Mining genetic epidemiology data with Bayesian networks I: Bayesian networks and example application (plasma apoE levels)

Bioinformatics

Volumn 21, Issue 15, 2005, Pages 3273-3278

  Rodin, Andrei S ^a,c   Boerwinkle, Eric ^a,b  

^a UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

^b UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

^c Human Genetics Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN E; APOLIPOPROTEIN E2; NUCLEOTIDE;

ALLELE; ARTICLE; BAYES THEOREM; CONTROLLED STUDY; DATA ANALYSIS; GENETIC ALGORITHM; GENETIC CODE; GENETIC EPIDEMIOLOGY; GENOTYPE; HUMAN; INFORMATION PROCESSING; LEARNING; LIPOPROTEIN BLOOD LEVEL; MATHEMATICAL MODEL; MULTIVARIATE ANALYSIS; PHENOTYPE; PRIORITY JOURNAL; PROBABILITY; SAMPLING; SCORING SYSTEM; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL SIGNIFICANCE; UNITED STATES; BIOLOGICAL MODEL; BLOOD; CHROMOSOME MAP; COMPUTER SIMULATION; DATA BASE; EPIDEMIOLOGY; EVALUATION; GENETIC DATABASE; GENETICS; INFORMATION RETRIEVAL; METHODOLOGY; NUCLEOTIDE SEQUENCE; STATISTICAL MODEL;

APOLIPOPROTEINS E; BAYES THEOREM; CHROMOSOME MAPPING; COMPUTER SIMULATION; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; DNA MUTATIONAL ANALYSIS; EPIDEMIOLOGIC METHODS; GENOTYPE; HUMANS; INFORMATION STORAGE AND RETRIEVAL; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 25144441907     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti505     Document Type: Article

References (25)

1. Akaike,H. (1973) Information theory and an extension of the maximum likelihood principle. In Petrov,B.N. and Csaki,F. (eds), [i#Proceedings of the 2nd International Symposium on Information Theory#1i], Akademiai Kiado, Budapest, Hungary.
2. Boerwinkle,E. and Utermann,G. (1988) Simultaneous effects of the apolipoprotein E polymorphism on apolipoprotein E, apolipoprotein B, and cholesterol metabolism. [i#Am. J. Hum. Genet.#1i], [b#42#1b], 104-112.
3. Boerwinkle,E. [i#et al.#1i] (1994) Apolipoprotein E polymorphism influences postprandial retinyl palmitate but not triglyceride concentrations. [i#Am. J. Hum. Genet.#1i], [b#54#1b], 341-360.
4. Cooper,G. and Herskovits,E. (1992) A Bayesian method for the induction of the probabilistic networks from data. [i#Machine Learning#1i], [b#9#1b] 309-347.
5. Dergunov,A.D. and Rosseneu,M. (1994) The significance of apolipoprotein E structure to the metabolism of plasma triglyceride-rich lipoproteins. [i#Biol. Chem. Hoppe Seyler#1i], [b#375#1b], 485-495.
6. Efron,B. and Tibshirani,R.J. (1993) [i#An Introduction to the Bootstrap#1i] Chapman and Hall, London.
7. Friedman,N. [i#et al.#1i] (2000) Using Bayesian network to analyze expression data. [i#J. Comput. Biol.#1i], [b#7#1b], 601-620.
8. Geiger,D. and Heckerman,D. (1994) A characterization of the Dirichlet distribution through global and local independence. [i#Technical Report MSR-TR-94-16#1i], Microsoft Research.
9. Hartemink,A.J. [i#et al.#1i] (2001) Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. [i#Pac. Symp. Biocomput.#1i], [b#6#1b], 422-433.
10. Heckerman,D. (1995) A tutorial on learning with Bayesian networks. [i#Technical Report MSR-TR-95-06#1i], Microsoft Research.
11. Hoeting,J.A. [i#et al.#1i] (1999) Bayesian model averaging: A tutorial (with Discussion). [Erratum (1999) [i#Stat. Sci.#1i], [b#15#1b], 193-195]. [i#Stat. Sci.#1i], [b#14#1b], 382-401.
12. Hoh,J. and Ott,J. (2001) A train of thoughts on gene mapping. [i#Theor. Popul. Biol.#1i], [b#60#1b], 149-153.
13. Martin,E.R. [i#et al.#1i] (2000) SNPing away at complex diseases: analysis of single-nucleotide polymorphisms around [i#APOE#1i] in Alzheimer disease. [i#Am. J. Hum. Genet.#1i], [b#67#1b], 383-394.
14. Myllymaki,P. [i#et al.#1i] (2002) B-Course: A web-based tool for Bayesian and causal data analysis. [i#Int. J. Artif. Intell. Tools#1i], [b#3#1b], 369-387.
15. Nelson,M.R. [i#et al.#1i] (2001) A combinatorial partitioning method to identify multi-locus genotypic partitions that predict quantitative trait variation. [i#Genome Res.#1i], [b#11#1b], 458-470.
16. Nickerson,D.A. [i#et al.#1i] (2000) Sequence diversity and large-scale typing of SNPs in the human apolipoprotein E gene. [i#Genome Res.#1i], [b#10#1b], 1532-1545.
17. Ong,I.M. [i#et al.#1i] (2002) Modelling regulatory pathways in [i#E.coli#1i] from time series expression profiles. [i#Bioinformatics#1i], [b#18#1b], S241-S248.
18. Pearl,J. (1988) [i#Probabilistic Reasoning in Intelligent Systems#1i]. Morgan Kaufmann, San Mateo, CA.
19. Piontkivska,H. (2004) Efficiencies of maximum likelihood methods of phylogenetic inferences when different substitution models are used. [i#Mol. Phylogenet. Evol.#1i], [b#31#1b], 865-873.
20. Province,M.A. (2001) Sequential methods of analysis for genome scans. [i#Adv. Genet.#1i], [b#42#1b], 499-514.
21. Rall,S.C.,Jr. [i#et al.#1i] (1989) Type III hyperlipoproteinemia associated with apolipoprotein E phenotype E3/3. Structure and genetics of an apolipoprotein E3 variant. [i#J. Clin. Invest.#1i], [b#83#1b], 1095-1101.
22. Sprites,P. and Meek,C. (1995). Learning Bayesian with discrete variables from data. In [i#Proceedings of First International Conference on Knowledge Discovery and Data Mining#1i]. Montreal, QU, Canada. Morgan Kaufmann.
23. Xiong,M. [i#et al.#1i] (2002). Generalized t2 test for genome association studies. [i#Am. J. Hum. Genet.#1i] [b#70#1b], 1257-1268.
24. Weisgraber,K.H. [i#et al.#1i] (1982). Abnormal lipoprotein receptor-binding activity of the human. E apoprotein due to cysteine-arginine interchange at a single site. [i#J. Biol. Chem.#1i] [b#257#1b], 2518-2521.
25. Zharkikh,A. and Li,W.H. (1995). Estimation of confidence in phylogeny: the complete- and-partial bootstrap technique. [i#Mol. Phylogenet. Evol.#1i] [b#4#1b], 44-63.