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Volumn 32, Issue 4, 2016, Pages 523-532

MT-HESS: An efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; ANTIBODY SPECIFICITY; BAYES THEOREM; COMPUTER LANGUAGE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; GENOMICS; HUMAN; INFLAMMATION; INFLAMMATORY BOWEL DISEASE; INSULIN DEPENDENT DIABETES MELLITUS; PROCEDURES; QUANTITATIVE TRAIT LOCUS; RAT; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE; THEORETICAL MODEL; TISSUE DISTRIBUTION;

EID: 84959860765     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv568     Document Type: Article
Times cited : (31)

References (35)
  • 1
    • 77953006646 scopus 로고    scopus 로고
    • The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
    • Atanur, S. S. et al. (2010) The genome sequence of the spontaneously hypertensive rat: analysis and functional significance. Genome Res., 20, 791-803.
    • (2010) Genome Res. , vol.20 , pp. 791-803
    • Atanur, S.S.1
  • 2
    • 79951540621 scopus 로고    scopus 로고
    • Evolutionary Stochastic search for Bayesian model exploration
    • Bottolo, L. and Richardson, S. (2010) Evolutionary Stochastic search for Bayesian model exploration. Bayesian Anal., 5, 583-618.
    • (2010) Bayesian Anal. , vol.5 , pp. 583-618
    • Bottolo, L.1    Richardson, S.2
  • 3
    • 83455198480 scopus 로고    scopus 로고
    • Bayesian detection of expression quantitative trait loci hot spots
    • Bottolo, L. et al. (2011) Bayesian detection of expression quantitative trait loci hot spots. Genetics, 189, 1449-1459.
    • (2011) Genetics , vol.189 , pp. 1449-1459
    • Bottolo, L.1
  • 4
    • 84884626511 scopus 로고    scopus 로고
    • GUESS-ing polygenic associations with multiple phenotypes using a GPU-based evolutionary stochastic search algorithm
    • Bottolo, L. et al. (2013) GUESS-ing polygenic associations with multiple phenotypes using a GPU-based evolutionary stochastic search algorithm. PLoS Genet., 9, e1003657.
    • (2013) PLoS Genet. , vol.9 , pp. e1003657
    • Bottolo, L.1
  • 5
    • 8844236882 scopus 로고    scopus 로고
    • A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments
    • Broët, P. et al. (2004) A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments. Bioinformatics, 20, 2562-2571.
    • (2004) Bioinformatics , vol.20 , pp. 2562-2571
    • Broët, P.1
  • 6
    • 0000857113 scopus 로고    scopus 로고
    • Multivariate Bayesian variable selection and prediction
    • Brown, P. J. et al. (1998) Multivariate Bayesian variable selection and prediction. J. R. Stat. Soc. B, 60, 627-641.
    • (1998) J. R. Stat. Soc. B , vol.60 , pp. 627-641
    • Brown, P.J.1
  • 7
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Dunham, I. et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Dunham, I.1
  • 8
    • 84860317030 scopus 로고    scopus 로고
    • Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles
    • Fairfax, B. P. et al. (2012) Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nat. Genet., 44, 502-510.
    • (2012) Nat. Genet. , vol.44 , pp. 502-510
    • Fairfax, B.P.1
  • 9
    • 84878476783 scopus 로고    scopus 로고
    • A statistical framework for joint eQTL analysis in multiple tissues
    • Flutre, T. et al. (2013) A statistical framework for joint eQTL analysis in multiple tissues. PLoS Genet., 9, e1003486.
    • (2013) PLoS Genet. , vol.9 , pp. e1003486
    • Flutre, T.1
  • 10
    • 84857467272 scopus 로고    scopus 로고
    • Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies
    • Fusi, N. et al. (2012) Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies. PLoS Comput. Biol., 8, e1002330.
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002330
    • Fusi, N.1
  • 11
    • 0000079228 scopus 로고
    • Model determination using predictive distributions with implementation via sampling-based-methods (with discussion)
    • Bernardo, J. (eds.), Oxford: Oxford University Press
    • Gelfand, A. et al. (1992) Model determination using predictive distributions with implementation via sampling-based-methods (with discussion). In: Bernardo, J. (eds.), Bayesian Statistics, vol. 4, Oxford: Oxford University Press, pp. 147-167.
    • (1992) Bayesian Statistics , vol.4 , pp. 147-167
    • Gelfand, A.1
  • 12
    • 77953808473 scopus 로고    scopus 로고
    • Next-generation genomics: An integrative approach
    • Hawkins, R. D. et al. (2010) Next-generation genomics: an integrative approach. Nat. Rev. Genet., 11, 476-486.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 476-486
    • Hawkins, R.D.1
  • 13
    • 77957126059 scopus 로고    scopus 로고
    • A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk
    • Heinig, M. et al. (2010) A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature, 467, 460-464.
    • (2010) Nature , vol.467 , pp. 460-464
    • Heinig, M.1
  • 14
    • 20144377218 scopus 로고    scopus 로고
    • Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease
    • Hubner, N. et al. (2005) Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat. Genet., 37, 243-253.
    • (2005) Nat. Genet. , vol.37 , pp. 243-253
    • Hubner, N.1
  • 15
    • 84899530032 scopus 로고    scopus 로고
    • Principles and methods of integrative genomic analyses in cancer
    • Kristensen, V. N. et al. (2014) Principles and methods of integrative genomic analyses in cancer. Nat. Rev. Cancer, 14, 299-313.
    • (2014) Nat. Rev. Cancer , vol.14 , pp. 299-313
    • Kristensen, V.N.1
  • 16
    • 84896759364 scopus 로고    scopus 로고
    • Common genetic variants modulate pathogen-sensing responses in human dendritic cells
    • Lee, M. N. et al. (2014) Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science, 343, 1246980.
    • (2014) Science , vol.343 , pp. 1246980
    • Lee, M.N.1
  • 17
    • 80755126865 scopus 로고    scopus 로고
    • Mapping a dynamic innate immunity protein interaction network regulating type i interferon production
    • Li, S. et al. (2011a) Mapping a dynamic innate immunity protein interaction network regulating type I interferon production. Immunity, 35, 426-440.
    • (2011) Immunity , vol.35 , pp. 426-440
    • Li, S.1
  • 18
    • 79959834606 scopus 로고    scopus 로고
    • Integrative analysis of many weighted co-expression networks using tensor computation
    • Li, W. et al. (2011b) Integrative analysis of many weighted co-expression networks using tensor computation. PLoS Comput. Biol., 7, e1001106.
    • (2011) PLoS Comput. Biol. , vol.7 , pp. e1001106
    • Li, W.1
  • 19
    • 0034403006 scopus 로고    scopus 로고
    • Evolutionary Monte Carlo: Applications to cp model sampling and change point problem
    • Liang, F. and Wong, W. H. (2000) Evolutionary Monte Carlo: applications to cp model sampling and change point problem. Stat. Sin., 10, 317-342.
    • (2000) Stat. Sin. , vol.10 , pp. 317-342
    • Liang, F.1    Wong, W.H.2
  • 20
    • 42349089655 scopus 로고    scopus 로고
    • Mixtures of g priors for Bayesian variable selection
    • Liang, F. et al. (2008) Mixtures of g priors for Bayesian variable selection. J. Am. Stat. Assoc., 103, 410-423.
    • (2008) J. Am. Stat. Assoc. , vol.103 , pp. 410-423
    • Liang, F.1
  • 21
    • 84903957321 scopus 로고    scopus 로고
    • Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression
    • Marttinen, P. et al. (2014) Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression. Bioinformatics, 30, 2026-2034.
    • (2014) Bioinformatics , vol.30 , pp. 2026-2034
    • Marttinen, P.1
  • 22
    • 84929015296 scopus 로고    scopus 로고
    • The human transcriptome across tissues and individuals
    • Melé, M. et al. (2015) The human transcriptome across tissues and individuals. Science, 348, 660-665.
    • (2015) Science , vol.348 , pp. 660-665
    • Melé, M.1
  • 24
    • 46549099940 scopus 로고
    • A new statistic in the one-way multivariate analysis of variance
    • Nath, R. and Pavur, R. (1985) A new statistic in the one-way multivariate analysis of variance. Comput. Stat. Data Anal., 2, 297-315.
    • (1985) Comput. Stat. Data Anal. , vol.2 , pp. 297-315
    • Nath, R.1    Pavur, R.2
  • 25
    • 33750481513 scopus 로고    scopus 로고
    • Heritability and tissue specificity of expression quantitative trait loci
    • Petretto, E. et al. (2006) Heritability and tissue specificity of expression quantitative trait loci. PLoS Genet., 2, e172.
    • (2006) PLoS Genet. , vol.2 , pp. e172
    • Petretto, E.1
  • 26
    • 77952588387 scopus 로고    scopus 로고
    • New insights into the genetic control of gene expression using a Bayesian multi-tissue Approach
    • Petretto, E., et al. (2010) New insights into the genetic control of gene expression using a Bayesian multi-tissue Approach. PLoS Comput. Biol., 6, 587-588.
    • (2010) PLoS Comput. Biol. , vol.6 , pp. 587-588
    • Petretto, E.1
  • 27
    • 84900338300 scopus 로고    scopus 로고
    • Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes
    • Raj, T. et al. (2014) Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science, 344, 519-523.
    • (2014) Science , vol.344 , pp. 519-523
    • Raj, T.1
  • 28
    • 84879234389 scopus 로고    scopus 로고
    • Bayesian models for sparse regression analysis of high dimensional data
    • Bernardo, J. (eds). Oxford University Press, Oxford
    • Richardson, S. et al. (2010) Bayesian models for sparse regression analysis of high dimensional data. In: Bernardo, J. (eds) Bayesian Statistics 9, volume 9. Oxford University Press, Oxford, pp. 539-569
    • (2010) Bayesian Statistics 9 , vol.9 , pp. 539-569
    • Richardson, S.1
  • 29
    • 84861904178 scopus 로고    scopus 로고
    • Genome regulation by long noncoding RNAs
    • Rinn, J. L. and Chang, H. Y. (2012) Genome regulation by long noncoding RNAs. Annu. Rev. Biochem., 81, 145-166.
    • (2012) Annu. Rev. Biochem. , vol.81 , pp. 145-166
    • Rinn, J.L.1    Chang, H.Y.2
  • 30
    • 60149084519 scopus 로고    scopus 로고
    • PASTAA: Identifying transcription factors associated with sets of co-regulated genes
    • Roider, H. G. et al. (2009) PASTAA: identifying transcription factors associated with sets of co-regulated genes. Bioinformatics, 25, 435-442.
    • (2009) Bioinformatics , vol.25 , pp. 435-442
    • Roider, H.G.1
  • 31
    • 84872111954 scopus 로고    scopus 로고
    • An integrated hierarchical Bayesian model for multivariate eQTL mapping
    • Scott-Boyer, M. P. et al. (2012) An integrated hierarchical Bayesian model for multivariate eQTL mapping. Stat. Appl. Genet. Mol. Biol., 11.
    • (2012) Stat. Appl. Genet. Mol. Biol. , pp. 11
    • Scott-Boyer, M.P.1
  • 32
    • 84861153094 scopus 로고    scopus 로고
    • Matrix eQTL: Ultra fast eQTL analysis via large matrix operations
    • Shabalin, A. A. (2012) Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics, 28, 1353-1358.
    • (2012) Bioinformatics , vol.28 , pp. 1353-1358
    • Shabalin, A.A.1
  • 33
    • 84861734626 scopus 로고    scopus 로고
    • Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
    • Stegle, O. et al. (2012) Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nat. Protoc., 7, 500-507.
    • (2012) Nat. Protoc. , vol.7 , pp. 500-507
    • Stegle, O.1
  • 34
    • 80054851243 scopus 로고    scopus 로고
    • A Bayesian graphical modeling approach to microRNA regulatory network inference
    • Stingo, F. C. et al. (2010) A Bayesian graphical modeling approach to microRNA regulatory network inference. Ann. Appl. Stat., 4, 20242048.
    • (2010) Ann. Appl. Stat. , vol.4 , pp. 20242048
    • Stingo, F.C.1
  • 35
    • 84885018609 scopus 로고    scopus 로고
    • Systematic identification of trans eQTLs as putative drivers of known disease associations
    • Westra, H.-J. et al. (2013) Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat. Genet., 45, 1238-1243.
    • (2013) Nat. Genet. , vol.45 , pp. 1238-1243
    • Westra, H.-J.1


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