IDEAS home Printed from https://ideas.repec.org/a/taf/jnlasa/v110y2015i512p1350-1361.html
   My bibliography  Save this article

Bayesian Partition Models for Identifying Expression Quantitative Trait Loci

Author

Listed:
  • Bo Jiang
  • Jun S. Liu

Abstract

Expression quantitative trait loci (eQTLs) are genomic locations associated with changes of expression levels of certain genes. By assaying gene expressions and genetic variations simultaneously on a genome-wide scale, scientists wish to discover genomic loci responsible for expression variations of a set of genes. The task can be viewed as a multivariate regression problem with variable selection on both responses (gene expression) and covariates (genetic variations), including also multi-way interactions among covariates. Instead of learning a predictive model of quantitative trait given combinations of genetic markers, we adopt an inverse modeling perspective to model the distribution of genetic markers conditional on gene expression traits. A particular strength of our method is its ability to detect interactive effects of genetic variations with high power even when their marginal effects are weak, addressing a key weakness of many existing eQTL mapping methods. Furthermore, we introduce a hierarchical model to capture the dependence structure among correlated genes. Through simulation studies and a real data example in yeast, we demonstrate how our Bayesian hierarchical partition model achieves a significantly improved power in detecting eQTLs compared to existing methods. Supplementary materials for this article are available online.

Suggested Citation

  • Bo Jiang & Jun S. Liu, 2015. "Bayesian Partition Models for Identifying Expression Quantitative Trait Loci," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 110(512), pages 1350-1361, December.
    • Handle: RePEc:taf:jnlasa:v:110:y:2015:i:512:p:1350-1361
    DOI: 10.1080/01621459.2015.1049746
    as

    Download full text from publisher

    File URL: http://hdl.handle.net/10.1080/01621459.2015.1049746
    Download Restriction: Access to full text is restricted to subscribers.
    File URL: https://libkey.io/10.1080/01621459.2015.1049746?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Eric E. Schadt & Stephanie A. Monks & Thomas A. Drake & Aldons J. Lusis & Nam Che & Veronica Colinayo & Thomas G. Ruff & Stephen B. Milligan & John R. Lamb & Guy Cavet & Peter S. Linsley & Mao Mao & R, 2003. "Genetics of gene expression surveyed in maize, mouse and man," Nature, Nature, vol. 422(6929), pages 297-302, March.
    2. C. M. Kendziorski & M. Chen & M. Yuan & H. Lan & A. D. Attie, 2006. "Statistical Methods for Expression Quantitative Trait Loci (eQTL) Mapping," Biometrics, The International Biometric Society, vol. 62(1), pages 19-27, March.
    3. Wei Zhang & Jun Zhu & Eric E Schadt & Jun S Liu, 2010. "A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules," PLOS Computational Biology, Public Library of Science, vol. 6(1), pages 1-10, January.
    4. Bryan N Howie & Peter Donnelly & Jonathan Marchini, 2009. "A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies," PLOS Genetics, Public Library of Science, vol. 5(6), pages 1-15, June.
    5. Michael Morley & Cliona M. Molony & Teresa M. Weber & James L. Devlin & Kathryn G. Ewens & Richard S. Spielman & Vivian G. Cheung, 2004. "Genetic analysis of genome-wide variation in human gene expression," Nature, Nature, vol. 430(7001), pages 743-747, August.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Lin Yuan & Chang-An Yuan & De-Shuang Huang, 2017. "FAACOSE: A Fast Adaptive Ant Colony Optimization Algorithm for Detecting SNP Epistasis," Complexity, Hindawi, vol. 2017, pages 1-10, September.
    2. Enrico Petretto & Leonardo Bottolo & Sarah R Langley & Matthias Heinig & Chris McDermott-Roe & Rizwan Sarwar & Michal Pravenec & Norbert Hübner & Timothy J Aitman & Stuart A Cook & Sylvia Richardson, 2010. "New Insights into the Genetic Control of Gene Expression using a Bayesian Multi-tissue Approach," PLOS Computational Biology, Public Library of Science, vol. 6(4), pages 1-13, April.
    3. Chang, Yu-Ling & Zou, Fei & Wright, Fred A., 2010. "An approximate Bayesian approach for quantitative trait loci estimation," Computational Statistics & Data Analysis, Elsevier, vol. 54(2), pages 565-574, February.
    4. Urmo Võsa & Tõnu Esko & Silva Kasela & Tarmo Annilo, 2015. "Altered Gene Expression Associated with microRNA Binding Site Polymorphisms," PLOS ONE, Public Library of Science, vol. 10(10), pages 1-24, October.
    5. Wei Zhang & Jun Zhu & Eric E Schadt & Jun S Liu, 2010. "A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules," PLOS Computational Biology, Public Library of Science, vol. 6(1), pages 1-10, January.
    6. Brown Andrew Anand & Richardson Sylvia & Whittaker John, 2011. "Application of the Lasso to Expression Quantitative Trait Loci Mapping," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-35, March.
    7. Daniel Svensson & Matilda Rentoft & Anna M Dahlin & Emma Lundholm & Pall I Olason & Andreas Sjödin & Carin Nylander & Beatrice S Melin & Johan Trygg & Erik Johansson, 2020. "A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences," PLOS ONE, Public Library of Science, vol. 15(9), pages 1-18, September.
    8. Chuan Gao & Nan Wang & Xiuqing Guo & Julie T Ziegler & Kent D Taylor & Anny H Xiang & Yang Hai & Steven J Kridel & Jerry L Nadler & Fouad Kandeel & Leslie J Raffel & Yii-Der I Chen & Jill M Norris & J, 2015. "A Comprehensive Analysis of Common and Rare Variants to Identify Adiposity Loci in Hispanic Americans: The IRAS Family Study (IRASFS)," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-17, November.
    9. Julia Schröder & Vitalia Schüller & Andrea May & Christian Gerges & Mario Anders & Jessica Becker & Timo Hess & Nicole Kreuser & René Thieme & Kerstin U Ludwig & Tania Noder & Marino Venerito & Lothar, 2019. "Identification of loci of functional relevance to Barrett’s esophagus and esophageal adenocarcinoma: Cross-referencing of expression quantitative trait loci data from disease-relevant tissues with gen," PLOS ONE, Public Library of Science, vol. 14(12), pages 1-12, December.
    10. Paul S de Vries & Maria Sabater-Lleal & Daniel I Chasman & Stella Trompet & Tarunveer S Ahluwalia & Alexander Teumer & Marcus E Kleber & Ming-Huei Chen & Jie Jin Wang & John R Attia & Riccardo E Mario, 2017. "Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study," PLOS ONE, Public Library of Science, vol. 12(1), pages 1-22, January.
    11. Rakesh Chettier & Lesa Nelson & James W Ogilvie & Hans M Albertsen & Kenneth Ward, 2015. "Haplotypes at LBX1 Have Distinct Inheritance Patterns with Opposite Effects in Adolescent Idiopathic Scoliosis," PLOS ONE, Public Library of Science, vol. 10(2), pages 1-11, February.
    12. Michel S. Naslavsky & Marilia O. Scliar & Guilherme L. Yamamoto & Jaqueline Yu Ting Wang & Stepanka Zverinova & Tatiana Karp & Kelly Nunes & José Ricardo Magliocco Ceroni & Diego Lima Carvalho & Carlo, 2022. "Whole-genome sequencing of 1,171 elderly admixed individuals from Brazil," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    13. Steinrücken, Matthias & Paul, Joshua S. & Song, Yun S., 2013. "A sequentially Markov conditional sampling distribution for structured populations with migration and recombination," Theoretical Population Biology, Elsevier, vol. 87(C), pages 51-61.
    14. Anshuman Sewda & A J Agopian & Elizabeth Goldmuntz & Hakon Hakonarson & Bernice E Morrow & Fadi Musfee & Deanne Taylor & Laura E Mitchell & on behalf of the Pediatric Cardiac Genomics Consortium, 2020. "Gene-based analyses of the maternal genome implicate maternal effect genes as risk factors for conotruncal heart defects," PLOS ONE, Public Library of Science, vol. 15(6), pages 1-15, June.
    15. Yixin Fang & Yang Feng & Ming Yuan, 2014. "Regularized principal components of heritability," Computational Statistics, Springer, vol. 29(3), pages 455-465, June.
    16. Wei Sun, 2012. "A Statistical Framework for eQTL Mapping Using RNA-seq Data," Biometrics, The International Biometric Society, vol. 68(1), pages 1-11, March.
    17. Witten Daniela M & Tibshirani Robert J., 2009. "Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-27, June.
    18. Lingxue Zhang & Seyoung Kim, 2014. "Learning Gene Networks under SNP Perturbations Using eQTL Datasets," PLOS Computational Biology, Public Library of Science, vol. 10(2), pages 1-20, February.
    19. Carl Nettelblad, 2013. "Breakdown of Methods for Phasing and Imputation in the Presence of Double Genotype Sharing," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-5, March.
    20. Viinikainen, Jutta & Bryson, Alex & Böckerman, Petri & Kari, Jaana T. & Lehtimäki, Terho & Raitakari, Olli & Viikari, Jorma & Pehkonen, Jaakko, 2022. "Does better education mitigate risky health behavior? A mendelian randomization study," Economics & Human Biology, Elsevier, vol. 46(C).

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:taf:jnlasa:v:110:y:2015:i:512:p:1350-1361. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Chris Longhurst (email available below). General contact details of provider: http://www.tandfonline.com/UASA20 .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.