.: Evolution of the Human ASPM Gene, a Major Determinant of Brain Size. Genetics 165, 2063–2070 (2003)

    Google Scholar 

  3. Evans, P.D., Anderson, J.R., Vallender, E.J., Gilbert, S.L., Malcom, Ch.M. et al.: Adaptive Evolution of ASPM, a Major Determinant of Cerebral Cortical Size in Humans. Human Molecular Genetics 13, 489–494 (2004)

    Article  Google Scholar 

  4. Fu, Y.X., Li, W.H.: Statistical Tests of Neutrality of Mutations. Genetics 133, 693–709 (1993)

    Google Scholar 

  5. Fu, Y.X.: Statistical Tests of Neutrality of Mutations Against Population Growth, Hitchhiking and Background Selection. Genetics 147, 915–925 (1997)

    Google Scholar 

  6. Kelly, J.K.: A Test of Neutrality Based on Interlocus Associations. Genetics 146, 1197–1206 (1997)

    Google Scholar 

  7. Wall, J.D.: Recombination and the Power of Statistical Tests of Neutrality. Genet. Res. 74, 65–79 (1999)

    Article  Google Scholar 

  8. Nielsen, R.: Statistical Tests of Selective Neutrality in the Age of Genomics. Heredity 86, 641–647 (2001)

    Article  Google Scholar 

  9. Cyran, K.A., Polañska, J., Kimmel, M.: Testing for Signatures of Natural Selection at Molecular Genes Level. J. Med. Inf. Techn. 8, 31–39 (2004)

    Google Scholar 

  10. Dhillon, K.K., Sidorova, J., Saintigny, Y., Poot, M., Gollahon, K., Rabinovitch, P.S., Mon-nat Jr., R.J.: Functional Role of the Werner Syndrome RecQ Helicase in Human Fibroblasts. Aging Cell 6, 53–61 (2007)

    Article  Google Scholar 

  11. Karmakar, P., Seki, M., Kanamori, M., Hashiguchi, K., Ohtsuki, M., Murata, E., Inoue, E., Tada, S., Lan, L., Yasui, A., Enomoto, T.: BLM is an Early Responder to DNA Double-strand Breaks. Biochem. Biophys. Res. Commun. 348, 62–69 (2006)

    Article  Google Scholar 

  12. Golding, S.E., Rosenberg, E., Neill, S., Dent, P., Povirk, L.F., Valerie, K.: Extracellular Signal-Related Kinase Positively Regulates Ataxia Telangiectasia Mutated, Homologous Recombination Repair, and the DNA Damage Response. Cancer Res. 67, 1046–1053 (2007)

    Article  Google Scholar 

  13. Schneider, J., Philipp, M., Yamini, P., Dork, T., Woitowitz, H.J.: ATM Gene Mutations in Former Uranium Miners of SDAG Wismut: a Pilot Study. Oncol. Rep. 17, 477–482 (2007)

    Google Scholar 

  14. Polanska, J.: The EM Algorithm and its Implementation for the Estimation of the Frequencies of SNP-Haplotypes. Int. J. Appl. Math. Comp. Sci. 13, 419–429 (2003)

    MATH  MathSciNet  Google Scholar 

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Marzena Kryszkiewicz James F. Peters Henryk Rybinski Andrzej Skowron

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© 2007 Springer-Verlag Berlin Heidelberg

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Cyran, K. (2007). Rough Sets in the Interpretation of Statistical Tests Outcomes for Genes Under Hypothetical Balancing Selection. In: Kryszkiewicz, M., Peters, J.F., Rybinski, H., Skowron, A. (eds) Rough Sets and Intelligent Systems Paradigms. RSEISP 2007. Lecture Notes in Computer Science(), vol 4585. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73451-2_75

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  • DOI: https://doi.org/10.1007/978-3-540-73451-2_75

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-73450-5

  • Online ISBN: 978-3-540-73451-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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