Detection and interpretation of expression quantitative trait loci (eQTL)

Methods

Volumn 48, Issue 3, 2009, Pages 265-276

  Michaelson, Jacob J ^a   Loguercio, Salvatore ^a   Beyer, Andreas ^a,b  

^a DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^b CENTER FOR REGENERATIVE THERAPIES DRESDEN   (Germany)

Author keywords

eQTL; Expression QTL; Expression quantitative trait locus; Genetic association study; Linkage analysis; Random forest; Transcriptional regulation

Indexed keywords

BAYES THEOREM; CIS TRANS ISOMERISM; DNA MICROARRAY; FALSE POSITIVE RESULT; GENE EXPRESSION; GENE MAPPING; GENETIC ASSOCIATION; GENETIC EPISTASIS; GENETIC SUSCEPTIBILITY; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; REGRESSION ANALYSIS; REVIEW;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; ANIMALS; CHROMOSOME MAPPING; DATABASES, GENETIC; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC DISEASES, INBORN; HUMANS; MALE; PHENOTYPE; POLYMORPHISM, GENETIC; QUANTITATIVE TRAIT LOCI; REGRESSION ANALYSIS; SEX FACTORS;

EID: 67649867440     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2009.03.004     Document Type: Review

References (61)

1. The Wellcome Trust Case Control Consortium, Nature 447 (2007) 661-678.
2. McCarthy M.I., Abecasis G.R., Cardon L.R., Goldstein D.B., Little J., Ioannidis J.P., and Hirschhorn J.N. Nat. Rev. Genet. 9 (2008) 356-369
3. Schadt E.E., et al. Nat. Genet. 37 (2005) 710-717
4. Schadt E.E., et al. Nature 422 (2003) 297-302
5. Eaves I.A., Wicker L.S., Ghandour G., Lyons P.A., Peterson L.B., Todd J.A., and Glynne R.J. Genome Res. 12 (2002) 232-243
6. Karp C.L., et al. Nat. Immunol. 1 (2000) 221-226
7. Jansen R.C., and Nap J.P. Trends Genet. 17 (2001) 388-391
8. Rockman M.V., and Kruglyak L. Nat. Rev. Genet. 7 (2006) 862-872
9. Abiola O., et al. Nat. Rev. Genet. 4 (2003) 911-916
10. McClurg P., et al. Genetics 176 (2007) 675-683
11. Ghazalpour A., et al. PLoS Genet. 4 (2008) e1000149
12. Dixon A.L., et al. Nat. Genet. 39 (2007) 1202-1207
13. Goring H.H., et al. Nat. Genet. 39 (2007) 1208-1216
14. Stranger B.E., et al. Nat. Genet. 39 (2007) 1217-1224
15. Shifman S., Bell J.T., Copley R.R., Taylor M.S., Williams R.W., Mott R., and Flint J. PLoS Biol. 4 (2006) e395
16. Bolstad B.M., Collin F., Simpson K.M., Irizarry R.A., and Speed T.P. Int. Rev. Neurobiol. 60 (2004) 25-58
17. Allison D.B., Cui X., Page G.P., and Sabripour M. Nat. Rev. Genet. 7 (2006) 55-65
18. Wilhelm B.T., et al. Nature 453 (2008) 1239-1243
19. Brem R.B., Yvert G., Clinton R., and Kruglyak L. Science 296 (2002) 752-755
20. Kang H.M., Zaitlen N.A., Wade C.M., Kirby A., Heckerman D., Daly M.J., and Eskin E. Genetics 178 (2008) 1709-1723
21. Lander E.S., and Botstein D. Genetics 121 (1989) 185-199
22. Haley C.S., and Knott S.A. Heredity 69 (1992) 315-324
23. K.W. Broman, H. Wu, G.A. Churchill, S. Sen, B.S. Yandell, qtl: Tools for analyzing QTL experiments. R package version 1.09-43, 2008.
24. Flint J., Valdar W., Shifman S., and Mott R. Nat. Rev. Genet. 6 (2005) 271-286
25. Chesler E.J., Rodriguez-Zas S.L., and Mogil J.S. Science 294 (2001) 2423
26. Darvasi A. Science 294 (2001) 2423
27. Bogue M.A., and Grubb S.C. Genetica 122 (2004) 71-74
28. McClurg P., Pletcher M.T., Wiltshire T., and Su A.I. BMC Bioinformatics 7 (2006) 61
29. Pletcher M.T., et al. PLoS Biol. 2 (2004) e393
30. Zeng Z.B. Genetics 136 (1994) 1457-1468
31. Breiman L. Mach. Learn. 45 (2001) 5-32
32. Bureau A., Dupuis J., Falls K., Lunetta K.L., Hayward B., Keith T.P., and Van Eerdewegh P. Genet. Epidemiol. 28 (2005) 171-182
33. Bureau A., Dupuis J., Hayward B., Falls K., and Van Eerdewegh P. BMC Genet. 4 Suppl. 1 (2003) S64
34. Lee S.S., Sun L., Kustra R., and Bull S.B. Bioinformatics 24 (2008) 1603-1610
35. Motsinger-Reif A.A., Reif D.M., Fanelli T.J., and Ritchie M.D. Genet. Epidemiol. 32 (2008) 767-778
36. Liaw A., and Wiener M. R News 2 (2002) 18-22
37. Wang S., Yehya N., Schadt E.E., Wang H., Drake T.A., and Lusis A.J. PLoS Genet. 2 (2006) e15
38. Yang X., et al. Genome Res. 16 (2006) 995-1004
39. Bystrykh L., et al. Nat. Genet. 37 (2005) 225-232
40. Walter N.A., McWeeney S.K., Peters S.T., Belknap J.K., Hitzemann R., and Buck K.J. Nat. Methods 4 (2007) 679-680
41. Alberts R., Terpstra P., Bystrykh L.V., de Haan G., and Jansen R.C. Genetics 171 (2005) 1437-1439
42. Alberts R., Vera G., and Jansen R.C. Bioinformatics 24 (2008) 433-434
43. Akey J.M., Biswas S., Leek J.T., and Storey J.D. Nat. Genet. 39 (2007) 807-808 author reply 808-809.
44. Branham W.S., Melvin C.D., Han T., Desai V.G., Moland C.L., Scully A.T., and Fuscoe J.C. BMC Biotechnol. 7 (2007) 8
45. Johnson W.E., Li C., and Rabinovic A. Biostatistics 8 (2007) 118-127
46. Leek J.T., and Storey J.D. PLoS Genet. 3 (2007) 1724-1735
47. H.M. Kang, C. Ye, E. Eskin, Genetics 180 (2008) 1909-1925.
48. Ronald J., Brem R.B., Whittle J., and Kruglyak L. PLoS Genet. 1 (2005) e25
49. Yvert G., et al. Nat. Genet. 35 (2003) 57-64
50. Zhu J., et al. Nat. Genet. 40 (2008) 854-861
51. Wu C., et al. PLoS Genet. 4 (2008) e1000070
52. Kulp D.C., and Jagalur M. BMC Genomics 7 (2006) 125
53. Zhu J., et al. Cytogenet. Genome Res. 105 (2004) 363-374
54. Beyer A., Bandyopadhyay S., and Ideker T. Nat. Rev. Genet. 8 (2007) 699-710
55. Suthram S., Beyer A., Karp R.M., Eldar Y., and Ideker T. Mol. Syst. Biol. 4 (2008) 162
56. Lee S.I., Dudley A.M., Drubin D., Silver P.A., Krogan N.J., Pe'er D., and Koller D. PLoS Genet. 5 (2009) e1000358
57. Chen Y., et al. Nature 452 (2008) 429-435
58. Cookson W., Liang L., Abecasis G., Moffatt M., and Lathrop M. Nat. Rev. Genet. 10 (2009) 184-194
59. Emilsson V., et al. Nature 452 (2008) 423-428
60. Schadt E.E., et al. PLoS Biol. 6 (2008) e107
61. Chesler E.J., Lu L., Wang J., Williams R.W., and Manly K.F. Nat. Neurosci. 7 (2004) 485-486