Divergence in the spatial pattern of gene expression between human duplicate genes

Genome Research

Volumn 13, Issue 7, 2003, Pages 1638-1645

  Makova, Kateryna D ^a,b   Li, Wen Hsiung ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; DNA MICROARRAY; DUPLICATE GENE; GENE EXPRESSION; GENE FUNCTION; GENETIC CODE; GENETIC VARIABILITY; HUMAN; INFORMATION; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE; YEAST;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES, DUPLICATE; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; VARIATION (GENETICS);

EUKARYOTA;

EID: 0038486898     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1133803     Document Type: Article

References (21)

1. Camon, E., Magrane, M., Barrell, D., Binns, D., Fleischmann, W., Kersey, P., Mulder, N., Oinn, T., Maslen, J., Cox, A., et al. 2003. The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res. 13: 662-672.
2. Cho, R.J., Huang, M., Campbell, M.J., Dong, H., Steinmetz, L., Sapinoso, L., Hampton, G., Elledge, S.J., Davis, R.W., and Lockhart, D.J. 2001. Transcriptional regulation and function during the human cell cycle. Nat. Genet. 27: 48-54.
3. Gu, Z., Cavalcanti, A., Chen, F.-C., Bouman, P., and Li, W.-H. 2002a. Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol. Biol. Evol. 19: 256-262.
4. Gu, Z., Nicolae, D., Lu, H.H., and Li, W.-H. 2002b. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 18: 609-613.
5. Huang, L., Guan, R.J., and Pardee, A.B. 1999. Evolution of transcriptional control from prokaryotic beginnings to eukaryotic complexities. Crit. Rev. Eukaryot. Gene Expr. 9: 175-182.
6. Hughes, A.L. and Nei, M. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167-170.
7. Lercher, M.J., Williams, E.J., and Hurst, L.D. 2001. Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: Implications for understanding the mechanistic basis of the male mutation bias. Mol. Biol. Evol. 18: 2032-2039.
8. Li, W.-H. 1997. Molecular evolution. Snauer Associates, Sunderland, MA.
9. Ly, D.H., Lockhart, D.J., Lerner, R.A., and Schultz, P.G. 2000. Mitotic misregulation and human aging. Science 287: 2486-2492.
10. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, New York.
11. Rost, B. 1999. Twilight zone of protein sequence alignments. Protein Eng. 12: 85-94.
12. Su, A.I., Cooke, M.P., Ching, K.A., Hakak, Y., Walker, J.R., Wiltshire, T., Orth, A.P., Vega, R.G., Sapinoso, L.M., Moqrich, A., et al. 2002. Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. 99: 4465-4470.
13. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: 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.
14. Urrutia, A.O. and Hurst, L.D. 2001. Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics 159: 1191-1199.
15. Wagner, A. 2000. Decoupled evolution of coding region and mRNA expression patterns after gene duplication: Implications for the neutralist-selectionist debate. Proc. Natl. Acad. Sci. 97: 6579-6584.
16. Williams, E.J. and Hurst, L.D. 2002. Is the synonymous substitution rate in mammals gene-specific? Mol. Biol. Evol. 19: 1395-1398.
17. Wodicka, L., Dong, H., Mittmann, M., Ho, M.H., and Lockhart, D.J. 1997. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 15: 1359-1367.
18. Wolfe, K. H. and Li, W.-H. 2003. Molecular evolution meets the genomics revolution. Nat. Genet. 33: 255-265.
19. Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. CABIOS 13: 555-556.
20. Yang, Z. and Nielsen, R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17: 32-43.
21. Yi, S., Ellsworth, D.L., and Li, W.-H. 2002. Slow molecular clocks in old world monkeys, apes, and humans. Mol. Biol. Evol. 19: 2191-2198.