Relationship between gene expression and GC-content in mammals: Statistical significance and biological relevance

Human Molecular Genetics

Volumn 14, Issue 3, 2005, Pages 421-427

  Sémon, Marie ^a   Mouchiroud, Dominique ^a   Duret, Laurent ^a  

^a UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; COMPUTER SIMULATION; COMPUTER SYSTEM; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; DATA BASE; DNA MICROARRAY; GC RICH SEQUENCE; GENE EXPRESSION; GENE LIBRARY; GENOME ANALYSIS; HUMAN; HUMAN CELL; HUMAN GENOME; HUMAN TISSUE; INTERMETHOD COMPARISON; ISOCHORE; METHODOLOGY; NONHUMAN; NUCLEIC ACID STRUCTURE; PREDICTION; PRIORITY JOURNAL; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE;

ANIMALS; BASE COMPOSITION; EXPRESSED SEQUENCE TAGS; GC RICH SEQUENCE; GENE EXPRESSION; GENOME; HUMANS; ISOCHORES; MICE; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

GENETTA; MAMMALIA;

EID: 13544254591     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/ddi038     Document Type: Article

References (28)

1. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., Fitzhugh, W. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
2. Mouchiroud, D., D'Onofrio, G., Aissani, B., Macaya, G., Gautier, C. and Bernardi, G. (1991) The distribution of genes in the human genome. Gene, 100, 181-187.
3. Duret, L., Mouchiroud, D. and Gautier, C. (1995) Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol., 40, 308-317.
4. Watanabe, Y., Fujiyama, A., Ichiba, Y., Hattori, M., Yada, T., Sakaki, Y. and Ikemura, T. (2002) Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions. Hum. Mol. Genet., 11, 13-21.
5. Kong, A., Gudbjartsson, D.F., Sainz, J., Jonsdottir, G.M., Gudjonsson, S.A., Richardsson, B., Sigurdardottir, S., Barnard, J., Hallbeck, B., Masson, G. et al. (2002) A high-resolution recombination map of the human genome. Nat. Genet., 31, 241-247.
6. Jabbari, K., Rayko, E. and Bernardi, G. (2003) The major shifts of human duplicated genes. Gene, 317, 203-208.
7. Smit, A.F. (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9, 657-663.
8. Bernardi, G., Olofsson, B., Filipski, J., Zerial, M., Salinas, J., Cuny, G., Meunier-Rotival, M. and Rodier, F. (1985) The mosaic genome of warm-blooded vertebrates. Science, 228, 953-958.
9. Bernardi, G. (2000) Isochores and the evolutionary genomics of vertebrates. Gene, 241, 3-17.
10. Galtier, N., Piganeau, G., Mouchiroud, D. and Duret, L. (2001) GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. Genetics, 159, 907-911.
11. Eyre-Walker, A. and Hurst, L.D. (2001) The evolution of isochores. Nat. Rev. Genet., 2, 549-555.
12. Goncalves, I., Duret, L. and Mouchiroud, D. (2000) Nature and structure of human genes that generate retropseudogenes. Genome Res. 10, 672-678.
13. Duret, L. (2002) Evolution of synonymous codon usage in metazoans. Curr. Opin. Genet. Dev., 12, 640-649.
14. Ponger, L., Duret, L. and Mouchiroud, D. (2001) Determinants of CpG islands: expression in early embryo and isochore structure. Genome. Res., 11, 1854-1860.
15. Vinogradov, A.E. (2003) Isochores and tissue-specificity. Nucleic Acids Res., 31, 5212-5220.
16. Urrutia, A.O. and Hurst, L.D. (2003) The signature of selection mediated by expression on human genes. Genome Res., 13 2260-2264.
17. Versteeg, R., van Schaik, B.D., van Batenburg, M.F., Roos, M., Monajemi, R., Caron, H., Bussemaker, H.J. and van Kampen, A.H. (2003) The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res., 13, 1998-2004.
18. Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2003) NCBI reference sequence project: update and current status. Nucleic Acids Res., 31, 34-37.
19. Lercher, M.J., Urrutia, A.O., Pavlicek, A. and Hurst, L.D. (2003) A unification of mosaic structures in the human genome. Hum. Mol. Genet., 12, 2411-2415.
20. Caron, H., van Schaik, B., van der Mee, M., Baas, F., Riggins, G., van Sluis, P., Hermus, M.C., van Asperen, R., Boon, K., Voute, P.A. et al. (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science, 291 1289-1292.
21. Lercher, M.J., Urrutia, A.O. and Hurst, L.D. (2002) Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet., 31, 180-183.
22. Birney, E., Andrews, T.D., Bevan, P., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cuff, J., Curwen, V., Cutts, T. et al. (2004) An overview of Ensembl. Genome Res., 14, 925-928
23. Duret, L., Mouchiroud, D. and Gouy, M. (1994) HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Res., 22 2360-2365.
24. Liang, P. (2002) SAGE Genie: a suite with panoramic view of gene expression. Proc. Natl Acad. Sci. USA, 99, 11547-11548.
25. Edgar, R., Domrachev, M. and Lash, A.E. (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210.
26. Zhang, Z., Schwartz, S., Wagner, L. and Miller, W. (2000) A greedy algorithm for aligning DNA sequences. J. Comput. Biol., 7 203-214.
27. 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. USA, 99, 4465-4470.
28. Ihaka, R. (1996) R: a language for data analysis and graphics. J. Comp. Graph. Genet., 16, 418-420.