Froehlich, Holger and Beissbarth, Tim and Tresch, Achim and Kostka, Dennis and Jacob, Juby and Spang, Rainer and Markowetz, F. (2008) Analyzing gene perturbation screens with nested effects models in R and bioconductor. BIOINFORMATICS, 24 (21). pp. 2549-2550. ISSN 1367-4803,
Full text not available from this repository.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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | ; |
| Subjects: | 600 Technology > 610 Medical sciences Medicine |
| Divisions: | Medicine > Institut für Funktionelle Genomik > Lehrstuhl für Statistische Bioinformatik (Prof. Spang) |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 19 Oct 2020 08:38 |
| Last Modified: | 19 Oct 2020 08:38 |
| URI: | https://pred.uni-regensburg.de/id/eprint/30077 |
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