IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v12y2013i4p469-487n4.html
   My bibliography  Save this article

A graphical model method for integrating multiple sources of genome-scale data

Author

Listed:
  • Dvorkin Daniel

    (Computational Bioscience Program, University of Colorado School of Medicine, Mail Stop 8303, 12801 E. 17th Ave., RC1S-L18 6103, Aurora, CO 80045–0511, USA)

  • Biehs Brian

    (Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143–2711, USA)

  • Kechris Katerina

    (Computational Bioscience Program, University of Colorado School of Medicine, Mail Stop 8303, 12801 E. 17th Ave., RC1S-L18 6103, Aurora, CO 80045–0511, USA Department of Biostatistics and Informatics, Colorado School of Public Health, 13001 E. 17th Place, B-119, Aurora, CO 80045, USA)

Abstract

Making effective use of multiple data sources is a major challenge in modern bioinformatics. Genome-wide data such as measures of transcription factor binding, gene expression, and sequence conservation, which are used to identify binding regions and genes that are important to major biological processes such as development and disease, can be difficult to use together due to the different biological meanings and statistical distributions of the heterogeneous data types, but each can provide valuable information for understanding the processes under study. Here we present methods for integrating multiple data sources to gain a more complete picture of gene regulation and expression. Our goal is to identify genes and cis-regulatory regions which play specific biological roles. We describe a graphical mixture model approach for data integration, examine the effect of using different model topologies, and discuss methods for evaluating the effectiveness of the models. Model fitting is computationally efficient and produces results which have clear biological and statistical interpretations. The Hedgehog and Dorsal signaling pathways in Drosophila, which are critical in embryonic development, are used as examples.

Suggested Citation

  • Dvorkin Daniel & Biehs Brian & Kechris Katerina, 2013. "A graphical model method for integrating multiple sources of genome-scale data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 12(4), pages 469-487, August.
    • Handle: RePEc:bpj:sagmbi:v:12:y:2013:i:4:p:469-487:n:4
    DOI: 10.1515/sagmb-2012-0051
    as

    Download full text from publisher

    File URL: https://doi.org/10.1515/sagmb-2012-0051
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.1515/sagmb-2012-0051?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. Cinzia Viroli, 2010. "Dimensionally Reduced Model-Based Clustering Through Mixtures of Factor Mixture Analyzers," Journal of Classification, Springer;The Classification Society, vol. 27(3), pages 363-388, November.
    2. Adelchi Azzalini, 2005. "The Skew‐normal Distribution and Related Multivariate Families," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 32(2), pages 159-188, June.
    3. John D. Storey, 2002. "A direct approach to false discovery rates," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 64(3), pages 479-498, 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. Youngchao Ge & Sandrine Dudoit & Terence Speed, 2003. "Resampling-based multiple testing for microarray data analysis," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 12(1), pages 1-77, June.
    2. Bajgrowicz, Pierre & Scaillet, Olivier, 2012. "Technical trading revisited: False discoveries, persistence tests, and transaction costs," Journal of Financial Economics, Elsevier, vol. 106(3), pages 473-491.
    3. Redivo, Edoardo & Nguyen, Hien D. & Gupta, Mayetri, 2020. "Bayesian clustering of skewed and multimodal data using geometric skewed normal distributions," Computational Statistics & Data Analysis, Elsevier, vol. 152(C).
    4. Toshihiro Abe & Arthur Pewsey, 2011. "Sine-skewed circular distributions," Statistical Papers, Springer, vol. 52(3), pages 683-707, August.
    5. Wen Shi & Xi Chen & Jennifer Shang, 2019. "An Efficient Morris Method-Based Framework for Simulation Factor Screening," INFORMS Journal on Computing, INFORMS, vol. 31(4), pages 745-770, October.
    6. Dørum Guro & Snipen Lars & Solheim Margrete & Saebo Solve, 2011. "Smoothing Gene Expression Data with Network Information Improves Consistency of Regulated Genes," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-26, August.
    7. Jianqing Fan & Xu Han, 2017. "Estimation of the false discovery proportion with unknown dependence," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 79(4), pages 1143-1164, September.
    8. Egozcue, Martín & García, Luis Fuentes & Wong, Wing-Keung & Zitikis, Ricardas, 2011. "Do investors like to diversify? A study of Markowitz preferences," European Journal of Operational Research, Elsevier, vol. 215(1), pages 188-193, November.
    9. A Bottle & P Aylin, 2011. "Predicting the false alarm rate in multi-institution mortality monitoring," Journal of the Operational Research Society, Palgrave Macmillan;The OR Society, vol. 62(9), pages 1711-1718, September.
    10. Van Hanh Nguyen & Catherine Matias, 2014. "On Efficient Estimators of the Proportion of True Null Hypotheses in a Multiple Testing Setup," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 41(4), pages 1167-1194, December.
    11. Shigeyuki Matsui & Hisashi Noma, 2011. "Estimating Effect Sizes of Differentially Expressed Genes for Power and Sample-Size Assessments in Microarray Experiments," Biometrics, The International Biometric Society, vol. 67(4), pages 1225-1235, December.
    12. Lianming Wang & David B. Dunson, 2010. "Semiparametric Bayes Multiple Testing: Applications to Tumor Data," Biometrics, The International Biometric Society, vol. 66(2), pages 493-501, June.
    13. Ebrahimi, Nader, 2008. "Simultaneous control of false positives and false negatives in multiple hypotheses testing," Journal of Multivariate Analysis, Elsevier, vol. 99(3), pages 437-450, March.
    14. B. Moerkerke & E. Goetghebeur & J. De Riek & I. Roldán‐Ruiz, 2006. "Significance and impotence: towards a balanced view of the null and the alternative hypotheses in marker selection for plant breeding," Journal of the Royal Statistical Society Series A, Royal Statistical Society, vol. 169(1), pages 61-79, January.
    15. Zaili Fang & Inyoung Kim & Jeesun Jung, 2018. "Semiparametric Kernel-Based Regression for Evaluating Interaction Between Pathway Effect and Covariate," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 23(1), pages 129-152, March.
    16. Mark Rempel, 2016. "Improving Overnight Loan Identification in Payments Systems," Journal of Money, Credit and Banking, Blackwell Publishing, vol. 48(2-3), pages 549-564, March.
    17. Timothy B. Armstrong, 2014. "Adaptive Testing on a Regression Function at a Point," Cowles Foundation Discussion Papers 1957R, Cowles Foundation for Research in Economics, Yale University, revised Feb 2015.
    18. Nucera, Federico & Valente, Giorgio, 2013. "Carry trades and the performance of currency hedge funds," Journal of International Money and Finance, Elsevier, vol. 33(C), pages 407-425.
    19. Nickole Moon & Christopher P. Morgan & Ruth Marx-Rattner & Alyssa Jeng & Rachel L. Johnson & Ijeoma Chikezie & Carmen Mannella & Mary D. Sammel & C. Neill Epperson & Tracy L. Bale, 2024. "Stress increases sperm respiration and motility in mice and men," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    20. Axel Gandy & Georg Hahn, 2016. "A Framework for Monte Carlo based Multiple Testing," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 43(4), pages 1046-1063, December.

    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:bpj:sagmbi:v:12:y:2013:i:4:p:469-487:n:4. 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: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    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.