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Volumn 7, Issue 2, 2006, Pages 87-96

Predicting type-I (Rate-Shift) functional divergence of protein sequences and applications in functional genomics

Author keywords

Amino Acid Residues; Caspases; Cluster Specific Functional Divergence; JAK Proteins; Mitochondria Genes; Vertebrate Mitochondrial Genomes

Indexed keywords

AMINO ACID; CASPASE; JANUS KINASE;

EID: 33746869721     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920206777304623     Document Type: Review
Times cited : (2)

References (35)
  • 2
    • 0002402035 scopus 로고
    • In: Nei, M. and Keohn, R.K. (eds) Sinauer Associates, Sunderland, MA
    • Li, W.H. In: Nei, M. and Keohn, R.K. (eds) Evolution of Genes and Proteins. Sinauer Associates, Sunderland, MA, 1983, pp14-37.
    • (1983) Evolution of Genes and Proteins , pp. 14-37
    • Li, W.H.1
  • 3
    • 0028348636 scopus 로고
    • Invasion and maintenance of a gene duplication
    • Clark, A.G. Invasion and maintenance of a gene duplication. Proc. Natl. Acad. Sci. USA 1994, 91: 2950-2954.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 2950-2954
    • Clark, A.G.1
  • 4
    • 0028342845 scopus 로고
    • The evolution of functionally novel proteins after gene duplication
    • Hughes, A.L. The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. B. Biol. Sci. 1994, 256: 119-124.
    • (1994) Proc. R. Soc. Lond. B. Biol. Sci. , vol.256 , pp. 119-124
    • Hughes, A.L.1
  • 5
    • 0030249746 scopus 로고    scopus 로고
    • The coevolution of gene family trees
    • Fryxell, K.J. The coevolution of gene family trees. Trends Genet. 1996, 12: 364-369.
    • (1996) Trends Genet , vol.12 , pp. 364-369
    • Fryxell, K.J.1
  • 6
    • 0030791307 scopus 로고    scopus 로고
    • Evolution by the birth-and-death process in multigene families of the vertebrate immune system
    • Nei, M., Gu, X., Sitnikova, T. Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc. Natl. Acad. Sci. USA 1997, 94: 7799-7806.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 7799-7806
    • Nei, M.1    Gu, X.2    Sitnikova, T.3
  • 7
    • 0032893932 scopus 로고    scopus 로고
    • Preservation of duplicate genes by complementary, degenerative mutations
    • Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.L., Postlethwait, J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 1999, 151: 1531-1545.
    • (1999) Genetics , vol.151 , pp. 1531-1545
    • Force, A.1    Lynch, M.2    Pickett, F.B.3    Amores, A.4    Yan, Y.L.5    Postlethwait, J.6
  • 8
    • 0032728408 scopus 로고    scopus 로고
    • Statistical methods for testing functional divergence after gene duplication
    • Gu, X. Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 1999, 16: 1664-1674.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1664-1674
    • Gu, X.1
  • 9
    • 0035061686 scopus 로고    scopus 로고
    • Maximum-likelihood approach for gene family evolution under functional divergence
    • Gu, X. Maximum-likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol. 2001, 18: 453-464.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 453-464
    • Gu, X.1
  • 10
    • 0035895207 scopus 로고    scopus 로고
    • Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors
    • Gaucher, E.A., iyamoto, M.M., Benner, S.A. Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors. Proc. Natl. Acad. Sci. USA 2001, 98: 548-552.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 548-552
    • Gaucher, E.A.1    Iyamoto, M.M.2    Benner, S.A.3
  • 11
    • 0035065391 scopus 로고    scopus 로고
    • Differential selection after duplication in mammalian developmental genes
    • Dermitzakis, E.T., Clark, A.G. Differential selection after duplication in mammalian developmental genes. Mol. Biol. Evol. 2001,18: 557-562.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 557-562
    • Dermitzakis, E.T.1    Clark, A.G.2
  • 12
    • 0034922711 scopus 로고    scopus 로고
    • Functional divergence in the caspase gene family and altered functional constraints: Statistical analysis and prediction
    • Wang, Y., Gu, X. Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction. Genetics 2001, 158: 1311-1320.
    • (2001) Genetics , vol.158 , pp. 1311-1320
    • Wang, Y.1    Gu, X.2
  • 13
    • 0036107253 scopus 로고    scopus 로고
    • Evolutionary analysis for functional divergence of Jak protein kinase domains and tissue-specific genes
    • Gu, J., Wang, Y., Gu, X. Evolutionary analysis for functional divergence of Jak protein kinase domains and tissue-specific genes. J. Mol. Evol. 2002, 54: 725-733.
    • (2002) J. Mol. Evol. , vol.54 , pp. 725-733
    • Gu, J.1    Wang, Y.2    Gu, X.3
  • 14
    • 34548534411 scopus 로고    scopus 로고
    • Evolutionary analysis for functional divergence of Toll-like receptor gene family and altered functional constraints
    • (in press)
    • Zhou, H., Gu, J., Lamont, S.J., Gu, X. Evolutionary analysis for functional divergence of Toll-like receptor gene family and altered functional constraints. J. Mol. Evol. 2006 (in press).
    • (2006) J. Mol. Evol.
    • Zhou, H.1    Gu, J.2    Lamont, S.J.3    Gu, X.4
  • 15
    • 0014860857 scopus 로고
    • An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
    • Fitch, W.M., Markowitz, E. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 1970, 4: 579-593.
    • (1970) Biochem. Genet. , vol.4 , pp. 579-593
    • Fitch, W.M.1    Markowitz, E.2
  • 16
    • 0029889222 scopus 로고    scopus 로고
    • Identification of functional residues and secondary structure from protein multiple sequence alignment
    • Livingstone, C.D., Barton, G.J. Identification of functional residues and secondary structure from protein multiple sequence alignment. Methods Enzymol. 1996, 266: 497-512.
    • (1996) Methods Enzymol. , vol.266 , pp. 497-512
    • Livingstone, C.D.1    Barton, G.J.2
  • 17
    • 0029587166 scopus 로고
    • A method to predict functional residues in proteins
    • Casari, G., Sander, C., Valencia, A. A method to predict functional residues in proteins. Nat. Struct. Biol. 1995, 2: 171-178.
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 171-178
    • Casari, G.1    Sander, C.2    Valencia, A.3
  • 18
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge, O., Bourne, H.R., Cohen, F.E. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 1996, 257: 342-358.
    • (1996) J. Mol. Biol. , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 19
    • 0032711731 scopus 로고    scopus 로고
    • Analysis of heregulin symmetry by weighted evolutionary tracing
    • Landgraf, R., Fischer, D., Eisenberg, D. Analysis of heregulin symmetry by weighted evolutionary tracing. Protein Eng. 1999, 12: 943-951.
    • (1999) Protein Eng. , vol.12 , pp. 943-951
    • Landgraf, R.1    Fischer, D.2    Eisenberg, D.3
  • 20
    • 0036205440 scopus 로고    scopus 로고
    • DIVERGE: Phylogeny-based Analysis for Functional-Structural Divergence of a Protein Family
    • Gu, X., Vander Velden K DIVERGE: Phylogeny-based Analysis for Functional-Structural Divergence of a Protein Family. Bioinformatics 2002, 18: 500-501.
    • (2002) Bioinformatics , vol.18 , pp. 500-501
    • Gu, X.1    Vander Velden, K.2
  • 21
    • 0023480940 scopus 로고
    • Evolution of animal mitochondrial DNA: Relevance for population biology and systematics
    • Moritz, C., Dowling, T.E., Brown, W.M. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Ann. Rev. Ecol. Syst. 1987, 18: 269-292.
    • (1987) Ann. Rev. Ecol. Syst. , vol.18 , pp. 269-292
    • Moritz, C.1    Dowling, T.E.2    Brown, W.M.3
  • 23
    • 0027525104 scopus 로고
    • The C. elegans cell death gene ced-3 encodes a protein similar to mammalian interleukin-1 beta-converting enzyme
    • Yuan, J., Shaham, S., Ledoux, S., Ellis, H.M., Horvitz, H.R. The C. elegans cell death gene ced-3 encodes a protein similar to mammalian interleukin-1 beta-converting enzyme. Cell 1993, 75: 641-652.
    • (1993) Cell , vol.75 , pp. 641-652
    • Yuan, J.1    Shaham, S.2    Ledoux, S.3    Ellis, H.M.4    Horvitz, H.R.5
  • 24
  • 25
    • 0032548919 scopus 로고    scopus 로고
    • Murine caspase-11, an ICE-interacting protease, is essential for the activation of ICE
    • Wang, S., Miura, M., Jung, Y.K., Zhu, H., Li, E., Yuan, J. Murine caspase-11, an ICE-interacting protease, is essential for the activation of ICE. Cell 1998, 92: 501-509.
    • (1998) Cell , vol.92 , pp. 501-509
    • Wang, S.1    Miura, M.2    Jung, Y.K.3    Zhu, H.4    Li, E.5    Yuan, J.6
  • 28
    • 0023375195 scopus 로고
    • The neighbor joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N., and Nei, M. The neighbor joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4: 406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 29
    • 85047698990 scopus 로고    scopus 로고
    • Evolutionary patterns of gene families generated in the early stage of vertebrates
    • Wang, Y., and Gu, X. Evolutionary patterns of gene families generated in the early stage of vertebrates. J. Mol. Evol. 2000, 51: 88-96.
    • (2000) J. Mol. Evol. , vol.51 , pp. 88-96
    • Wang, Y.1    Gu, X.2
  • 31
    • 0032227861 scopus 로고    scopus 로고
    • Cloning and expression of human eNOS and nNOS using the baculovirus-insect cell system
    • Charles, I.G., Foxwell, N., Chubb, A. Cloning and expression of human eNOS and nNOS using the baculovirus-insect cell system. Methods Mol. Biol. 1998, 100: 51-60.
    • (1998) Methods Mol. Biol. , vol.100 , pp. 51-60
    • Charles, I.G.1    Foxwell, N.2    Chubb, A.3
  • 32
    • 0033551402 scopus 로고    scopus 로고
    • The myb gene family in cell growth, differentiation and apoptosis
    • Oh, I.H., and Reddy, E.P. The myb gene family in cell growth, differentiation and apoptosis. Oncogene 1999, 18: 3017-3033.
    • (1999) Oncogene , vol.18 , pp. 3017-3033
    • Oh, I.H.1    Reddy, E.P.2
  • 33
    • 0033582946 scopus 로고    scopus 로고
    • Coevolving protein residues: Maximum likelihood identification and relationship to structure
    • Pollock, D., Taylor, W.R., Goldman, N. Coevolving protein residues: maximum likelihood identification and relationship to structure. J. Mol. Biol. 1999, 287: 187-198.
    • (1999) J. Mol. Biol. , vol.287 , pp. 187-198
    • Pollock, D.1    Taylor, W.R.2    Goldman, N.3
  • 34
    • 0031966661 scopus 로고    scopus 로고
    • The structural basis of molecular adaptation
    • Golding, G.B., Dean, A.M. The structural basis of molecular adaptation. Mol. Biol. Evol. 1998, 15: 355-369.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 355-369
    • Golding, G.B.1    Dean, A.M.2
  • 35
    • 0032849322 scopus 로고    scopus 로고
    • A method for detecting positive selection at single amino acid sites
    • Suzuki, Y., Gojobori, T. A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 1999, 16: 1315-1328.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1315-1328
    • Suzuki, Y.1    Gojobori, T.2


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