Bioinformatics. 2008 Nov 1;24(21):2549-50. Epub 2008 Aug 21.

Analyzing gene perturbation screens with nested effects models in R and bioconductor.

Fröhlich H, Beissbarth T, Tresch A, Kostka D, Jacob J, Spang R, Markowetz F.

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German Cancer Research Center, INF 580, 69120 Heidelberg, Germany.

Abstract

Nested effects models (NEMs) are a class of probabilistic models introduced to analyze the effects of gene perturbation screens visible in high-dimensional phenotypes like microarrays or cell morphology. NEMs reverse engineer upstream/downstream relations of cellular signaling cascades. NEMs take as input a set of candidate pathway genes and phenotypic profiles of perturbing these genes. NEMs return a pathway structure explaining the observed perturbation effects. Here, we describe the package nem, an open-source software to efficiently infer NEMs from data. Our software implements several search algorithms for model fitting and is applicable to a wide range of different data types and representations. The methods we present summarize the current state-of-the-art in NEMs. AVAILABILITY: Our software is written in the R language and freely avail-able via the Bioconductor project at http://www.bioconductor.org.

PMID:: 18718939; [PubMed - indexed for MEDLINE]
PMCID: PMC2732276

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