Correction: A unified framework for association analysis with multiple related phenotypes (PLoS ONE (2013) 8:7 (e65245) DOI: 10.1371/journal.pone.0065245);A Unified Framework for Association Analysis with Multiple Related Phenotypes

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Stephens, Matthew ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIPID;

ARTICLE; BAYES THEOREM; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; GENOTYPE PHENOTYPE CORRELATION; HUMAN; LIPID BLOOD LEVEL; PHENOTYPE; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84879818733     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0213951     Document Type: Erratum

References (63)

1. Willer C, Sanna S, Jackson A, Scuteri A, Bonnycastle L, et al. (2008) Newly identified loci that inuence lipid concentrations and risk of coronary artery disease. Nature genetics 40: 161-169.
2. Verzilli CJ, Stallard N, Whittaker JC, (2005) Bayesian modelling of multivariate quantitative traits using seemingly unrelated regressions. Genet Epidemiol 28: 313-25.
3. Banerjee S, Yandell BS, Yi N, (2008) Bayesian quantitative trait loci mapping for multiple traits. Genetics 179: 2275-89.
4. Kim S, Sohn KA, Xing EP, (2009) A multivariate regression approach to association analysis of a quantitative trait network. Bioinformatics 25: i204-12.
5. Kim S, Xing EP, (2009) Statistical estimation of correlated genome associations to a quantitative trait network. PLoS Genet 5: e1000587.
6. Baker AR, Goodloe RJ, Larkin EK, Baechle DJ, Song YE, et al. (2009) Multivariate association analysis of the components of metabolic syndrome from the framingham heart study. BMC Proc 3Suppl 7: S42.
7. Zhang L, Pei YF, Li J, Papasian CJ, Deng HW, (2009) Univariate/multivariate genome-wide association scans using data from families and unrelated samples. PLoS One 4: e6502.
8. Ferreira MAR, Purcell SM, (2009) A multivariate test of association. Bioinformatics 25: 132-3.
9. Petretto E, Bottolo L, Langley SR, Heinig M, McDermott-Roe C, et al. (2010) New insights into the genetic control of gene expression using a Bayesian multi-tissue approach. PLoS Comput Biol 6: e1000737.
10. O'Reilly PF, Hoggart CJ, Pomyen Y, Calboli FCF, Elliott P, et al. (2012) Multiphen: Joint model of multiple phenotypes can increase discovery in gwas. PLoS One 7: e34861.
11. Shriner D, (2012) Moving toward system genetics through multiple trait analysis in genome-wide association studies. Front Genet 3: 1.
12. Yang Q, Wang Y (2012) Methods for analyzing multivariate phenotypes in genetic association studies. Journal of Probability and Statistics 2012.
13. Hoggart CJ, Whittaker JC, De Iorio M, Balding DJ, (2008) Simultaneous analysis of all snps in genome-wide and re-sequencing association studies. PLoS Genet 4: e1000130.
14. Guan Y, Stephens M, (2011) Bayesian variable selection regression for genome-wide association studies and other large-scale problems. Annals of Applied Statistics 5: 1780-1815.
15. Anderson TW (1984) An Introduction to Multivariate Statistical Analysis. New York: John Wiley and Son, second edition.
16. Huberty C, Morris J, (1989) Multivariate analysis versus multiple univariate analyses. Journal of Counseling Psychology 33: 15.
17. Tiao G, Zellner A (1964) On the Bayesian estimation of multivariate regression. Journal of the Royal Statistical Society Series B (Methodological): 277-285.
18. Minka T (1999) Bayesian linear regression. Unpublished manuscript. Available: http://research.microsoft.com/en-us/um/people/minka/papers/linear.html. Accessed 2013 June 3.
19. Lauritzen S (1996) Graphical models, volume 17. Oxford University Press, USA.
20. Davey Smith G, Ebrahim S, (2003) 'Mendelian randomization': can genetic epidemiology contribute to understanding environmental determinants of disease? International Journal of Epidemiology 32: 1.
21. Spirtes P, Glymour C, Scheines R (2000) Causation, prediction, and search, volume 81. The MIT Press.
22. Geiger D, Heckerman D, (2002) Parameter priors for directed acyclic graphical models and the characterization of several probability distributions. Annals of statistics 30: 1412-1440.
23. Neyman J, Pearson E, (1933) On the problem of the most efficient tests of statistical hypotheses. Philosophical Transactions of the Royal Society of London Series A, Containing Papers of a Mathematical or Physical Character 231: 289.
24. Tiao G, Zellner A, (1964) On the Bayesian estimation of multivariate regression. Journal of the Royal Statistical Society Series B (Methodological) 26: 277-285.
25. Box G, Tiao G (1973) Bayesian inference in statistical inference. Wiley & Sons, New York.
26. Press S (1982) Applied multivariate analysis: using Bayesian and frequentist methods of inference. Malabar, FL (EUA).
27. Brown P, Vannucci M, Fearn T, (1998) Multivariate Bayesian variable selection and prediction. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 60: 627-641.
28. Rothenberg T (1963) A Bayesian analysis of simultaneous equation systems. Econometric Institute Report 6315.
29. Kshirsagar A, (1960) A note on the derivation of some exact multivarlate tests. Biometrika 47: 480.
30. Dickey J, (1967) Matricvariate generalizations of the multivariate t distribution and the inverted multivariate t distribution. The Annals of Mathematical Statistics 38: 511-518.
31. Dawid A, (1981) Some matrix-variate distribution theory: notational considerations and a Bayesian application. Biometrika 68: 265.
32. Wakefield J, (2009) Bayes factors for genome-wide association studies: comparison with p-values. Genet Epidemiol 33: 79-86.
33. Stephens M, Balding DJ, (2009) Bayesian statistical methods for genetic association studies. Nat Rev Genet 10: 681-690.
34. Teslovich TM, Musunuru K, Smith AV, Edmondson AC, Stylianou IM, et al. (2010) Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466: 707-13.
35. Friedewald W, Levy R, Fredrickson D, (1972) Estimation of the concentration of low-density lipoprotein cholesterol in plasma, without use of the preparative ultracentrifuge. Clinical chemistry 18: 499-502.
36. Martínez-Royo A, Ordovas L, Zaragoza P, Altarriba J, Serrano M, et al. (2010) The bovine annexin 9 gene (anxa9) is significantly associated with milk-fat yield in a spanish holstein-friesian population. Res Vet Sci 88: 452-5.
37. Huang J, Iqbal J, Saha PK, Liu J, Chan L, et al. (2007) Molecular characterization of the role of orphan receptor small heterodimer partner in development of fatty liver. Hepatology 46: 147-57.
38. Li R, Oteiza A, Sørensen KK, McCourt P, Olsen R, et al. (2011) Role of liver sinusoidal endothelial cells and stabilins in elimination of oxidized low-density lipoproteins. Am J Physiol Gastrointest Liver Physiol 300: G71-81.
39. Kzhyshkowska J, Gratchev A, Goerdt S, (2006) Stabilin-1, a homeostatic scavenger receptor with multiple functions. J Cell Mol Med 10: 635-49.
40. Adachi H, Tsujimoto M, (2002) Feel-1, a novel scavenger receptor with in vitro bacteria-binding and angiogenesis-modulating activities. J Biol Chem 277: 34264-70.
41. Al-Kateb H, Mirea L, Xie X, Sun L, Liu M, et al. (2007) Multiple variants in vascular endothelial growth factor (vegfa) are risk factors for time to severe retinopathy in type 1 diabetes: the dcct/edic genetics study. Diabetes 56: 2161-8.
42. Abhary S, Burdon KP, Gupta A, Lake S, Selva D, et al. (2009) Common sequence variation in the vegfa gene predicts risk of diabetic retinopathy. Invest Ophthalmol Vis Sci 50: 5552-8.
43. Yang X, Deng Y, Gu H, Lim A, Altankhuyag A, et al. (2011) Polymorphisms in the vascular endothelial growth factor gene and the risk of diabetic retinopathy in chinese patients with type 2 diabetes. Mol Vis 17: 3088-96.
44. Yu Y, Bhangale TR, Fagerness J, Ripke S, Thorleifsson G, et al. (2011) Common variants near frk/col10a1 and vegfa are associated with advanced age-related macular degeneration. Hum Mol Genet 20: 3699-709.
45. Russell DW, (2003) The enzymes, regulation, and genetics of bile acid synthesis. Annu Rev Biochem 72: 137-74.
46. Sarria AJ, Panini SR, Evans RM, (1992) A functional role for vimentin intermediate filaments in the metabolism of lipoprotein-derived cholesterol in human sw-13 cells. J Biol Chem 267: 19455-63.
47. Browman DT, Resek ME, Zajchowski LD, Robbins SM, (2006) Erlin-1 and erlin-2 are novel members of the prohibitin family of proteins that define lipid-raft-like domains of the er. J Cell Sci 119: 3149-60.
48. Yuan X, Waterworth D, Perry JRB, Lim N, Song K, et al. (2008) Population-based genome-wide association studies reveal six loci inuencing plasma levels of liver enzymes. Am J Hum Genet 83: 520-8.
49. Ganji SH, Tavintharan S, Zhu D, Xing Y, Kamanna VS, et al. (2004) Niacin noncompetitively inhibits dgat2 but not dgat1 activity in hepg2 cells. J Lipid Res 45: 1835-45.
50. Hu M, Chu WCW, Yamashita S, Yeung DKW, Shi L, et al. (2012) Liver fat reduction with niacin is inuenced by dgat-2 polymorphisms in hypertriglyceridemic patients. J Lipid Res 53: 802-9.
51. Zellner A, (1962) An efficient method of estimating seemingly unrelated regressions and tests for aggregation bias. Journal of the American Statistical Association 57: 348-368.
52. Smith M, Kohn R, (2000) Nonparametric seemingly unrelated regression. Journal of Econometrics 98: 257-281.
53. Holmes C, Denison D, Mallick B, (2002) Accounting for model uncertainty in seemingly unrelated regressions. Journal of Computational and Graphical Statistics 11: 533-551.
54. Finegold M, Drton M (2011) Robust graphical modeling of gene networks using classical and alternative t-distributions. The Annals of Applied Statistics 5: 1057{1080.
55. Vogel D, Fried R (2011) Elliptical graphical modelling. Biometrika 98: 935{951.
56. Maranville JC, Luca F, Richards AL, Wen X, Witonsky DB, et al. (2011) Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes. PLoS Genet 7: e1002162.
57. Engelhardt BE, Stephens M (2010) Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet 6.
58. Devlin B, Roeder K, (1999) Genomic control for association studies. Biometrics 55: 997-1004.
59. Chelala C, Khan A, Lemoine NR, (2009) Snpnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. Bioinformatics 25: 655-61.
60. Dayem Ullah AZ, Lemoine NR, Chelala C, (2012) Snpnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update). Nucleic Acids Res 40: W65-70.
61. R Core Team (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. Available: http://www.R-project.org/. Accessed 2013 June 3.
62. Wickham H (2009) ggplot2: elegant graphics for data analysis. Springer New York.
63. Pe'er D, (2005) Bayesian network analysis of signaling networks: a primer. Sci STKE 2005: pl4.