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Statistical Applications in Genetics and Molecular Biology

Editor-in-Chief: Stumpf, Michael P.H.

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Volume 7, Issue 1 (Mar 2008)

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Structure Learning in Nested Effects Models

Achim Tresch
  • Johannes Gutenberg University Mainz
/ Florian Markowetz
  • Princeton University
Published Online: 2008-03-01 | DOI: https://doi.org/10.2202/1544-6115.1332

Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-dimensional outputs of phenotyping studies, e.g., the effects showing in gene expression profiles or as morphological features of the perturbed cell.In this paper we expand the statistical basis of NEMs in four directions. First, we derive a new formula for the likelihood function of a NEM, which generalizes previous results for binary data. Second, we prove model identifiability under mild assumptions. Third, we show that the new formulation of the likelihood allows efficiency in traversing model space. Fourth, we incorporate prior knowledge and an automated variable selection criterion to decrease the influence of noise in the data.

Keywords: gene perturbation; pathway reconstruction; model identifiability; feature selection

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Published Online: 2008-03-01


Citation Information: Statistical Applications in Genetics and Molecular Biology, ISSN (Online) 1544-6115, DOI: https://doi.org/10.2202/1544-6115.1332.

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