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A Model-Based Analysis to Infer the Functional Content of a Gene List

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  • Newton Michael A.

    (University of Wisconsin, Madison)

  • He Qiuling

    (University of Wisconsin, Madison)

  • Kendziorski Christina

    (University of Wisconsin, Madison)

Abstract

An important challenge in statistical genomics concerns integrating experimental data with exogenous information about gene function. A number of statistical methods are available to address this challenge, but most do not accommodate complexities in the functional record. To infer activity of a functional category (e.g., a gene ontology term), most methods use gene-level data on that category, but do not use other functional properties of the same genes. Not doing so creates undue errors in inference. Recent developments in model-based category analysis aim to overcome this difficulty, but in attempting to do so they are faced with serious computational problems. This paper investigates statistical properties and the structure of posterior computation in one such model for the analysis of functional category data. We examine the graphical structures underlying posterior computation in the original parameterization and in a new parameterization aimed at leveraging elements of the model. We characterize identifiability of the underlying activation states, describe a new prior distribution, and introduce approximations that aim to support numerical methods for posterior inference.

Suggested Citation

  • Newton Michael A. & He Qiuling & Kendziorski Christina, 2012. "A Model-Based Analysis to Infer the Functional Content of a Gene List," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(2), pages 1-27, January.
  • Handle: RePEc:bpj:sagmbi:v:11:y:2012:i:2:n:9
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    References listed on IDEAS

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    1. Liang, Kun & Nettleton, Dan, 2010. "A Hidden Markov Model Approach to Testing Multiple Hypotheses on a Tree-Transformed Gene Ontology Graph," Journal of the American Statistical Association, American Statistical Association, vol. 105(492), pages 1444-1454.
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