Universal 1/f noise, crossovers of scaling exponents, and chromosome-specific patterns of guanine-cytosine content in DNA sequences of the human genome

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 71, Issue 4, 2005, Pages

  Li, Wentian ^a   Holste, Dirk ^b  

^a Robert S Boas Ctr Genom/Hum G   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE CONTENT; HUMAN CHROMOSOMES; HUMAN GENOME; POWER SPECTRUM;

BACTERIA; CONCENTRATION (PROCESS); CORRELATION METHODS; ELECTRIC CURRENTS; GENES; MATHEMATICAL MODELS; MUTAGENESIS; PROTEINS;

DNA SEQUENCES;

DNA;

AUTOMATED PATTERN RECOGNITION; BIOLOGICAL MODEL; CHEMICAL MODEL; CHROMOSOME MAP; COMPUTER SIMULATION; CROSSING OVER; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; HUMAN; HUMAN CHROMOSOME; NUCLEOTIDE SEQUENCE; PROCEDURES; STATISTICAL MODEL; STATISTICS;

BASE COMPOSITION; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN; COMPUTER SIMULATION; CROSSING OVER, GENETIC; DNA; DNA MUTATIONAL ANALYSIS; HUMANS; MODELS, CHEMICAL; MODELS, GENETIC; MODELS, STATISTICAL; PATTERN RECOGNITION, AUTOMATED; SEQUENCE ANALYSIS, DNA; STOCHASTIC PROCESSES;

EID: 37649027056     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.71.041910     Document Type: Article

References (70)

1. J. B. Johnson, Phys. Rev. 26, 71 (1925).
2. A. van der Ziel, Adv. Electron. Electron Phys. 49, 225 (1979); P. Dutta and P. M. Horn, Rev. Mod. Phys. 53, 497 (1981); M. B. Weissman, ibid. 60, 537 (1988); H. Wong, Microelectron. Reliab. 43, 585 (2003).
3. A. van der Ziel, Adv. Electron. Electron Phys. 49, 225 (1979); P. Dutta and P. M. Horn, Rev. Mod. Phys. 53, 497 (1981); M. B. Weissman, ibid. 60, 537 (1988); H. Wong, Microelectron. Reliab. 43, 585 (2003).
4. A. van der Ziel, Adv. Electron. Electron Phys. 49, 225 (1979); P. Dutta and P. M. Horn, Rev. Mod. Phys. 53, 497 (1981); M. B. Weissman, ibid. 60, 537 (1988); H. Wong, Microelectron. Reliab. 43, 585 (2003).
5. A. van der Ziel, Adv. Electron. Electron Phys. 49, 225 (1979); P. Dutta and P. M. Horn, Rev. Mod. Phys. 53, 497 (1981); M. B. Weissman, ibid. 60, 537 (1988); H. Wong, Microelectron. Reliab. 43, 585 (2003).
6. M. Gardner, Sci. Am. 238(4), 16 (1978); W. Press, Comments. Astrophys. 7,103 (1978); B. J. West and M. F. Shlesinger, Am. Sci. 78, 40 (1990); E. Milotti, e-print physics/0204033.
7. M. Gardner, Sci. Am. 238(4), 16 (1978); W. Press, Comments. Astrophys. 7,103 (1978); B. J. West and M. F. Shlesinger, Am. Sci. 78, 40 (1990); E. Milotti, e-print physics/0204033.
8. M. Gardner, Sci. Am. 238(4), 16 (1978); W. Press, Comments. Astrophys. 7,103 (1978); B. J. West and M. F. Shlesinger, Am. Sci. 78, 40 (1990); E. Milotti, e-print physics/0204033.
9. M. Gardner, Sci. Am. 238(4), 16 (1978); W. Press, Comments. Astrophys. 7,103 (1978); B. J. West and M. F. Shlesinger, Am. Sci. 78, 40 (1990); E. Milotti, e-print physics/0204033.
10. W. Li, http://www.nslij-genetics.org/wli/lfnoise/
11. H. Herzel and I. Grosse, Physica A 216, 518 (1995); S. V. Buldyrev, A. L. Goldberger, S. Havlin, R. N. Mantegna, M. E. Matsa, C. K. Peng, M. Simons, and H. E. Stanley, Phys. Rev. E 51, 5084 (1995).
12. H. Herzel and I. Grosse, Physica A 216, 518 (1995); S. V. Buldyrev, A. L. Goldberger, S. Havlin, R. N. Mantegna, M. E. Matsa, C. K. Peng, M. Simons, and H. E. Stanley, Phys. Rev. E 51, 5084 (1995).
13. D. Holste, I. Grosse, and H. Herzel, Phys. Rev. E 64, 041917 (2001);
14. D. Holste, I. Grosse, S. Beirer, P. Schieg, and H. Herzel, ibid. 67, 061913 (2003).
15. W. Li, Europhys. Lett. 10, 395 (1989); Phys. Rev. A 43, 5240 (1991).
16. W. Li, Europhys. Lett. 10, 395 (1989); Phys. Rev. A 43, 5240 (1991).
17. W. Li, Int. J. Bifurcation Chaos Appl. Sci. Eng. 2, 137 (1992); W. Li and K. Kaneko, Europhys. Lett. 17, 655 (1992).
18. W. Li, Int. J. Bifurcation Chaos Appl. Sci. Eng. 2, 137 (1992); W. Li and K. Kaneko, Europhys. Lett. 17, 655 (1992).
19. R. F. Voss, Phys. Rev. Lett. 68, 3805 (1992).
20. X. Lu, Z. Sun, H. Chen, and Y. Li, Phys. Rev. E 58, 3578 (1998); M. de Sousa Vieira, ibid. 60, 5932 (1999).
21. X. Lu, Z. Sun, H. Chen, and Y. Li, Phys. Rev. E 58, 3578 (1998); M. de Sousa Vieira, ibid. 60, 5932 (1999).
22. W. Li, G. Stolovitzky, P. Bernaola-Galván, and J. L. Oliver, Genome Res. 8, 916 (1998).
23. A. Fukushima, Ph.D. thesis, Nara Institute of Science and Technology, 2003; A. Fukushima, T. Ikemura, M. Kinouchi, T. Oshima, Y. Kudo, H. Mori, and S. Kanaya, Gene 300, 203 (2002).
24. A. Fukushima, Ph.D. thesis, Nara Institute of Science and Technology, 2003; A. Fukushima, T. Ikemura, M. Kinouchi, T. Oshima, Y. Kudo, H. Mori, and S. Kanaya, Gene 300, 203 (2002).
25. G. Cuny, P. Soriano, G. Macaya, and G. Bernardi, Eur. J. Biochem. 115, 227 (1981); G. Bernardi, B. Olofsson, J. Filipski, M. Zerial, J. Salinas, G. Cuny, M. Meunier-Rotival, and F. Rodier, Science 228, 953 (1985); G. Bernardi, Gene 241, 3 (2000).
26. G. Cuny, P. Soriano, G. Macaya, and G. Bernardi, Eur. J. Biochem. 115, 227 (1981); G. Bernardi, B. Olofsson, J. Filipski, M. Zerial, J. Salinas, G. Cuny, M. Meunier-Rotival, and F. Rodier, Science 228, 953 (1985); G. Bernardi, Gene 241, 3 (2000).
27. G. Cuny, P. Soriano, G. Macaya, and G. Bernardi, Eur. J. Biochem. 115, 227 (1981); G. Bernardi, B. Olofsson, J. Filipski, M. Zerial, J. Salinas, G. Cuny, M. Meunier-Rotival, and F. Rodier, Science 228, 953 (1985); G. Bernardi, Gene 241, 3 (2000).
28. O. Clay, N. Carels, C. Douady, G. Macaya, and G. Bernardi, Gene 276, 15 (2001); O. Clay and G. Bernardi, ibid. 276, 25 (2001).
29. O. Clay, N. Carels, C. Douady, G. Macaya, and G. Bernardi, Gene 276, 15 (2001); O. Clay and G. Bernardi, ibid. 276, 25 (2001).
30. W. Li, P. Bernaola-Galván, P. Carpena, and J. L. Oliver, Comput. Biol. Chem. 27, 5 (2003).
31. O. Clay, Gene 276, 33 (2001).
32. W. Li, Gene 300, 129 (2002).
33. W. Li, Complexity 3, 33 (1997).
34. E. S. Lander et al., Nature (London) 409, 860 (2001).
35. P. Bernaola-Galván, P. Carpena, R. Román-Roldán, and J. L. Oliver, Gene 300, 105 (2002).
36. Z.Abellah et al., Nature (London) 431, 931 (2004); J. Schmutz et al., ibid. 429, 365 (2004).
37. Z.Abellah et al., Nature (London) 431, 931 (2004); J. Schmutz et al., ibid. 429, 365 (2004).
38. A. F. A. Smit and P. Green, computer code REPEATMASKER, University of Washington, available at http:// repeatmasker.genome.washington.edu/
39. P. J. Daniell, Suppl. J. R. Stat. Soc. 8, 88 (1946).
40. J. R. Korenberg and M. C. Rykowski, Cell 53, 391 (1988); P. Medstrand, L. N. van de Lagemaat, and D. L. Mager, Genome Res. 12, 1483 (2002); M.-A. Hakimi, D. A. Bochar, J. A. Schmiesing, Y. Dong, O. G. Barak, D. W. Speicher, K. Yokomori, and R. Shiekhattar, Nature (London) 418, 994 (2002); J. S. Han, S. T. Szak, and J. D. Boeke, ibid. 429, 268 (2004).
41. J. R. Korenberg and M. C. Rykowski, Cell 53, 391 (1988); P. Medstrand, L. N. van de Lagemaat, and D. L. Mager, Genome Res. 12, 1483 (2002); M.-A. Hakimi, D. A. Bochar, J. A. Schmiesing, Y. Dong, O. G. Barak, D. W. Speicher, K. Yokomori, and R. Shiekhattar, Nature (London) 418, 994 (2002); J. S. Han, S. T. Szak, and J. D. Boeke, ibid. 429, 268 (2004).
42. J. R. Korenberg and M. C. Rykowski, Cell 53, 391 (1988); P. Medstrand, L. N. van de Lagemaat, and D. L. Mager, Genome Res. 12, 1483 (2002); M.-A. Hakimi, D. A. Bochar, J. A. Schmiesing, Y. Dong, O. G. Barak, D. W. Speicher, K. Yokomori, and R. Shiekhattar, Nature (London) 418, 994 (2002); J. S. Han, S. T. Szak, and J. D. Boeke, ibid. 429, 268 (2004).
43. J. R. Korenberg and M. C. Rykowski, Cell 53, 391 (1988); P. Medstrand, L. N. van de Lagemaat, and D. L. Mager, Genome Res. 12, 1483 (2002); M.-A. Hakimi, D. A. Bochar, J. A. Schmiesing, Y. Dong, O. G. Barak, D. W. Speicher, K. Yokomori, and R. Shiekhattar, Nature (London) 418, 994 (2002); J. S. Han, S. T. Szak, and J. D. Boeke, ibid. 429, 268 (2004).
44. O. Clay, C. J. Douady, N. Carels, S. Hughes, G. Bucciarelli, and G. Bernardi, Eur. Biophys. J. 32, 418 (2003).
45. G. Macaya, J. P. Thiery, and G. Bernardi, J. Mol. Biol. 108, 237 (1976).
46. W. Li, Progress in Bioinformatics (Nova Science, Hauppauge, in press).
47. J. Beran, Statistics for Long-Memory Processes (Chapman and Hall, London, 1994).
48. B. Audit and C. A. Ouzounis, J. Mol. Biol. 332, 617 (2003).
49. P. Bernaola-Galván, J. L. Oliver, P. Carpena, O. Clay, and G. Bernardi, Gene 333, 121 (2004).
50. G. W. Snedecor and W. G. Cochran, Statistical Methods, 7th ed. (Iowa State University Press, Ames, 1980).
51. R. F. Voss and J. Clarke, Nature (London) 258, 317 (1975); K. J. Hsu and A. Hsu, Proc. Nad. Acad. Sci. U.S.A. 88, 3507 (1991).
52. R. F. Voss and J. Clarke, Nature (London) 258, 317 (1975); K. J. Hsu and A. Hsu, Proc. Nad. Acad. Sci. U.S.A. 88, 3507 (1991).
53. W. Li and D. Holste, Comput. Biol. Chem. 28, 393 (2004).
54. W. Li and D. Holste, Fluct. Noise Lett. 4, L453 (2004).
55. G. Bejerano, M. Pheasant, I. Makunin, S. Stephen, W. J. Kent, J. S. Mattick, and D. Haussler, Science 304, 1321 (2004).
56. P. Pevzner and G. Tesler, Genome Res. 13, 37 (2003).
57. S. Ohno, Evolution by Gene Duplication (Springer-Verlag, Berlin, 1970).
58. A. Meyer and Y. van de Peer, J. Struct Funct. Genomics 3, vii (2003).
59. G. Bernardi, Annu. Rev. Genet. 23, 637 (1989);
60. 29, 445 (1995).
61. G. Bernardi, Structural and Evolutionary Genomics (Elsevier, Amsterdam, 2004).
62. M. J. Lercher, A. O. Urrutia, and L. D. Hurst, Nat. Genet. 31, 180 (2002); M. J. Lercher, A. O. Urrutia, A. Pavlicek, and L. D. Hurst, Hum. Mol. Genet. 12, 2411 (2003); R. Versteeg, B. D. van Schaik, M. F. van Batenburg, M. Roos, R. Monajemi, H. Caron, H. J. Bussemaker, and A. H. van Kampen, Genome Res. 13, 1998 (2003).
63. M. J. Lercher, A. O. Urrutia, and L. D. Hurst, Nat. Genet. 31, 180 (2002); M. J. Lercher, A. O. Urrutia, A. Pavlicek, and L. D. Hurst, Hum. Mol. Genet. 12, 2411 (2003); R. Versteeg, B. D. van Schaik, M. F. van Batenburg, M. Roos, R. Monajemi, H. Caron, H. J. Bussemaker, and A. H. van Kampen, Genome Res. 13, 1998 (2003).
64. M. J. Lercher, A. O. Urrutia, and L. D. Hurst, Nat. Genet. 31, 180 (2002); M. J. Lercher, A. O. Urrutia, A. Pavlicek, and L. D. Hurst, Hum. Mol. Genet. 12, 2411 (2003); R. Versteeg, B. D. van Schaik, M. F. van Batenburg, M. Roos, R. Monajemi, H. Caron, H. J. Bussemaker, and A. H. van Kampen, Genome Res. 13, 1998 (2003).
65. Y. Niimura and T. Gojobori, Proc. Natl. Acad. Sci. U.S.A. 99, 797 (2002).
66. P. A. Dijkwel and J. L. Harnlin, Int. Rev. Cytol. 162A, 455 (1995); S. V. Razin, I. I. Gromova, and O. V. Iarovaia, ibid. 162B, 405 (1995).
67. P. A. Dijkwel and J. L. Harnlin, Int. Rev. Cytol. 162A, 455 (1995); S. V. Razin, I. I. Gromova, and O. V. Iarovaia, ibid. 162B, 405 (1995).
68. S. Boyle, S. Gilchrist, J. M. Bridger, N. L. Mahy, J. A. Ellis, and W. A. Bickmore, Hum. Mol. Genet. 10, 211 (2001); S. Saccone, C. Federico, and G. Bernardi, Gene 300, 169 (2002).
69. S. Boyle, S. Gilchrist, J. M. Bridger, N. L. Mahy, J. A. Ellis, and W. A. Bickmore, Hum. Mol. Genet. 10, 211 (2001); S. Saccone, C. Federico, and G. Bernardi, Gene 300, 169 (2002).
70. Human Genome browser, available at http://genome.ucsc.edu/