The environmental contribution to gene expression profiles

Nature Reviews Genetics

Volumn 9, Issue 8, 2008, Pages 575-581

  Gibson, Greg ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ENVIRONMENT; GENE CONTROL; GENE EXPRESSION; GENE MAPPING; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; MICROARRAY ANALYSIS; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; REVIEW;

ADAPTATION, BIOLOGICAL; ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; CLUSTER ANALYSIS; ENVIRONMENT; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; MODELS, BIOLOGICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PEDIGREE; TRANSCRIPTION, GENETIC; VARIATION (GENETICS);

EID: 47649132170     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg2383     Document Type: Review

References (41)

1. Pennisi, E. Breakthrough of the year: human genetic variation. Science 318, 1842-1843 (2007).
2. Ranz, J. M. & Machado, C. A. Uncovering evolutionary patterns of gene expression using microarrays. Trends Ecol. Evol. 21, 29-37 (2006).
3. Pietiläinen, K. H. et al. Global transcript profiles of fat in monozygotic twins discordant for BMI: pathways behind acquired obesity. PLoS Medicine 5, e51 (2008).
4. Montano, M. et al. Gene-expression profiling of HIV-1 infection and perinatal transmission in Botswana. Genes Immun. 7, 298-309 (2006).
5. Leek, J. T. & Storey, J. D. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 3, e161 (2007).
6. Fink, J. et al. Host gene expression profiling of Dengue virus infection in cell lines and patients. PLoS Negl. Trop. Dis. 1, e86 (2007).
7. Fry, R. C. et al. Activation of inflammation/NF-kappa B signaling in infants born to arsenic-exposed mothers. PLoS Genet. 3, e207 (2007).
8. Peretz, A. et al. Diesel exhaust inhalation and assessment of peripheral blood mononuclear cell gene transcription effects: an exploratory study of healthy human volunteers. Inhal. Toxicol. 19, 1107-1119 (2007).
9. Kawai, T. et al. Gene expression signature in peripheral blood cells from medical students exposed to chronic psychological stress. Biol. Psychol. 76, 147-155 (2007).
10. Dvornyk, V. et al. Effect of menopause on gene expression profiles of circulating monocytes: a pilot in vivo microarray study. J. Genet. Genom. 34, 974-983 (2007).
11. Crawford, D. L. & Oleksiak, M. F. The biological importance of measuring individual variation. J. Exp. Biol. 210, 1613-1621 (2007).
12. Kennerly, E. et al. A gene expression signature of confinement in peripheral blood of red wolves (Canis rufus). Mol. Ecol. 17, 2782-2791 (2008).
13. Lindberg, J. et al. Selection for tameness has changed brain gene expression in silver foxes. Curr. Biol. 15, R915-R916 (2005).
14. Gulick, P. J. et al. Transcriptome comparison of winter and spring wheat responding to low temperature. Genome 48, 913-923 (2005).
15. Joosen, R. V. et al. Correlating gene expression to physiological parameters and environmental conditions during cold acclimation of Pinus sylvestris, identification of molecular markers using cDNA microarrays. Tree Physiol. 26, 1297-1313 (2006).
16. Rifkin, S. A., Kim, J. & White, K. P. Evolution of gene expression in the Drosophila melanogaster subgroup. Nature Genet. 33, 138-144 (2003).
17. Hsieh, W.-P., Chu, T.-M., Wolfinger, R. D. & Gibson, G. Mixed-model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles. Genetics 165, 747-757 (2003).
18. Somel, M. et al. Human and chimpanzee gene expression differences replicated in mice fed different diets. PLoS ONE 1, e1504 (2008).
19. Visscher, P. M., Hill, W. G. & Wray, N. R. Heritability in the genomics era - concepts and misconceptions. Nature Rev. Genet. 9, 255-266 (2008).
20. Idaghdour, Y., Storey, J. D., Jadallah, S. & Gibson, G. A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs. PLoS Genet. 4, e100052 (2008).
21. Dermitzakis, E. T. & Stranger, B. E. Genetic variation in human gene expression. Mamm. Genome 17, 503-508 (2006).
22. Torcia, M. G. et al. Functional deficit of T regulatory cells in Fulani, an ethnic group with low susceptibility to Plasmodium falciparum malaria. Proc. Natl Acad. Sci. USA 105, 646-651 (2008).
23. Monks, S. A. et al. Genetic inheritance of gene expression in human cell lines. Am. J. Hum. Genet. 75, 1094-1105 (2004).
24. Dixon, A. L. et al. A genome-wide association study of global gene expression. Nature Genet. 39, 1202-1207 (2007).
25. Göring, H. H. et al. Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nature Genet. 39, 1208-1216 (2007).
26. Stranger, B. E. et al. Population genomics of human gene expression. Nature Genet. 39, 1217-1224 (2007).
27. Emilsson, V. et al. Genetics of gene expression and its effect on disease. Nature 452, 423-428 (2008).
28. Solinas, G. et al. JNK1 in hematopoietically derived cells contributes to diet-induced inflammation and insulin resistance without affecting obesity. Cell Metab. 6, 386-397 (2007).
29. Jansen, R. C. & Nap, J. P. Genetical genomics: the added value from segregation. Trends Genet. 17, 388-391 (2001).
30. Rockman, M. V. & Kruglyak, L. Genetics of global gene expression. Nature Rev. Genet. 7, 862-872 (2007).
31. Chen, Y. et al. Variations in DNA elucidate molecular networks that cause disease. Nature 452, 429-435 (2008).
32. Li, Y., et al. Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet. 2, e222 (2007).
33. Smith, E. N. & L. Kruglyak. Gene-environment interaction in yeast gene expression. PLoS Biol. 6, e83 (2008).
34. Yu, J., et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genet. 38, 203-208 (2006).
35. Visscher, P. M. et al. Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings. PLoS Genet. 2, e41 (2006).
36. Frentiu, F. D. et al. Pedigree-free animal models: the relatedness matrix reloaded. Proc. Biol. Sci. 275, 639-647 (2008).
37. West-Eberhard, M. J. Developmental plasticity and evolution (Oxford Univ. Press, Oxford, 2003).
38. Crispo, E. The Baldwin effect and genetic assimilation: revisiting two mechanisms of evolutionary change mediated by phenotypic plasticity. Evolution 61, 2469-2479 (2007).
39. Wang, H., Zhang, H., Gao, F., Li, J. & Li, Z. Comparison of gene expression between upland and lowland rice cultivars under water stress using cDNA microarray. Theor. Appl. Genet. 115, 1109-1126 (2007).
40. Waddington, C. H. Canalization of development and genetic assimilation of acquired characters. Nature 183, 1654-1655 (1959).
41. Wittkopp, P. J., Haerum, B. K. & Clark, A. G. Regulatory changes underlying expression differences within and between Drosophila species. Nature Genet. 40, 346-350 (2008).