A preliminary analysis of gene pleiotropy estimated from protein sequences

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Volumn 314 B, Issue 2, 2010, Pages 115-122

  Su, Zhixi ^a   Zeng, Yanwu ^a   Gu, Xun ^a,b  

^a FUDAN UNIVERSITY   (China)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALLELE; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CATTLE; DOG; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; HUMAN; MOLECULAR EVOLUTION; MOUSE; NUCLEOTIDE SEQUENCE; PHENOTYPE; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; VERTEBRATE;

ALLELES; AMINO ACID SEQUENCE; ANIMALS; CATTLE; CONSERVED SEQUENCE; DOGS; EVOLUTION, MOLECULAR; GENETIC VARIATION; HUMANS; MICE; MODELS, GENETIC; PHENOTYPE; PROTEINS; SELECTION, GENETIC; SEQUENCE ANALYSIS, PROTEIN; SPECIES SPECIFICITY; VERTEBRATES;

VERTEBRATA;

EID: 76749096400     PISSN: 15525007     EISSN: 15525015     Source Type: Journal    
DOI: 10.1002/jez.b.21315     Document Type: Article

References (28)

1. Albert AYK, Sawaya S, Vines TH, Knecht AK, Miller CT, Summers BR, Balabhadra S, Kingsley DM, Schluter D. 2008. The genetics of adaptive shape shift in stickleback: pleiotropy and effect size. Evolution 62:76-85.
2. Barton NH. 1990. Pleiotropic models of quantitative variation. Genetics 124:773-782.
3. Dudley AM, Janse DM, Tanay A, Shamir R, Church GM. 2005. A global view of pleiotropy and phenotypically derived gene function in yeast. Mol Syst Biol 1:2005;0001.
4. Fisher RA. 1930. The genetical theory of natural selection. Oxford: The Clarendon Press.
5. Griswold CK, Whitlock MC. 2003. The genetics of adaptation: the roles of pleiotropy, stabilizing selection and drift in shaping the distribution of bidirectional fixed mutational effects. Genetics 165:2181-2192.
6. Gu X. 2007a. Evolutionary framework for protein sequence evolution and gene pleiotropy. Genetics 175:1813-1822.
7. Gu X. 2007b. Stabilizing selection of protein function and distribution of selection coefficient among sites. Genetica 130:93-97.
8. Gu X, Su Z. 2007. Tissue-driven hypothesis of genomic evolution and sequence-expression correlations. Proc Natl Acad Sci USA 104:2779-2784.
9. Gu X, Zhang J. 1997. A simple method for estimating the parameter of substitution rate variation among sites. Mol Biol Evol 14:1106-1113.
10. Gu X, Fu YX, Li WH. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol 12:546-557.
11. Hahn MW, Kern AD. 2005. Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 22:803-806.
12. He X, Zhang J. 2006. Toward a molecular understanding of pleiotropy. Genetics 173:1885-1891.
13. Hubbell E, Liu WM, Mei R. 2002. Robust estimators for expression analysis. Bioinformatics 18:1585-1592.
14. Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E. 2004. EnsMart: a generic system for fast and flexible access to biological data. Genome Res 14:160-169.
15. Orr HA. 2000. Adaptation and the cost of complexity. Evolution 54:13-20.
16. Otto SP. 2004. Two steps forward, one step back: the pleiotropic ffects of favoured alleles. Proc Biol Sci 271:705-714.
17. Promislow DEL. 2004. Protein networks, pleiotropy and the evolution of senescence. Proc R Soc (London) 271:1225-1234.
18. Salathe M, Ackermann M, Bonhoeffer S. 2006. The effect of multifunctionality on the rate of evolution in yeast. Mol Biol Evol 23:721-722.
19. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB. 2004. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101:6062-6067.
20. The Gene Ontology Consortium. 2002. Gene Ontology: tool for the unification of biology. Nat Genet 25:25-29.
21. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.
22. Wagner GP. 1989. Multivariate mutation-selection balance with constrained pleiotropic effects. Genetics 122:223-234.
23. Wagner GP, Kenney-Hunt JP, Pavlicev M, Peck JR, Waxman D, Cheverud JM. 2008. Pleiotropic scaling of gene effects and the ''cost of complexity''. Nature 452:470-472.
24. Waxman D, Peck JR. 1998. Pleiotropy and the preservation of perfection. Science 279:1210-1213.
25. Williams GC. 1957. Pleiotropy, natural selection, and the evolution of senescence. Evolution 11:398-411.
26. Wright S. 1968. Evolution and the genetics of populations; a treatise. Chicago: University of Chicago Press.
27. Yang J, Su AI, Li WH. 2005. Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol Biol Evol 22:2113-2118.
28. Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556.