Multiple locus linkage analysis of genomewide expression in yeast

PLoS Biology

Volumn 3, Issue 8, 2005, Pages

  Storey, John D ^a   Akey, Joshua M ^a   Kruglyak, Leonid ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CALCULATION; CONFIDENCE INTERVAL; EPISTASIS; FUNGAL GENETICS; FUNGAL STRAIN; GENE EXPRESSION; GENE INTERACTION; GENE LOCUS; GENE MAPPING; GENETIC LINKAGE; GENETIC TRAIT; GENETIC VARIABILITY; GENOME; LINKAGE ANALYSIS; NONHUMAN; QUANTITATIVE TRAIT LOCUS; SACCHAROMYCES CEREVISIAE; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; YEAST; CHROMOSOME MAP; COMPARATIVE STUDY; EVALUATION; GENE EXPRESSION PROFILING; GENETIC EPISTASIS; GENETICS; METHODOLOGY; PHENOTYPE; PROBABILITY;

SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

CHROMOSOME MAPPING; EPISTASIS, GENETIC; GENE EXPRESSION PROFILING; GENOME, FUNGAL; LINKAGE (GENETICS); PHENOTYPE; PROBABILITY; QUANTITATIVE TRAIT LOCI; SACCHAROMYCES CEREVISIAE;

EID: 23644434473     PISSN: 15449173     EISSN: None     Source Type: Journal    
DOI: 10.1371/journal.pbio.0030267     Document Type: Article

References (42)

1. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470.
2. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotech 14: 1675-1680.
3. MacBeath G, Schreiber SL (2000) Printing proteins as microarrays for highthroughput function determination. Science 289: 1760-1763.
4. Lan H, Stoehr JP, Nadler ST, Schueler KL, Yandell BS, et al. (2003) Dimension reduction for mapping mrna abundance as quantitative traits. Genetics 164: 1607-1614.
5. Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
6. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, et al. (2003) Genetics of gene expression surveyed in maize, mouse, and man. Nature 422: 297-302.
7. Yvert G, Brem RB, Whittle J, Akey JM, Foss E, et al. (2003) Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 35: 57-64.
8. Cowles CR, Hirschhorn JN, Altshuler D, Lander ES (2002) Detection of regulatory variation in mouse genomes. Nat Genet 32: 432-437.
9. Oleksiak MF, Churchill GA, Crawford DL (2002) Variation in gene expression within and among natural populations. Nat Genet 32: 261-266.
10. Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, et al. (2002) The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet 29: 389-395.
11. Yan H, Yuan W, Velculescu VE, Vogelstein B, Kinzler KW (2002) Allelic variation in human gene expression. Science 297: 1143.
12. Rockman MV, Wray GA (2002) Abundant raw material for cis-regulatory evolution in humans. Mol Biol Evol 19: 1991-2004.
13. Cheung VG, Conlin LK, Weber TM, Arcaro M, Jen KY, et al. (2003) Natural variation in human gene expression assessed in lymphoblastoid cells. Nat Genet 33: 422-425.
14. Brem RB, Kruglyak L (2005) The landscape of genetic complexity across 5700 gene expression traits in yeast. Proc Natl Acad Sci U S A 102: 1572-1577.
15. Zeng ZB, Kao CH, Basten CJ (1999) Estimating the genetic architecture of quantitative traits. Genet Res 74: 279-289.
16. Ball RD (2001) Bayesian methods for quantitative trait loci mapping based on model selection: Approximate analysis using the Bayesian information criterion. Genetics 159: 1351-1364.
17. Piepho HP, Gauch HG (2001) Marker pair selection for mapping quantitative trait loci. Genetics 157: 433-444.
18. Broman KW, Speed TP (2002) A model selection approach for the identi.cation of quantitative trait loci in experimental crosses (with discussion). J R Stat Soc [Ser B] 64: 641-656.
19. Zeng ZB (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci U S A 90: 10972-10976.
20. Jansen R (1993) A general mixture model for mapping quantitative trait loci by using molecular markers. Theor Appl Genet 85: 252-260.
21. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.
22. Jansen RC, Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136: 1447-1455.
23. Kao CH, Zeng ZB, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152: 1203-1216.
24. Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sunderland (Massachusetts): Sinauer. 980 p.
25. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
26. Doerge RW, Churchill GA (1996) Permutation tests for multiple loci affecting a quantitative character. Genetics 142: 285-294.
27. Storey JD (2002) A direct approach to false discovery rates. J R Stat Soc [Ser B] 64: 479-498.
28. Storey JD, Tibshirani R (2003) Statistical signi.cance for genome-wide studies. Proc Natl Acad Sci U S A 100: 9440-9445.
29. Frankel WN, Schork NJ (1996) Who's afraid of epistasis? Nat Genet 14: 371-373.
30. Storey JD (2003) The positive false discovery rate: A Bayesian interpretation and the q-value. Annals of Statistics 31: 2013-2035.
31. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, et al. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature 430: 743-747.
32. Brem RB, Storey JD, Whittle J, Kruglyak L (2005) Genetic interactions between polymorphisms that affect gene expression in yeast. Nature: In press.
33. Tanaka K, Matsumoto K, Tohe A (1989) IRA1, an inhibitory regulator of the RAS-cyclic AMP pathway in Saccharomyces cerevisiae. Mol Cell Biol 9: 757-768.
34. Fazzio TG, Kooperberg C, Goldmark JP, Neal C, Basom R, et al. (2001) Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Mol Cell Biol 21: 6450-6460.
35. Talla E, Tekaia F, Brino L, Dujon B (2003) A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes crosshybridization. BMC Genomics 4: 38.
36. Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
37. Anderson JA, Blair V (1982) Penalized maximum likelihood estimation in logistic regression and discrimination. Biometrika 69: 123-136.
38. Green PJ, Silverman BW (1994) Nonparametric regression and generalized linear models: A roughness penalty approach. New York: Chapman and Hall. 182 p.
39. Efron B, Tibshirani R, Storey JD, Tusher V (2001) Empirical Bayes analysis of a microarray experiment. J Am Stat Assoc 96: 1151-1160.
40. Genovese C, Wasserman L (2002) Bayesian and frequentist multiple hypothesis testing. Bayesian Statistics 7: 145-162.
41. Newton MA, Noueiry A, Sarkar D, Ahlquist P (2004) Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics 5: 155-176.
42. Storey JD, Taylor JE, Siegmund D (2004) Strong control, conservative point estimation, and simultaneous conservative consistency of false discovery rates: A unified approach. J R Stat Soc [Ser B] 66: 187-205.