Analyzing gene perturbation screens with nested effects models in R and bioconductor
2008-11-01 | journal article
Jump to: Cite & Linked | Documents & Media | Details | Version history
Documents & Media
Details
- Authors
- Fröhlich, Holger; Beißbarth, Tim ; Tresch, Achim; Kostka, Dennis; Jacob, Juby; Spang, Rainer; Markowetz, F
- 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.
- Issue Date
- 1-November-2008
- Journal
- Bioinformatics
- ISSN
- 1367-4803; 1460-2059
- eISSN
- 1367-4811
- Language
- English