Evolutionary dynamics of oncogenes and tumor suppressor genes: Higher intensities of purifying selection than other genes

Molecular Biology and Evolution

Volumn 20, Issue 6, 2003, Pages 964-968

  Thomas, Michael A ^a,c,d   Weston, Benjamin ^a   Joseph, Moltu ^a   Wu, Wenhua ^a   Nekrutenko, Anton ^b,d   Tonellato, Peter J ^a  

^a MEDICAL COLLEGE OF WISCONSIN   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c Nucl Eng Idaho State University   (United States)

^d PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Darwinian selection; Disease gene; Oncogene; Purifying selection; Synonymous and nonsynonymous substitutions

Indexed keywords

AMINO ACID SUBSTITUTION; ANALYSIS OF VARIANCE; ARTICLE; CARCINOGENESIS; GENE EXPRESSION; GENE FUNCTION; GENETIC ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; ONCOGENE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TUMOR SUPPRESSOR GENE;

EVOLUTION, MOLECULAR; GENES, TUMOR SUPPRESSOR; HUMANS; NEOPLASMS; ONCOGENES; SELECTION (GENETICS);

DARWINIA;

EID: 0038586458     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg110     Document Type: Article

References (27)

1. Bielawski, J. P., K. A. Dunn, and Z. Yang. 2000. Rates of nucleotide substitution and mammalian nuclear gene evolution: approximate and maximum-likelihood methods lead to different conclusions. Genetics 156:1299-1308.
2. Fearon, E. R. 1997. Human cancer syndromes: clues to the origin and nature of cancer. Science 278:1043-1050.
3. Fortini, M. E., M. P. Skupski, M. S. Boguski, and I. K. Hariharan. 2000. A survey of human disease gene counterparts in the Drosophila genome. J. Cell. Biol. 150:F23-30.
4. Gentleman, R., and R. Ihaka. 1996. R: a language for data analysis and graphics. J. Comp. Graph. Stat. 5:299-314.
5. Gojobori, T., and S. Yokoyama. 1987. Molecular evolutionary rates of oncogenes. J. Mol. Evol. 26:148-156.
6. Hirsh, A. E., and H. B. Fraser. 2001. Protein dispensability and rate of evolution. Nature 411:1046-1049.
7. Hurst, L. D., and C. Pal. 2001. Evidence for purifying selection acting on silent sites in BRCA1. Trends Genet. 17: 62-65.
8. Hurst, L. D., and N. G. Smith. 1999. Do essential genes evolve slowly? Curr. Biol. 9:747-750.
9. Ina, Y. 1995. New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J. Mol. Evol. 40:190-226.
10. Jimenez-Sanchez, G., B. Childs, and D. Valle. 2001. Human disease genes. Nature 409:853-855.
11. Kumar, S., and S. B. Hedges. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920.
12. Kumar, S., and S. Subramanian. 2002. Mutation rates in mammalian genomes. Proc. Natl. Acad. Sci. USA 99: 803-808.
13. Liberles, D. A. 2001. Evaluation of methods for determination of a reconstructed history of gene sequence evolution. Mol. Biol. Evol. 18:2040-2047.
14. Makalowski, W., and M. S. Boguski. 1998. Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. Proc. Natl. Acad. Sci. USA 95:9407-9412.
15. Mann, H., and D. Whitney. 1947. On a test of whether one of two random variables is stochastically larger than the other. Ann. Math. Statist. 18:50-60.
16. Mushegian, A. R., D. E. Bassett Jr., M. S. Boguski, P. Bork, and E. V. Koonin. 1997. Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs. Proc. Natl. Acad. Sci. USA 94:5831-5836.
17. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
18. Nei, M., and S. Kumar. 2000. Molecular evolution and phylogenetics. Oxford University Press, New York.
19. Nei, M., P. Xu, and G. Glazko. 2001. Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms. Proc. Natl. Acad. Sci. USA 98:2497-2502.
20. S ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Res. 12:198-202.
21. Nesse, R. M. 2001. How is Darwinian medicine useful? West. J. Med. 174:358-360.
22. Reiter, L. T., L. Potocki, S. Chien, M. Gribskov, and E. Bier. 2001. A systematic analysis of human disease-associated gene sequences in Drosophila melanogaster. Genome Res. 11: 1114-1125.
23. Rubin, G. M., M. D. Yandell, J. R. Wortman et al. (50 coauthors) 2000. Comparative genomics of the eukaryotes. Science 287:2204-2215.
24. Stearns, S. C., and D. Ebert. 2001. Evolution in health and disease: work in progress. Q. Rev. Biol. 76:417-432.
25. Yang, Z., and J. P. Bielawski. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15:496-503.
26. Yang, Z., and R. Nielsen. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17:32-43.
27. Zar, J. H. 1999. Biostatistical analysis. Prentice Hall, Upper Saddle River, N.J.