Bayesian detection of expression quantitative trait

Genetics

Volumn 189, Issue 4, 2011, Pages 1449-1459

  Spots, Loci Hot ^a   Bottolo, Leonardo ^a   Petretto, Enrico ^b   Blankenberg, Stefan ^a   Cambien, François ^c   Cook, Stuart A ^d   Tiret, Laurence ^e   Richardson, Sylvia ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY HEART CENTER HAMBURG   (Germany)

^c INSERM   (France)

^d NATIONAL HEART AND LUNG INSTITUTE   (United Kingdom)

^e HAREFIELD HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC MARKER; HEREDITY; HUMAN; MOUSE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SIMULATION;

BAYES THEOREM; GENE EXPRESSION; HUMANS; QUANTITATIVE TRAIT LOCI;

EID: 83455198480     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.111.131425     Document Type: Article

References (38)

1. Altshuler, D., L. D. Brooks, A. Chakravarti, F. S. Collins, M. D. Daly et al., 2005 A haplotype map of the human genome. Nature 437: 1299-1320.
2. Banerjee, S., B. S. Yandell, and N. Yi, 2008 Bayesian quantitative trait loci mapping for multiple traits. Genetics 179: 2275-2289.
3. Bottolo, L., and S. Richardson, 2010 Evolutionary stochastic search for Bayesian model exploration. Bayesian Anal. 5: 583-618.
4. Bottolo, L., M. Chadeau-Hyam, D. I. Hastie, S. R. Langley, E. Petretto et al., 2011 ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration. Bioinformatics 27: 587-588.
5. Breitling, R., Y. Li, B. M. Tesson, J. Fu, T. Wiltshire et al., 2008 Genetical genomics: spotlight on QTL hotspots. PLoS Genet. 4: e1000232.
6. Broman, K. W., and S. Sen, 2009 A Guide to QTL Mapping with R/qtl. Springer-Verlag, Berlin.
7. Chen, Y., J. Zhu, P. Y. Lum, X. Yang, S. Pinto et al., 2008 Variations in DNA elucidate molecular networks that cause disease. Nature 452: 429-435.
8. Chun, H., and S. Kelesx, 2009 Expression quantitative trait loci mapping with multivariate sparse partial least squares regression. Genetics 182: 79-90.
9. Cookson, W., L. Liang, G. Abecasis, M. Moffatt, and M. Lathrop, 2009 Mapping complex disease traits with global gene expression. Nat. Rev. Genet. 10: 184-194.
10. George, E. I., and R. E. McCulloch, 1997 Approaches for Bayesian variable selection. Statist. Sinica 7: 339-373.
11. Ghosh, D., W. Chen, and T. Raghunathan, 2006 The false discovery rate: a variable selection perspective. J. Statist. Plann. Inference 136: 2668-2684.
12. Gramacy, R. B., R. J. Samworth, and R. King, 2010 Importance tempering. Stat. Comput. 20: 1-7.
13. Hall, R. J., J. E. Hollis-Moffatt, M. E. Merriman, R. A. Green, D. Baker et al., 2003 An autoimmune diabetes locus (Idd21) on mouse chromosome 18. Mamm. Genome 14: 335-339.
14. Heinig, M., E. Petretto, C. Wallace, L. Bottolo, M. Rotival et al., 2010 A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature 467: 460-464.
15. Jia, Z., and S. Xu, 2007 Mapping quantitative trait loci for expression abundance. Genetics 176: 611-623.
16. Kass, R. E., and A. E. Raftery, 2007 Bayes factor. J. Am. Stat. Assoc. 90: 773-795.
17. Kendziorski, C. M., M. Chen, M. Yuan, H. Lan, and A. D. Attie, 2006 Statistical methods for expression quantitative trait loci (eQTL) mapping. Biometrics 62: 19-27.
18. Kohn, R., M. Smith, and D. Chan, 2001 Nonparametric regression using linear combinations of basis functions. Stat. Comput. 11: 313-322.
19. Korstanje, R., R. Li, T. Howard, P. Kelmenson, J. Marshall et al., 2004 Influence of sex and diet on quantitative trait loci for hdl cholesterol levels in an SM/J by NZB/BlNJ intercross population. J. Lipid Res. 45: 881-888.
20. Lan, H., M. Chen, J. B. Flowers, B. S. Yandell, D. S. Stapleton et al., 2006 Combined expression trait correlations and expression quantitative trait locus mapping. PLoS Genet. 2: e6.
21. Lee, S. I., A. M. Dudley, D. Drubin, P. Silver, N. J. Krogan et al., 2009 Learning a prior on regulatory potential from eQTL data. PLoS Genet. 5: e1000358.
22. Majewski, J., and T. Pastinen, 2011 The study of eQTL variations by RNA-seq: from SNPs to phenotypes. Trends Genet. 27: 72-79.
23. Nakagawa, T., M. Setou, D. Seog, and N. Ogasawara Dohmae et al., 2000 A novel motor, KIF13A, transports mannose-6-phosphate receptor to plasma membrane through direct interaction with AP-1 complex. Cell 103: 569-581.
24. Petretto, E., L. Bottolo, S. R. Langley, M. Heinig, M. C. McDermott-Roe et al., 2010 New insights into the genetic control of gene expression using a Bayesian multi-tissue approach. PLOS Comput. Biol. 6: e1000737.
25. Richardson, S., A. Thomson, N. Best, and P. Elliott, 2004 Interpreting posterior relative risk estimates in disease mapping studies. Environ. Health Perspect. 112: 1016-1025.
26. Roberts, G. O., and J. S. Rosenthal, 2009 Examples of adaptive MCMC. J. Comput. Graph. Statist. 9: 349-367.
27. Schadt, E. E., 2009 A molecular networks as sensors and drivers of common human diseases. Nature 461: 218-223.
28. Scheet, P., and M. Stephens, 2006 A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet. 78: 629-644.
29. Sun, W., J. G. Ibrahim, and F. Zou, 2010 Genomewide multipleloci mapping in experimental crosses by iterative adaptive penalized regression. Genetics 185: 349-359.
30. Wang, P., J. A. Dawson, M. P. Keller, B. S. Yandell, N. A. Thornberry et al., 2011 A model selection approach for expression quantitative trait loci (eQTL) mapping. Genetics 187: 611-621.
31. Wu, C., D. L. Delano, N. Mitro, S. V. Su, J. Janes et al., 2008 Gene set enrichment in eqtl data identifies novel annotations and pathway regulators. PLoS Genet. 5: e1000070.
32. Xu, C., X. Wang, Z. Li, and S. Xu, 2008 Mapping QTL for multiple traits using Bayesian statistics. Genet. Res. Camb. 91: 23-37.
33. Yi, N., and D. Shriner, 2008 Advances in Bayesian multiple QTL mapping in experimental designs. Heredity 100: 240-252.
34. Yi, N., and S. Xu, 2008 Bayesian lasso for quantitative trait loci mapping. Genetics 179: 1045-1055.
35. Yi, N., D. Shriner, S. Banerjee, T. Mehta, D. Pomp et al., 2007 An efficient Bayesian model selection approach for interacting quantitative trait loci models with many effects. Genetics 176: 1865-1877.
36. Yvert, G., R. B. Brem, J. Whittle, J. M. Akey, E. Foss et al., 2003 Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat. Genet. 35: 57-64.
37. Zeller, T., P. Wild, S. Szymczak, M. Rotival, A. Schillert et al., 2010 Genetics and beyond: the transcriptome of human monocytes and disease susceptibility. PLoS ONE 5: e10693.
38. Zhang, W., J. Zhu, E. E. Schadt, and J. S. Liu, 2010 A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules. PLOS Comput. Biol. 6: e1000642.