Structure learning in Nested Effects Models

Stat Appl Genet Mol Biol. 2008;7(1):Article9. doi: 10.2202/1544-6115.1332. Epub 2008 Mar 1.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Animals
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / immunology
  • Gene Expression Profiling / statistics & numerical data
  • Genes, Insect
  • Genes, MHC Class II
  • Genomics / statistics & numerical data
  • Likelihood Functions
  • Models, Genetic
  • Models, Statistical*
  • Oligonucleotide Array Sequence Analysis / statistics & numerical data
  • Phenotype
  • RNA Interference