Scaling law in sizes of protein sequence families: From super-families to orphan genes

Proteins: Structure, Function and Genetics

Volumn 51, Issue 4, 2003, Pages 569-576

  Unger, Ron ^a   Uliel, Shai ^a   Havlin, Shlomo ^a  

^a BAR ILAN UNIVERSITY   (Israel)

Author keywords

Evolution; Power law; Protein families; Scaling; Size distribution

Indexed keywords

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CLUSTER ANALYSIS; DATA ANALYSIS; DATA BASE; EVOLUTION; GENOME; HUMAN; MODEL; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY;

ALGORITHMS; DATABASES, GENETIC; EVOLUTION, MOLECULAR; MODELS, GENETIC; PROTEINS;

EID: 0037941120     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10347     Document Type: Article

References (27)

1. Holm L, Sander C. Mapping the protein universe. Science 1996;273:595-603.
2. Gogarten JP, Olendzenski L. Orthologs, paralogs and genome comparisons. Curr Opin Genet Dev 1999;9:630-636.
3. Orengo CA, Jones DT, Thornton JM. Protein superfamilies and domain superfolds. Nature 1994;372:631-634.
4. Fischer D, Eisenberg D. Finding families for genomic ORFans. Bioinformatics 1999;15:759-762.
5. Zipf GK. Human behavior and the principle of least efforts. Cambridge MA: Addison-Wesley; 1949.
6. Makse HA, Havlini S, Stanley HE. Modelling urban growth patterns. Nature 1995;377:608-612.
7. Nagel K, Paczuski M. Emergent traffic jams. Physical Rev E 1995;51:2909-2918.
8. Huberman BA, Adamic L. Growth dynamics of the World-Wide Web. Nature 1999;401:131.
9. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL. The large-scale organization of metabolic networks. Nature 2000;407:651-654.
10. Stanley HE, Ostrowskyi N, editors. Correlations and connectivity: geometric aspects of physics, chemistry and biology. Dordrecht: Kluwer; 1990.
11. Hill B, Woodroofe M. Stronger forms of Zipf's law. J Am Stat Assoc 1975;70:349-355.
12. Barabasi AL, Albert R. Emergence of scaling in random networks. Science 1999;286:509-512.
13. Huynen MA, van Nimwegen E. The frequency distribution of gene family sizes in complete genomes. Mol Biol Evol 1998;15:583-589.
14. Yanai I, Camacho CJ, DeLisi C. Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification. Phys Rev Lett 2000;85:2641-2644.
15. Qian J, Luscombe NM, Gerstein M. Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. J Mol Biol 2001;313:673-681.
16. Corpet F, Gouzy J, Kahn D. The ProDom database of protein domain families. Nucleic Acids Res 1998;26:323-326.
17. Yona G, Linial N, Linial M. ProtoMap: automatic classification of protein sequences, a hier-archy of protein families, and local maps of the protein space. Proteins 1999;37:360-378.
18. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997;278:631-637.
19. Zipf GK. The psycho-biology of languages, an introduction to dynamic philology. Cambridge MA: MIT Press; 1965.
20. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
21. Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature 2000;405:299-304.
22. Lander ES, et. al. Initial sequencing and analysis of the human genome. Nature 2001;495:860-921.
23. Devos D, Valencia A. Practical limits of function prediction. Proteins 2000;41:98-107.
24. Dorogovtsev SN, Mendes JJF, Samukhin AN. Structure of growing networks with preferential linking. Phys Rev Let 2000;85:4633-4636.
25. Park J, Bolser D. Conservation of protein interaction network in evolution. Genome Inform 2001;12:135-140.
26. Coulson AF, Moult J. A unifold, mesofold, and superfold model of protein fold use. Proteins 2002;46:61-71.
27. Rubin GM. The draft sequences: comparing species. Nature 2001;495:820-821.