Design of microarray experiments for genetical genomics studies

Genetics

Volumn 174, Issue 2, 2006, Pages 945-957

  Bueno Filho, Júlio S S ^a   Gilmour, Steven G ^b   Rosa, Guilherme J M ^c,d  

^a FEDERAL UNIVERSITY OF LAVRAS   (Brazil)

^b QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^c MICHIGAN STATE UNIVERSITY   (United States)

^d UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE LOCUS; GENE STRUCTURE; GENE TARGETING; GENETIC ANALYSIS; GENETIC EPISTASIS; GENETIC VARIABILITY; GENOMICS; MATHEMATICAL ANALYSIS; MICROARRAY ANALYSIS; MOTIVATION; PRIORITY JOURNAL; PROMOTER REGION; STATISTICAL MODEL; TRANSGENE;

ANIMALS; GENOMICS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RESEARCH DESIGN;

EID: 33750469672     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.057281     Document Type: Article

References (36)

1. BAILEY, R. A., 1981 A unified approach to design of experiments. J. R. Stat. Soc. A 144: 214-223.
2. BAILEY, R. A., 1997 Statistics and mathematics: the appropriate use of mathematics within statistics (with discussion). Statistician 47: 261-271, 273-290.
3. BREM, R. B., G. YVERT, R. CLINTON and L. KRUGLYAK, 2002 Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
4. BUENO FILHO, J. S. S., and S. G. GILMOUR, 2003 Planning incomplete block experiments when treatments are genetically related. Biometrics 59: 375-381.
5. BYSTRYKH, L., E. WEERSING, B. DONTJE, S. SUTTON, M. T. PLETCHER et al., 2005 Uncovering regulatory pathways affecting hematopoietic stem cell function using "genetical genomics." Nat. Genet. 37: 225-232.
6. CHESLER, E. J., L. LU, J. WANG, R. W. WILLIAMS and K. F. MANLY, 2004 WebQTL: rapid exploratory analysis of gene expression and genetic networks for brain and behavior. Nat. Neurosci. 7: 485-486.
7. DARVASI, A., 2003 Gene expression meets genetics. Nature 422: 269-271.
8. DARVASI, A., and M. SOLLER, 1992 Selective genotyping for determination of linkage between a marker locus and a quantitative trait locus. Theor. Appl. Genet. 85: 353-359.
9. DRAPER, N. R., and I. GUTTMAN, 1997 Two-level factorial and fractional factorial designs in blocks of size two. J. Qual. Technol. 29: 71-75.
10. FEDOROV, V. V., 1972 Theory of Optimal Experiments. Academic Press, New York.
11. GLONEK, G. F. V., and P. J. SOLOMON, 2004 Factorial and time course designs for cDNA microarray experiments. Biostatistics 5: 89-111.
12. HENDERSON, C. R., 1976 Simple method for computing inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics 32: 69-83.
13. JANSEN, R. C., and J. NAP, 2001 Genetical genomics: the added value from segregation. Trends Genet. 17: 388-391.
14. JIN, C., H. LAN, A. D. ATTIE, G. A. CHURCHILL, D. BULUTOGLU et al., 2004 Selective phenotyping for increased efficiency in genetic mapping studies. Genetics 168: 2285-2293.
15. KERR, M. K., 2003 Design considerations for efficient and effective microarray studies. Biometrics 59: 822-828.
16. KERR, M. K., 2006 2∧k factorials in blocks of size 2, with application to two-color microarray experiments. UW Biostatistics Working Paper Series No. 227 (http://www.bepress.com/uwbiostat/paper227).
17. KERR, M. K., and G. A. CHURCHILL, 2001 Statistical design and the analysis of gene expression microarray data. Genet. Res. 77: 123-128.
18. KIEFER, J. C., and J. WOLFOWITZ, 1960 The equivalence of two extremum problems. Can. J. Math. 12: 363-366.
19. LANDER, E. S, and D. BOTSTEIN, 1989 Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
20. LOCKHART, D. J., H. L. DONG, M. C. BYRNE, M. T. FOLLETTIE, M. V. GALLO et al., 1996 Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotech. 14: 1675-1680.
21. LYNCH, M., and B. WALSH, 1998 Genetics and Analysis of Quantitative Traits. Sinauer, Sunderland, MA.
22. MEAD, R., 1990 The nonorthogonal design of experiments (with discussion). J. R. Stat. Soc. A 153: 151-201.
23. MONKS, S. A., A. LEONARDSON, H. ZHU, P. CUNDIFF, P. PIETRUSIAK et al., 2004 Genetic inheritance of gene expression in human cell lines. Am. J. Hum. Genet. 75: 1094-1105.
24. NOUEIRY, A. O., J. CHEN and P. AHLQUIST, 2000 A mutant allele of essential, general translation initiation factor DED1 selectively inhibits translation of a viral mRNA. Proc. Natl. Acad. Sci. USA 97: 12985-12990.
25. ROSA, G. J. M., J. P. STEIBEL and R. J. TEMPELMAN, 2005 Reassessing design and analysis of two-color microarray experiments using mixed effects models. Comp. Funct. Genomics 6: 123-131.
26. SCHADT, E. E., S. A. MONKS, T. A. DRAKE, A. J. LUSIS, N. CHE et al., 2003 Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
27. SCHENA, M., D. SHALON, R. W. DAVIS and P. O. BROWN, 1995 Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science 270: 467-470.
28. SORENSEN, D., and D. GIANOLA, 2002 Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics. Springer, New York.
29. STEIBEL, J. P., and G. J. M. ROSA, 2005 On reference designs for microarray experiments. Stat. Appl. Gen. Mol. Biol. 4(1): Article 36 (http://www.bepress.com/sagmb/vol4/issl/art36/).
30. TEMPELMAN, R. J., 2005 Assessing statistical precision, power, and robustness of alternative experimental designs for two color microarray platforms based on mixed effects models. Vet. Immunol. Immunopathol. 105: 175-186.
31. VINCIOTTI, V., R. KHANIN, D. D'ALIMONTE, X. LIU, N. CATTINI et al., 2005 An experimental evaluation of a loop versus a reference design for two-channel microarrays. Bioinformatics 21: 492-501.
32. WANG, P. C., 2004 Designing two-level fractional factorial experiments in blocks of size two. Sankhya 66: 327-342.
33. WIT, E., A. NOBILE and R. KHANIN, 2005 Near-optimal designs for dual channel microarray studies. Appl. Stat. 54: 817-830.
34. WOLFINGER, R. D., G. GIBSON, E. D. WOLFINGER, L. BENNETT, H. HAMADEH et al., 2001 Assessing gene significance from cDNA microarray expression data via mixed models. J. Comp. Biol. 8: 625-637.
35. YANG, Y. H., and T. SPEED, 2002 Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3: 570-588.
36. YANG, Y. J., and N. R. DRAPER, 2003 Two-level factorial and fractional factorial designs in blocks of size two. J. Qual. Technol. 35: 294-305.