Fractal properties of the human genome

Journal of Theoretical Biology

Volumn 230, Issue 2, 2004, Pages 251-260

  Garte, Seymour ^a,b  

^a UNIVERSITY OF MEDICINE AND DENTISTRY OF NEW JERSEY   (United States)

^b Genetics Research Institute   (Italy)

Author keywords

Dimension; Gene density; Self similarity

Indexed keywords

CHROMOSOME;

ARABIDOPSIS; ARTICLE; BACTERIUM; CALCULATION; DENSITY; EMPIRICISM; FRACTAL ANALYSIS; GENETIC ANALYSIS; GENOME; HUMAN CHROMOSOME; INTRON; PLANT; PRIORITY JOURNAL; SPECIES; THEORY; WORM; YEAST;

ANIMALS; FRACTALS; GENE DOSAGE; GENOME, BACTERIAL; GENOME, FUNGAL; GENOME, HUMAN; GENOME, PLANT; HUMANS; MODELS, GENETIC;

ARABIDOPSIS;

EID: 4043180539     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jtbi.2004.05.015     Document Type: Article

References (34)

1. Aravind L., Dixit V.M., Koonin E.V. Apoptotic molecular machinery. vastly increased complexity in vertebrates revealed by genome comparisons Science. 291:2001;1279-1284
2. Baish J.W., Jain R.K. Fractals and cancer. Cancer Res. 60:2000;3683-3688
3. Barakat A., Matassi G., Bernardi G. Distribution of genes in the genome of Arabidopsis thaliana and its implications or the genome organization of plants. Proc. Natl Acad. Sci. 95:1998;10044-10049
4. Charlesworth B., Charlesworth D. The degeneration of Y chromosomes. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 355:2000;1563-1572
5. Chatzidimitriou-Dreismann C.A., Streffer R.M., Larhammar D. A quantitative test of long-range correlations and compositional fluctuations in DNA sequences. Eur. J. Biochem. 224:1994;365-371
6. Dehal P., Predki P., Olsen A.S., Kobayashi A., Folta P., Lucas S., Land M., Terry A., Ecale Zhou C.L., Rash S., Zhang Q., Gordon L., Kim J., Elkin C., Pollard M.J., Richardson P., Rokhsar D., Uberbacher E., Hawkins T., Branscomb E., Stubbs L. Human chromosome 19 and related regions in mouse. conservative and lineage-specific evolution Science. 293:2001;104-111
7. Fedorov A., Cao X., Saxonov S., de Souza S.J., Roy S.W., Gilbert W. Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns. Proc. Natl Acad. Sci. USA. 98:2001;13177-13182
8. Gilbert W., de Souza S.J., Long M. Origin of genes. Proc. Natl Acad. Sci. USA. 94:1997;7698-7703
9. Gisiger T. Scale invariance in biology. coincidence or footprint of a universal mechanism? Biol. Rev. Cambridge Philos. Soc. 76:2001;161-209
10. Goldberger A.L. Non-linear dynamics for clinicians. chaos theory, fractals, and complexity at he bedside Lancet. 347:1996;1312-1314
11. Gregory T.R. Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol. Rev. Cambridge Philos. Soc. 76:2001;65-101
12. Heymans O., Fissette J., Vico P., Blacher S., Masset D., Brouers F. Is fractal geometry useful in medicine and biomedical sciences? Med Hypotheses. 54:2000;360-366
13. Karlin S., Brendel V. Patchiness and correlations in DNA sequences. Science. 259:1993;677-680
14. Kidwell M.G., Lisch D.R. Perspective. transposable elements, parasitic DNA, and genome evolution Evol. Int. J. Org. Evol. 55:2001;1-24
15. Koop B.F. Human and rodent DNA sequence comparisons. a mosaic model of genomic evolution Trends Genet. 11:1995;367-371
16. Kwiatowski J., Krawczyk M., Kornacki M., Bailey K., Ayala F.J. Evidence against the exon theory of genes derived from the triose-phosphate isomerase gene. Proc. Natl Acad. Sci. 92:1995;8503-8506
17. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J.P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J.C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R.H., Wilson, R.K., Hillier, L.W., McPherson, J.D., Marra, M.A., Mardis, E.R., Fulton, L.A., Chinwalla, A.T., Pepin, K.H., Gish, W.R., Chissoe, S.L., Wendl, M.C., Delehaunty, K.D., Miner, T.L., Delehaunty, A., Kramer, J.B., Cook, L.L., Fulton, R.S., Johnson, D.L., Minx, P.J., Clifton, S.W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J.F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E., Frazier, M., Gibbs, R.A., Muzny, D.M., Scherer, S.E., Bouck, J.B., Sodergren, E.J., Worley, K.C., Rives, C.M., Gorrell, J.H., Metzker, M.L., Naylor, S.L., Kucherlapati, R.S., Nelson, D.L., Weinstock, G.M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Smith, D.R., Doucette-Stamm, L., Rubenfield, M., Weinstock, K., Lee, H.M., Dubois, J., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H., Yu, J., Wang, J., Huang, G., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S., Davis, R.W., Federspiel, N.A., Abola, A.P., Proctor, M.J., Myers, R.M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D.R., Olson, M.V., Kaul, R., Raymond, C., Shimizu, N., Kawasaki, K., Minoshima, S., Evans, G.A., Athanasiou, M., Schultz, R., Roe, B.A., Chen, F., Pan, H., Ramser, J., Lehrach, H., Reinhardt, R., McCombie, W.R., de la Bastide, M., Dedhia, N., Blocker, H., Hornischer, K., Nordsiek, G., Agarwala, R., Aravind, L., Bailey, J.A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D.G., Burge, C.B., Cerutti, L., Chen, H.C., Church, D., Clamp, M., Copley, R.R., Doerks, T., Eddy, S.R., Eichler, E.E., Furey, T.S., Galagan, J., Gilbert, J.G., Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W., Johnson, L.S., Jones, T.A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W.J., Kitts, P., Koonin, E.V., Korf, I., Kulp, D., Lancet, D., Lowe, T.M., McLysaght, A., Mikkelsen, T., Moran, J.V., Mulder, N., Pollara, V.J., Ponting, C.P., Schuler, G., Schultz, J., Slater, G., Smit, A.F., Stupka, E., Szustakowski, J., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Wallis, J., Wheeler, R., Williams, A., Wolf, Y.I., Wolfe, K.H., Yang, S.P., Yeh, R.F., Collins, F., Guyer, M.S., Peterson, J., Felsenfeld, A., Wetterstrand, K.A., Patrinos, A., Morgan, M.J., Szustakowki, J., de Jong, P., Catanese, J.J., Osoegawa, K., Shizuya, H., Choi, S., Chen, Y.J., 2001. International human genome sequencing consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921.
18. Lang D., Thoma R., Henn-Sax M., Sterner R., Wilmanns M. Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. Science. 289:2000;1546-1550
19. Lynch M., Conery J.S. The evolutionary fate and consequences of duplicate genes. Science. 290:2000;1151-1155
20. Mandelbrot B.B. The Fractal Geometry of Nature. 1982;W.H. Freeman, New York
21. Nadir E., Margalit H., Gallily T., Ben-Sasson S.A. Microsatellite spreading in the human genome. evolutionary mechanisms and structural implications Proc. Natl Acad. Sci. USA. 93:1996;6470-6475
22. Ott, E., 1993. Chaos in Dynamical Systems. Cambridge University Press, New York, pp. 103-104.
23. Parkinson I.H., Fazzalari N.L. Methodological principles for fractal analysis of trabecular bone. J. Microsc. 198:2000;134-142
24. Peng C.K., Buldyrev S.V., Hausdorff J.M., Havlin S., Mietus J.E., Simons M., Stanley H.E., Goldberger A.L. Non-equilibrium dynamics as an indispensable characteristic of a healthy biological system. Integrative Physiol. Behav. Sci. 29:1994;283-293
25. Petrov D.A., Sangster T.A., Johnston J.S., Hartl D.L., Shaw K.L. Evidence for DNA loss as a determinant of genome size. Science. 287:2000;1060-1062
26. Pikkujamsa S.M., Makikallio T.H., Sourander L.B., Raiha I.J., Puukka P., Skytta J., Peng C.K., Goldberger A.L., Huikuri H.V. Cardiac interbeat interval dynamics from childhood to senescence. comparison of conventional and new measures based on fractals and chaos theory Circulation. 100:1999;393-399
27. Salzberg S.L., White O., Peterson J., Eisen J.A. Microbial genes in the human genome. lateral transfer or gene loss? Science. J292:2001;1903-1906
28. Smith T.G., Behar T.N. Comparative fractal analysis of cultured glia derived from optic nerve and brain demonstrate different rates of morphological differentiation. Brain Res. 634:1994;181-190
29. Sugihara G., Allan W., Sobel D., Allan K.D. Nonlinear control of heart rate variability in human infants. Proc. Natl Acad. Sci. USA. 93:1996;2608-2613
30. Tsonis A.A., Elsner J.B., Tsonis P.A. On the existence of scaling in DNA sequences. Biochem. Biophys. Res. Commun. 197:1993;1288-1295
31. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., Gocayne, J.D., Amanatides, P., Ballew, R.M., Huson, D.H., Wortman, J.R., Zhang, Q., Kodira, C.D., Zheng, X.H., Chen, L., Skupski, M., Subramanian, G., Thomas, P.D., Zhang, J., Gabor Miklos, G.L., Nelson, C., Broder, S., Clark, A.G., Nadeau, J., McKusick, V.A., Zinder, N., Levine, A.J., Roberts, R.J., Simon, M., Slayman, C., Hunkapiller, M., Bolanos, R., Delcher, A., Dew, I., Fasulo, D., Flanigan, M., Florea, L., Halpern, A., Hannenhalli, S., Kravitz, S., Levy, S., Mobarry, C., Reinert, K., Remington, K., Abu-Threideh, J., Beasley, E., Biddick, K., Bonazzi, V., Brandon, R., Cargill, M., Chandramouliswaran, I., Charlab, R., Chaturvedi, K., Deng, Z., Di Francesco, V., Dunn, P., Eilbeck, K., Evangelista, C., Gabrielian, A.E., Gan, W., Ge, W., Gong, F., Gu, Z., Guan, P., Heiman, T.J., Higgins, M.E., Ji, R.R., Ke, Z., Ketchum, K.A., Lai, Z., Lei, Y., Li, Z., Li, J., Liang, Y., Lin, X., Lu, F., Merkulov, G.V., Milshina, N., Moore, H.M., Naik, A.K., Narayan, V.A., Neelam, B., Nusskern, D., Rusch, D.B., Salzberg, S., Shao, W., Shue, B., Sun, J., Wang, Z., Wang, A., Wang, X., Wang, J., Wei, M., Wides, R., Xiao, C., Yan, C., Yao, A., Ye, J., Zhan, M., Zhang, W., Zhang, H., Zhao, Q., Zheng, L., Zhong, F., Zhong, W., Zhu, S., Zhao, S., Gilbert, D., Baumhueter, S., Spier, G., Carter, C., Cravchik, A., Woodage, T., Ali, F., An, H., Awe, A., Baldwin, D., Baden, H., Barnstead, M., Barrow, I., Beeson, K., Busam, D., Carver, A., Center, A., Cheng, M.L., Curry, L., Danaher, S., Davenport, L., Desilets, R., Dietz, S., Dodson, K., Doup, L., Ferriera, S., Garg, N., Gluecksmann, A., Hart, B., Haynes, J., Haynes, C., Heiner, C., Hladun, S., Hostin, D., Houck, J., Howland, T., Ibegwam, C., Johnson, J., Kalush, F., Kline, L., Koduru, S., Love, A., Mann, F., May, D., McCawley, S., McIntosh, T., McMullen, I., Moy, M., Moy, L., Murphy, B., Nelson, K., Pfannkoch, C., Pratts, E., Puri, V., Qureshi, H., Reardon, M., Rodriguez, R., Rogers, Y.H., Romblad, D., Ruhfel, B., Scott, R., Sitter, C., Smallwood, M., Stewart, E., Strong, R., Suh, E., Thomas, R., Tint, N.N., Tse, S., Vech, C., Wang, G., Wetter, J., Williams, S., Williams, M., Windsor, S., Winn-Deen, E., Wolfe, K., Zaveri, J., Zaveri, K., Abril, J.F., Guigo, R., Campbell, M.J., Sjolander, K.V., Karlak, B., Kejariwal, A., Mi, H., Lazareva, B., Hatton, T., Narechania, A., Diemer, K., Muruganujan, A., Guo, N., Sato, S., Bafna, V., Istrail, S., Lippert, R., Schwartz, R., Walenz, B., Yooseph, S., Allen, D., Basu, A., Baxendale, J., Blick, L., Caminha, M., Carnes-Stine, J., Caulk, P., Chiang, Y.H., Coyne, M., Dahlke, C., Mays, A., Dombroski, M., Donnelly, M., Ely, D., Esparham, S., Fosler, C., Gire, H., Glanowski, S., Glasser, K., Glodek, A., Gorokhov, M., Graham, K., Gropman, B., Harris, M., Heil, J., Henderson, S., Hoover, J., Jennings, D., Jordan, C., Jordan, J., Kasha, J., Kagan, L., Kraft, C., Levitsky, A., Lewis, M., Liu, X., Lopez, J., Ma, D., Majoros, W., McDaniel, J., Murphy, S., Newman, M., Nguyen, T., Nguyen, N., Nodell, M., Pan, S., Peck, J., Peterson, M., Rowe, W., Sanders, R., Scott, J., Simpson, M., Smith, T., Sprague, A., Stockwell, T., Turner, R., Venter, E., Wang, M., Wen, M., Wu, D., Wu, M., Xia, A., Zandieh, A., Zhu, X., 2001. The sequence of the human genome. Science 291, 1304-1351.
32. Watson J.D., Baker T.A., Bell S.P., Gann A., Levine M., Losick R. Molecular Biology of the Gene. 5th Edition:2003;Benjamin/Cummings, San Francisco
33. West G.B., Brown J.H., Enquist B.J. A general model for the origin of allometric scaling laws in biology. Science. 276:1997;122-126
34. West G.B., Brown J.H., Enquist B.J. The fourth dimension of life. fractal geometry and allometric scaling of organisms Science. 284:1999;1677-1679