Studying complex biological systems using multifactorial perturbation

Nature Reviews Genetics

Volumn 4, Issue 2, 2003, Pages 145-151

  Jansen, Ritsert C ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

GALACTOSE; TRANSCRIPTION FACTOR;

ARABIDOPSIS; BIOLOGICAL TRAIT; BIOLOGY; CLINICAL RESEARCH; COST; DNA MICROARRAY; DNA MODIFICATION; DROSOPHILA MELANOGASTER; GENE INTERACTION; GENE SEGREGATION; GENETIC ANALYSIS; GENETIC MANIPULATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOMICS; HUMAN; KNOCKOUT GENE; MODEL; MUTAGENESIS; NONHUMAN; PHENOTYPE; POINT MUTATION; POPULATION; PRIORITY JOURNAL; PROTEOMICS; QUANTITATIVE GENETICS; QUANTITATIVE TRAIT LOCUS; REVIEW; SACCHAROMYCES CEREVISIAE; SEGREGATION ANALYSIS; STATISTICAL ANALYSIS; TECHNIQUE; TRANSGENE; TRANSGENICS; YEAST;

ANIMALS; GENETIC RESEARCH; GENETIC TECHNIQUES; GENOMICS; HUMANS;

ARABIDOPSIS; DROSOPHILA MELANOGASTER; MELANOGASTER; SACCHAROMYCES CEREVISIAE;

EID: 0037306536     PISSN: 14710056     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrg996     Document Type: Review

References (44)

1. Chong, L. & Ray, L. B. Whole-istic biology. Science 295, 1661 (2002).
2. Kitano, H. Systems biology. Science 295, 1662-1668 (2002).
3. Knowlton, R. G. et al. A polymorphic DNA marker linked to cystic fibrosis is located on chromosome 7 Nature 318, 380-385 (1985).
4. Kerem, B.-S. et al. Identification of the cystic fibrosis gene: genetic analysis. Science 245, 1073-1080 (1989).
5. Gilliam, T. C. et al. Localization of the Huntington's disease gene to a small segment of chromosome 4 flanked by D4S10 and the telomere. Cell 50, 565-571 (1987).
6. Huntington's Disease Collaborative Research Group. A novel gene containing a trinucleotide repeat that is expanded and unstable in Huntington's disease chromosomes. Cell 72, 971-983 (1993).
7. Hughes, T. R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109-126 (2000).
8. Ideker, T. et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934 (2001).
9. Davidson, E. H. et al. A genomic regulatory network for development. Science 295, 1669-1678 (2002).
10. Ernest, S. et al. Genetic and molecular control of folatehomocysteine metabolism in mutant mice. Mamm. Genome 13, 259-267 (2002).
11. Jansen, R. C. & Nap, J. P. H. Genetical genomics: the added value from segregation. Trends Genet. 17, 388-391 (2001).
12. Brem, R. B., Yvert, G., Clinton, R. & Kruglyak, L. Genetic dissection of transcriptional regulation in budding yeast. Science 296, 752-756 (2002).
13. Klose, J. et al. Genetic analysis of the mouse brain proteome. Nature Genet. 30, 385-393 (2002).
14. Wayne, M. L. & McIntyre, L. M. Combining mapping and arraying: an approach to candidate gene identification. Proc. Natl Acad. Sci. USA 99, 14903-14906 (2002)
15. Demant, P. & Hart, A. A. M. Recombinant congenic strains - a new tool for analyzing genetic traits determined by more than one gene. Immunogenetics 24, 416-422 (1986).
16. Fijneman, R. J. A., Ophoff, R. A., Hart, A. A. M. & Demant, P. Kras-2 alleles, mutations, and lung tumor susceptibility in the mouse - an evaluation. Oncogene 9, 1417-1421 (1994).
17. Darvasi, A. Experimental strategies for the genetic dissection of complex traits in animal models. Nature Genet. 18, 19-24 (1998)
18. Nadeau, J. H., Singer, J. B., Matin, A. & Lander, E S. Analysing complex genetic traits with chromosome substitution strains. Nature Genet. 24, 221-225 (2000).
19. Threadgill, D. W., Hunter, K. W. & Williams, R. W. Genetic dissection of complex and quantitative traits: from fantasy to reality via a community effort. Mamm. Genome 13, 175-178 (2002).
20. Jannink, J. L. & Jansen, R. C. Mapping epistatic quantitative trait loci with one-dimensional genome searches. Genetics 6, 337-342 (2001).
21. Gygi, S. P., Rochon, Y., Franza, B. R. & Aebersold, R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19, 1720-1730 (1999).
22. Jansen, R. C., Nap, J. P. H. & Mlynarova, L. Errors in genomics and proteomics. Nature Biotechnol. 20, 19 (2002).
23. Mather K. & Jinks, J. L. Biometrical Genetics 3rd edn (Chapman & Hall, London, 1982)
24. Brenner, S. et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnol. 18, 630-634 (2000)
25. Nap, J. P., Conner, A. J., Mlynarova, M., Stiekema, W. J. & Jansen, R. C. Dissection of a synthesized quantitative trait to characterize transgene interactions. Genetics 147, 315-320 (1997).
26. Mlynarova, L., Loonen, A., Mietkiewska, E., Jansen, R. C. & Nap, J. P. Assembly of two transgenes in an artificial chromatin domain gives highly coordinated expression in tobacco. Genetics 160, 727-740 (2002).
27. Ozbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D. & van Oudenaarden. A Regulation of noise in the expression of a single gene. Nature Genet. 31, 69-73 (2002).
28. Claverie, J. M. Gene number - what if there are only 30,000 human genes? Science 291, 1255-1257 (2001).
29. Carlborg, O., Andersson, L. & Kinghorn, B. The use of genetic algorithm for simultaneous mapping of multiple interacting quantitative trait loci. Genetics 155, 2003-2010 (2000).
30. Broman, K. W. & Speed, T. A model selection approach for the identification of quantitative trait loci in experimental crosses. J. R. Statist. Soc. B 64, 1-6 (2002)
31. Ritchie, M. D. et al. Multifactorial-dimensionality reduction reveals high-order interactions among estrogenmetabolism genes in sporadic breast cancer. Am. J. Hum. Genet. 69, 138-147 (2001).
32. Nelson, M. R., Kardia, S. L. R., Ferrell, R. E. & Sing, C. F. A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. Genome Res. 11, 458-470 (2001).
33. Fijneman, R. J. A., de Vries, S. S., Jansen, R. C. & Demant, P. Complex interaction of new quantitative trait loci, Sluc1, Sluc2, Sluc3, and Sluc4, that influence the susceptibility to lung cancer in the mouse. Nature Genet. 14, 465-467 (1996).
34. de Boer, M. P., ter Braak, C. J. F. & Jansen, R. C. A penalized likelihood method for mapping epistatic quantitative trait loci with one-dimensional genome searches. Genetics 162, 951-960 (2002).
35. 2 easy steps. Bioinformatics 17, 1183-1197 (2001).
36. de la Fuente, A., Brazhnik, P. & Mendez, P. Linking the genes: inferring quantitative gene networks from microarray data. Trends Genet. 18, 395-398 (2002).
37. Stoll, M. et al. A genomic-systems biology map for cardiovascular function Science 294, 1723-1726 (2001).
38. Kerr, M. K. & Churchill, G. A. Statistical design and the analysis of gene expression microarray data. Genet. Res. 77, 123-128 (2001).
39. Fisher, R. A. The Design of Experiments (Oxford Univ. Press, Oxford, UK, 1935).
40. Kitami, T. & Nadeau, J. H. Biochemical networking contributes more to genetic buffering in human and mouse metabolic networks than does gene duplication. Nature Genet. 32, 191-194 (2002).
41. Yuh, C. H., Bolouri, H. & Davidson, E. H. Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 279, 1896-1902 (1998).
42. Fessele, S., Maier, H., Zischek, C., Nelson, P. J. & Werner, T. Regulatory context is a crucial part of gene function. Trends Genet. 18, 60-63 (2002).
43. Frankel, W. N. & Schork, N. J. Who is afraid of epistasis? Nature Genet. 14, 371-373 (1996).
44. Templeton, A. R. in Epistasis and the Evolutionary Process (ed. Wolf, J. B.) 41-57 (Oxford Univ. Press, Oxford, UK, 2000).