Copyright © 2007 Valia Shoja et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

1. A. Force, M. Lynch, F. B. Pickett, A. Amores, Y.-L. Yan, and J. Postlethwait, “Preservation of duplicate genes by complementary, degenerative mutations,” Genetics, vol. 151, no. 4, pp. 1531–1545, 1999.
2. X. He and J. Zhang, “Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution,” Genetics, vol. 169, no. 2, pp. 1157–1164, 2005. View at Publisher · View at Google Scholar · View at PubMed
3. L. Huminiecki and K. H. Wolfe, “Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse,” Genome Research, vol. 14, no. 10a, pp. 1870–1879, 2004. View at Publisher · View at Google Scholar · View at PubMed
4. A. van Hoof, “Conserved functions of yeast genes support the duplication, degeneration and complementation model for gene duplication,” Genetics, vol. 171, no. 4, pp. 1455–1461, 2005. View at Publisher · View at Google Scholar · View at PubMed
5. W. Wang, H. Yu, and M. Long, “Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species,” Nature Genetics, vol. 36, no. 5, pp. 523–527, 2004. View at Publisher · View at Google Scholar · View at PubMed
6. X. Gu, Z. Zhang, and W. Huang, “Rapid evolution of expression and regulatory divergences after yeast gene duplication,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 3, pp. 707–712, 2005. View at Publisher · View at Google Scholar · View at PubMed
7. Z. Gu, D. Nicolae, H. H.-S. Lu, and W.-H. Li, “Rapid divergence in expression between duplicate genes inferred from microarray data,” Trends in Genetics, vol. 18, no. 12, pp. 609–613, 2002. View at Publisher · View at Google Scholar
8. K. D. Makova and W.-H. Li, “Divergence in the spatial pattern of gene expression between human duplicate genes,” Genome Research, vol. 13, no. 7, pp. 1638–1645, 2003. View at Publisher · View at Google Scholar · View at PubMed
9. C. Rizzon, L. Ponger, and B. S. Gaut, “Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice,” PLoS Computational Biology, vol. 2, no. 9, p. e115, 2006. View at Publisher · View at Google Scholar · View at PubMed
10. V. Shoja and L. Zhang, “A roadmap of tandemly arrayed genes in the genomes of human, mouse, and rat,” Molecular Biology and Evolution, vol. 23, no. 11, pp. 2134–2141, 2006. View at Publisher · View at Google Scholar · View at PubMed
11. J. Yu, J. Wang, and W. Lin, et al., “The genomes of Oryza sativa: a history of duplications,” PLoS Biology, vol. 3, no. 2, p. e38, 2005. View at Publisher · View at Google Scholar · View at PubMed
12. L. Zhang and B. S. Gaut, “Does recombination shape the distribution and evolution of tandemly arrayed genes (TAGs) in the Arabidopsis thaliana genome?,” Genome Research, vol. 13, no. 12, pp. 2533–2540, 2003. View at Publisher · View at Google Scholar · View at PubMed
13. B. A. Cohen, R. D. Mitra, J. D. Hughes, and G. M. Church, “A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression,” Nature Genetics, vol. 26, no. 2, pp. 183–186, 2000. View at Publisher · View at Google Scholar · View at PubMed
14. M. J. Lercher, T. Blumenthal, and L. D. Hurst, “Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes,” Genome Research, vol. 13, no. 2, pp. 238–243, 2003. View at Publisher · View at Google Scholar · View at PubMed
15. P. T. Spellman and G. M. Rubin, “Evidence for large domains of similarly expressed genes in the Drosophila genome,” Journal of Biology, vol. 1, no. 1, pp. 5.1–5.8, 2002. View at Publisher · View at Google Scholar
16. E. J. B. Williams and D. J. Bowles, “Coexpression of neighboring genes in the genome of Arabidopsis thaliana,” Genome Research, vol. 14, no. 6, pp. 1060–1067, 2004. View at Publisher · View at Google Scholar · View at PubMed
17. A. I. Su, T. Wiltshire, and S. Batalov, et al., “A gene atlas of the mouse and human protein-encoding transcriptomes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 16, pp. 6062–6067, 2004. View at Publisher · View at Google Scholar · View at PubMed
18. E. Hubbell, W.-M. Liu, and R. Mei, “Robust estimators for expression analysis,” Bioinformatics, vol. 18, no. 12, pp. 1585–1592, 2002. View at Publisher · View at Google Scholar
19. A. I. Su, M. P. Cooke, and K. A. Ching, et al., “Large-scale analysis of the human and mouse transcriptomes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 7, pp. 4465–4470, 2002. View at Publisher · View at Google Scholar · View at PubMed
20. I. Yanai, D. Graur, and R. Ophir, “Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control,” OMICS, vol. 8, no. 1, pp. 15–24, 2004. View at Publisher · View at Google Scholar · View at PubMed
21. B.-Y. Liao and J. Zhang, “Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution,” Molecular Biology and Evolution, vol. 23, no. 6, pp. 1119–1128, 2006. View at Publisher · View at Google Scholar · View at PubMed
22. P. Rice, I. Longden, and A. Bleasby, “EMBOSS: the European molecular biology open software suite,” Trends in Genetics, vol. 16, no. 6, pp. 276–277, 2000. View at Publisher · View at Google Scholar
23. Z. Yang, “PAML: a program package for phylogenetic analysis by maximum likelihood,” Computer Applications in the Biosciences, vol. 13, no. 5, pp. 555–556, 1997.
24. A. Wagner, “Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 12, pp. 6579–6584, 2000. View at Publisher · View at Google Scholar · View at PubMed
25. V. Katju and M. Lynch, “The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome,” Genetics, vol. 165, no. 4, pp. 1793–1803, 2003.
26. V. Katju and M. Lynch, “On the formation of novel genes by duplication in the Caenorhabditis elegans genome,” Molecular Biology and Evolution, vol. 23, no. 5, pp. 1056–1067, 2006. View at Publisher · View at Google Scholar · View at PubMed
27. M. Long, “Evolution of novel genes,” Current Opinion in Genetics & Development, vol. 11, no. 6, pp. 673–680, 2001. View at Publisher · View at Google Scholar
28. M. J. Lercher, A. O. Urrutia, and L. D. Hurst, “Clustering of housekeeping genes provides a unified model of gene order in the human genome,” Nature Genetics, vol. 31, no. 2, pp. 180–183, 2002. View at Publisher · View at Google Scholar · View at PubMed
29. N. Chen and L. D. Stein, “Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans,” Genome Research, vol. 16, no. 5, pp. 606–617, 2006. View at Publisher · View at Google Scholar · View at PubMed