Log-linear models for gene association

Journal of the American Statistical Association

Volumn 104, Issue 486, 2009, Pages 597-607

  Hu, Jianhua ^a   Joshi, Adarsh ^b   Johnson, Valen E ^a  

^a UNIVERSITY OF TEXAS   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

Bayes factor; Deviance statistic; Ewens' sampling distribution; Gene interaction; Markov chain Monte Carlo

Indexed keywords

EID: 66549117792     PISSN: 01621459     EISSN: None     Source Type: Journal    
DOI: 10.1198/jasa.2009.0025     Document Type: Article

References (35)

1. Agresti, A. (2002), Categorical Data Analysis, Hoboken, N.J: Wiley.
2. Bertucci, F., Houlgatte, R., Benziane, A., Granjeaud, S., Adelaide, J., Tagett, R., Loriod, B., Jacquemier, J., Viens, P., Jordan, B., Birnbaum, D., and Nguyen, C. (2000), "Gene Expression Profiling of Primary Breast Carcinomas Using Arrays of Candidate Genes," Human Molecular Genetics, 9, 2981-2991.
3. Bishop, Y. M. M., Fienberg, S. E., and Holland, P. W. (1975), Discrete Multivariate Analysis: Theory and Practice, Cambridge, Mass.: MIT Press.
4. Carvalho, C. M., Massam, H., and West, M. (2007), "Simulation of Hyper-inverse Wishart Distributions in Graphical Models," Biometrika, 94, 647-659.
5. Chen, W., Ghosh, D., Raghunathan, T., and Kardia, S. (2004), "A Bayesian Method for Finding Interactions in Genomic Studies." The University of Michigan Department of Biostatistics Working Paper Series www.bepress. com/umichbiostat/paper48.
6. Chien, W., Kumagai, T, Miller, C. W., Desmond, J. C, Frank, J. M., Said, J. W., and Koeffler, H. P. (2004), "Cyr61 Suppresses Growth of Human Endometrial Cancer Cells," Journal of Biological Chemistry, 79, 53087-53096.
7. Cooper, C. S. (2001), "Applications of Microarray Technology in Breast Cancer Research," Breast Cancer Research, 3, 158-175.
8. Dobra, A., Han, C, Jones, B., Nevins, J., Yao, G, and West, M. (2004), "Sparse Graphical Models for Exploring Gene Expression Data," Journal of Multivariate Analysis, 90, 196-212.
9. Eeckhoute, J., Keeton, E. K., Lupien, M., Krum, S. A., Carroll, J. S., and Brown, M. (2007), "Positive Cross-Regulatory Loop Ties GATA-3 to Estrogen Receptor Alpha Expression in Breast Cancer," Cancer Research, 67, 6477-6483.
10. Ewens, W. (1972), "The Sampling Theory of Selectively Neutral Alleles," Theoretical Population Biology, 3, 87-112.
11. Ferguson, A. T, and Davidson, N. E. (1997), "Regulation of Estrogen Receptor AlphaFunction in Breast Cancer," Critical Reviews in Oncogenesis, 8,29-46. Genetwork. (2007 http://humgen.med.uu.nl/lude/ genenetwork/.
12. George, E. I., and McCulloch, R. E. (1993), "Variable Selection via Gibbs Sampling," Journal of the American Statistical Association, 88, 881-889.
13. - (1997), "Approaches for Bayesian Variable Selection," Statistica Sinica, 7, 339-374.
14. Haberman, S. J. (1974), The Analysis of Frequency Data, Chicago, Ill.: University of Chicago Press.
15. Harkin, D. P., Bean, J. M., Miklos, D., Song, Y H., Truong, V B., Englert, C, Christians, F. C, Ellisen, L. W., Maheswaran, S., Oliner, J. D., and Haber, D. A. (1999), "Induction of GADD45 and JNK/SAPK-Dependent Apoptosis Following Inducible Expression of BRCA1," Cell, 28, 575-586.
16. Hu, J., and Johnson, V E. (2008), "Bayesian Model Selection Using Test Statistics," Journal of the Royal Statistical Society, Ser. B, JRSS-B, 71, 143-158.
17. 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 (Oxford, England), 4, 249-264.
18. Johnson, V. E. (2005), "Bayes Factors Based on Test Statistics," Journal of the Royal Statistical Society, Ser. B, 67, 689-701.
19. -. (2008), "Properties of Bayes Factors Based on Test Statistics," Scandinavian Journal of Statistics, 35, 354-368.
20. Jones, B., and West, M. (2005), "Covariance Decomposition in Undirected Gaussian Graphical Models," Biometrika, 92, 779-786.
21. Lacroix, M., and Leclercq, G. (2004), "About GATA3, HNF3A, and XBP1: Three Genes Co-expressed With the Oestrogen Receptor-Alpha Gene (ESR1) in Breast Cancer," Molecular and Cellular Endocrinology, 219, 1-7.
22. Lauritzen, S. L. (1996), Graphical Models, Oxford: Clarendon Press.
23. Lee, K. E., Sha, N, Doughtery, E. R., Vannucci, M., and Mallick, B. (2003), "Gene Selection: A Bayesian Variable Selection Approach," Bioinformatics (Oxford, England), 19, 90-97.
24. Liang, F, Paulo, R., Molina, G., Clyde, M. A., and Berger, J. O. (2005): "Mixtures of g-Priors for Bayesian Variable Selection." In ISDS Discussion Paper. Vol. 05-12, Durham, NC: Duke University.
25. Narod, S., Lynch, H., Conway, T, Watson, P., Feunteun, J., and Lenoir, G (1993), "Increasing Incidence of Breast Cancer in Family With BRCA1 Mutation," Lancet, 24, 1101-1102.
26. Panet-Raymond, V, Gottlieb, B., Beitel, L. K., Pinsky, L., and Trifiro, M. A. (2000), "Interactions Between Androgen and Estrogen Receptors and the Effects on Their Transactivational Properties," Molecular and Cellular Endocrinology, 25, 139-150.
27. Potamias, G, Koumakis, L., and Moustakis, V (2004): "Gene Selection via Discretized Gene-Expression Profiles and Greedy Feature-Elimination." Methods and Applications of Artificial Intelligence 3025. Berlin: Springer.
28. Pubmed. (2007), "National Library of Medicine and National Institutes of Healthwww.ncbi.nlm.nih.gov/sites/entrez.
29. Quenneville, L. A., Trotter, M. J., Maeda, T, and Tron, V A. (2002), "P53-Dependent Regulation of Heat Shock Protein 72," British Journal of Dermatology, 146, 786-791.
30. Schafer, J., and Strimmer, K. (2005), "An Empirical Bayes Approach to Inferring Large-Scale Gene Association Networks," Bioinformatics (Oxford, England), 21, 754-764.
31. Spurdle, A. B., Chang, J., Byrnes, G. B., Chen, X., Dite, G S., McCredie, M. R E, Giles, G G, Southey, M. C, Chenevix-Trench, G, and Hopper, J. L. (2007), "A Systematic Approach to Analysing Gene-Gene Interactions: Polymorphisms at the Microsomal Epoxide Hydrolase EPHX and Glutathione S-transferase GSTM1, GSTT1, and GSTP1 Loci and Breast Cancer Risk," Cancer Epidemiology, Biomarkers & Prevention, 16, 769-774.
32. Tavare, S., and Ewens, W. J. (1997), "The Ewens Sampling Formula,"in Multivariate Discrete Distributions, eds. N. L. Johnson and N. Balakrish-anan, New York: Wiley.
33. West, M., Blanchette, C, Dressman, H., Huang, E., Ishida, S., Spang, R., Zuzan, H, Olson, J. A. Jr., Marks, J. R., andNevins, J. R. (2001), "Predicting the Clinical Status of Human Breast Cancer by Using Gene Expression Profiles," Proceedings of the National Academy of Sciences of the United States of America, 98, 11462-11467.
34. Wu, X., Yong, Y, and Kalpathi, R. S. (2003), "Interactive Analysis of Gene Interactions Using Graphical Gaussian Model." in 3rd ACM SIGKDD Workshop on Data Mining in Bioinformatics, Troy, NY: Rensselaer Polytechnic Institute, pp. 63-69.
35. Zhang, Y, and Liu, J. S. (2007), "Bayesian Inference of Epistatic Interactions in Case-Control Studies," Nature Genetics, 39, 1167-1173.