Analysis of the evolving proteomes: Predictions of the number of protein domains in nature and the number of genes in eukaryotic organisms

Journal of Biological Systems

Volumn 10, Issue 4, 2002, Pages 381-407

  Kuznetsov, Vladimir A ^a   Pickalov, Valery V ^b   Senko, Oleg V ^c   Knott, Gary D ^d  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b ENERGY SYSTEMS INSTITUTE   (Russian Federation)

^c RUSSIAN ACADEMY OF SCIENCES   (Russian Federation)

^d Civilized Software Inc   (United States)

Author keywords

Evolution; Number of genes; Number of protein domains; Pareto like distribution; Proteome complexity; Stochastic process

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 0037849814     PISSN: 02183390     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0218339002000767     Document Type: Article

References (24)

1. Apic G., Gough J., and Teichmann S. A., An insight into domain combinations, Bioinformatics 17 (suppl.1) (2001) pp. S83-S89.
2. Aravind L., Dixit, V. M. and Koonin E. V., Apoptotic molecular machinery: Vastly increased complexity in vertebrates revealed by genome comparisons, Science 291 (2001) pp. 1279-1284.
3. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S. R., Griffiths-Jones S., Howe K. L., Marshall M. and Sonnhammer E. L. L., The Pfam protein families database, Nucleic Acids Res. 30(1) (2002) pp. 276-280.
4. Copley R. R., Doerks T., Letunic I. and Bork P., Protein domain analysis in the era of complete genomes, FEBS Letters 513 (2002) pp. 129-134.
5. Daly M., Estimating the human gene count, Cell 109 (2002) pp. 283-284.
6. Douglas S., Zauner S., Fraunholz M., Beaton M., Penny S., Deng L.-T., Wu X., Reith M., Caveller-Smith T. and Maler U.-G., The highly reduced genome of an enslaved algal Nucleus, Nature 410 (2001) pp. 1091-1096.
7. Ewing B. and Green P., Analysis of expressed sequence tags indicates 35,000 human genes, Nat. Genet. 25 (2000) pp. 232-234.
8. Feller W., An Introduction to Probability Theory and Its Applications (Vol. 1, 3rd Edition) (Wiley, New York, 1968).
9. Hogenesch J. B., Ching K. A., Batalov S., Su A. I., Walker J. R., Zhou Y., Kay S. A., Schultz P. G. and Cooke M. P., A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes, Cell 106(4) (2001) pp. 413-415.
10. Irwin J. O., The place of mathematics in the medical and biological sciences, J. Royal Stat. Soc. A126 (1963) pp. 1-45.
11. Johnson N. L., Kotz S. and Kemp A. W., Univariate Discrete Distributions (Wiley and Sons, New York, 1993).
12. Kanapin A., Apweiler R., Biswas M., Fleischmann W., Karavidopoulou Y., Kersey P., Kriventseva E. V., Mittard V., Mulder N., Oinn T., Phan I., Servant F. and Zdobnov E., Interactive InterPro-based comparisons of proteins in whole genomes, Bioinformatics 18(2) (2002) pp. 374-375.
13. Kuznetsov V. A., Distribution associated with stochastic processes of gene expres-sion in a single eukaryotic cell, EURASIP J. on Applied Signal Processing 4 (2001) pp. 285-296.
14. Kuznetsov V. A., Statistics of the numbers of transcripts and protein sequences encoded hi the genome, Computational and Statistical Methods to Genomics, ed. by Zhang W. and Shmulevish I. (Kluwer Academic Press, Boston, 2002) pp. 125-171.
15. Kuznetsov V. A. and Pickalov V. V., The numbers of protein domain sequences and protein coding genes in the evolved proteomes, in Proc. Third Int. Conf. on Bioinformatics of Genome Regulation and Structure (BGRS'2002) (July 14-20, 2002, IC&G: Novosibirsk, Russia) 3 pp. 160-163.
16. Kuznetsov V. A., Knott G. D. and Bonner R. F., General statistics of stochastic process of gene expression in eukaryotic cells, Genetics 161(3) (2002) pp. 1321-1332.
17. Lander E. S., Linton L. M., Birren B., Nusbaum C., Zody M. C., Baldwin J., Devon K., Dewar K., Doyle M. and FitzHugh W. et al., Initial sequencing and analysis of the human genome. International Human Genome Sequencing Consortium, Nature 409 (2001) pp. 860-921.
18. Letunic I., Goodstadt G., Dickens G. N. J., Doerks T., Schultz J., Mott M., Ciccarelli F., Copley R. R., Ponting C. P. and Bork P., Recent improvements to the SMART domain-based sequence annotation resource, Nucl. Acids Res. 30 (2002) pp. 242-244.
19. Marchler-Bauer A., Panchenko A. R., Shoemaker B. A., Thiessen P. A., Geer L. V. and Bryant S. H., CDD: A database of conserved domain alignments with links to domain three-dimensional structure, Nucl. Acids Res. 30(1) (2002) pp. 281-283.
20. Rzhetsky A. and Gomez S. M., Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome, Bioinformatics 17 (2001) pp. 988-996.
21. 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. and Holt R. A. et al., The sequence of the human genome, Science 291 (2001) pp. 1304-1351.
22. Wolf Y. I., Grishin N. V. and Koonin E. V., Estimating the number of protein folds and families from complete genome data, J. Molec. Evolution 299 (2000) pp. 897-905.
23. Wuchty S., Scale-free behavior in protein domain networks, Molec. Biol. Evol. 18(9) (2001) pp. 1694-1702.
24. Yule G. U., A mathematical theory of evolution based on the conclusions of Dr. J. C. Willis, F.R.S., Philosophical Transactions of the Royal Society of London. Ser. B213 (1924) pp. 21-87.