Statistical methods for expression quantitative trait loci (eQTL) mapping

Biometrics

Volumn 62, Issue 1, 2006, Pages 19-27

  Kendziorski, C M ^a   Chen, M ^b   Yuan, M ^a   Lan, H ^c   Attie, A D ^c  

^a UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^b University of Wisconsin Madison   (United States)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Bayesian hierarchical mixture model; Expression trait loci (eQTL) mapping; Gene expression; Microarray; Quantitative trait loci (QTL) mapping

Indexed keywords

MAPPING; MICROARRAYS; PLANTS (BOTANY);

BAYESIAN; BAYESIAN HIERARCHICAL MIXTURE MODEL; EXPRESSION TRAIT LOCUS (EXPRESSION QUANTITATIVE TRAIT LOCUS) MAPPING; GENES EXPRESSION; HIERARCHICAL MIXTURES; MAPPING METHOD; MIXTURE MODELING; QUANTITATIVE TRAIT LOCI MAPPINGS; QUANTITATIVE TRAIT LOCUS;

GENE EXPRESSION;

GENE EXPRESSION;

ANIMAL MODEL; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; DIABETES MELLITUS; GENE EXPRESSION; GENE LOCATION; GENE MAPPING; GENOMICS; GENOTYPE; MARKER GENE; MEDICAL INFORMATION; NONHUMAN; QUANTITATIVE TRAIT LOCUS; SIMULATION; STATISTICAL ANALYSIS;

ANIMALIA;

EID: 33645068841     PISSN: 0006341X     EISSN: 15410420     Source Type: Journal    
DOI: 10.1111/j.1541-0420.2005.00437.x     Document Type: Article

References (37)

1. Baldi P. and Long A. D. 2001 A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes Bioinformatics 17 509 519
2. Brem R. B. Yvert G. Clinton R. and Kruglyak L. 2002 Genetic dissection of transcriptional regulation in budding yeast Science 296 752 755
3. Broman K. W. 2001 Review of statistical methods for QTL mapping in experimental crosses Laboratory Animal 30 44 52
4. Broman K. W. and Speed T. P. 2002 A model selection approach for the identification of quantitative trait loci in experimental crosses (with discussion) Journal of the Royal Statistical Society, Series B 64 641 656 and 737 775 discussion
5. Carlin B. and Louis T. 1998 Bayes and Empirical Bayes Methods for Data Analysis New York Chapman & Hall
6. Churchill G. A. and Doerge R. W. 1994 Empirical threshold values for quantitative trait mapping Genetics 138 963 971
7. Coleman D. L. and Hummel K. P. 1973 The influence of genetic background on the expression of the obese (Ob) gene in the mouse Diabetologia 9 287 293
8. Colinayo V. V. Qiao J. H. Wang X. Krass K. Schadt E. Lusis A. J. and Drake T. A. 2003 Genetic loci for diet-induced atherosclerotic lesions and plasma lipids in mice Mammalian Genome 14 464 471
9. Cox N. J. 2004 An expression of interest Nature 12 733 734
10. Dudoit S. Yang Y. H. Speed T. P. and Callow M. J. 2002 Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments Statistica Sinica 12 111 139
11. Dupuis J. and Siegmund D. 1999 Statistical methods for mapping quantitative trait loci from a dense set of markers Genetics 151 373 386
12. Efron B. 2004 Large-scale simultaneous hypothesis testing: The choice of a null hypothesis Journal of the American Statistical Association 99 96 104
13. Efron B. and Tibshirani R. 2002 Empirical Bayes methods and false discovery rates for microarrays Genetic Epidemiology 1 70 86
14. Efron B. Tibshirani R. Storey J. and Tusher V. 2001 Empirical Bayes analysis of a microarray experiment Journal of the American Statistical Association 96 1151 1160
15. Irizarry R. A. Hobbs B. Collin F. Beazer-Barclay Y. D. Antonellis K. J. Scherf U. and Speed T. P. 2003 Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostatistics 4 249 264
16. Jin C. Lan H. Attie A. D. Bulutuglo D. Churchill G. A. and Yandell B. S. 2004 Selective phenotyping for increased efficiency in genetic mapping studies Genetics 168 2285 2293
17. Kendziorski C. M. Newton M. A. Lan H. and Gould M. N. 2003 On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles Statistics in Medicine 22 3899 3914
18. Lan H. Rabaglia M. E. Stoehr J. P. Nadler S. T. Schueler K. L. Zou F. Yandell B. S. and Attie A. D. 2003a Gene expression profiles of non-diabetic and diabetic obese mice suggest a role of hepatic lipogenic capacity in diabetes susceptibility Diabetes 52 688 700
19. Lan H. Stoehr J. P. Nadler S. T. Schueler K. L. Yandell B. S. and Attie A. D. 2003b Dimension reduction for mapping mRNA abundance as quantitative traits Genetics 164 1607 1614
20. Lander E. S. and Botstein D. 1989 Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps Genetics 121 185 199
21. Lonnstedt I. and Speed T. P. 2002 Replicated microarray data Statistica Sinica 12 31 46
22. Lund M. S. Sorenson P. Guldbrandtsen B. and Sorensen D. A. 2003 Multitrait fine mapping of quantitative trait loci using combined linkage disequilibria and linkage analysis Genetics 163 405 410
23. Naggert J. K. Fricker L. D. Varlamov O. Nishina P. M. Rouille Y. Steiner D. F. Carroll R. J. Paigen B. J. and Leiter E. H. 1995 Hyperproinsulinaemia in obese fat/fat mice associated with a carboxypeptidase E mutation which reduces enzyme activity Nature Genetics 10 135 142
24. Newton M. A. and Kendziorski C. M. 2003 Parametric empirical Bayes methods for microarrays In The Analysis of Gene Expression Data: Methods and Software Parmigiani G. Garrett E. S. Irizarry R. and Zeger S. L. eds 254 271 New York Springer Verlag
25. Newton M. A. Kendziorski C. M. Richmond C. S. Blattner F. R. and Tsui K. W. 2001 On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data Journal of Computational Biology 8 37 52
26. Newton M. A. Noueiry A. Sarkar D. and Ahlquist P. 2004 Detecting differential gene expression with a semiparametric hierarchical mixture method Biostatistics 5 155 176
27. Parmigiani G. Garrett E. S. Irizarry R. and Zeger S. L. 2003 The Analysis of Gene Expression Data: Methods and Software New York Springer Verlag
28. R Development Core Team. 2004 R: A language and environment for statistical computing R Foundation for Statistical Computing Vienna Austria
29. Schadt E. Monks S. Drake T. A. et al. 2003 Genetics of gene expression surveyed in maize, mouse and man Nature 422 297 302
30. Stoehr J. P. Nadler S. T. Schueler K. L. Rabaglia M. E. Yandell B. S. Metz S. A. and Attie A. D. 2000 Genetic obesity unmasks nonlinear interactions between murine type 2 diabetes susceptibility loci Diabetes 49 1946 1954
31. Stoehr J. P. Byers J. E. Clee S. M. Lan H. Boronenkov I. V. Schueler K. L. Yandell B. S. and Attie A. D. 2004 Identification of major quantitative trait loci controlling body weight variation in ob/ob mice Diabetes 53 245 249
32. Storey J. D. 2003 The positive false discovery rate: A Bayesian interpretation and the q-value Annals of Statistics 31 2013 2035
33. Storey J. D. and Tibshirani R. 2003 Statistical significance for genomewide studies Proceedings of the National Academy of Sciences USA 100 9440 9445
34. Storey J. D. Taylor J. E. and Siegmund D. 2004 Strong control, conservative point estimation, and simultaneous conservative consistency of false discovery rates: A unified approach Journal of the Royal Statistical Society, Series B 66 187 205
35. Tusher V. Tibshirani R. and Chu G. 2001 Significance analysis of microarrays applied to the ionizing radiation response Proceedings of the National Academy of Sciences USA 98 5116 5121
36. Yvert G. Brem R. B. Whittle J. Akey J. M. Foss E. Smith E. N. Mackelprang R. and Kruglyak L. 2003 Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors Nature Genetics 35 57 64
37. Zhang Y. Proenca R. Maffei M. Barone M. Leopold L. and Friedman J. M. 1994 Positional cloning of the mouse obese gene and its human homologue Nature 372 425 431