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

Bioinformatics
Holger FröhlichFlorian Markowetz

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. Our software is written in the R language and freely avail-able via the Bioconductor project at http://www.bioconductor.org.

References

Nov 15, 2002·Developmental Cell·Michael BoutrosNorbert Perrimon
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Jul 13, 2007·BMC Bioinformatics·Janusz Dutkowski, Anna Gambin
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Citations

Mar 31, 2009·Proceedings of the National Academy of Sciences of the United States of America·Benedict AnchangRainer Spang
Nov 8, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mohammad J SadehRainer Spang
Jan 17, 2009·EURASIP Journal on Bioinformatics & Systems Biology·Cordula ZellerAchim Tresch
May 18, 2010·International Journal of Cancer. Journal International Du Cancer·Marian GradeThomas Ried
Nov 5, 2014·Frontiers in Cell and Developmental Biology·Frank Emmert-StreibBenjamin Haibe-Kains
Jun 28, 2012·PLoS Computational Biology·Theresa NiederbergerAchim Tresch
Apr 14, 2017·PLoS Computational Biology·Martin PirklFlorian Markowetz
Feb 14, 2020·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yuriy SverchkovMark Craven
Apr 15, 2018·Proceedings of the National Academy of Sciences of the United States of America·Benedict AnchangSylvia K Plevritis
May 1, 2021·Science·Josephine M BryantR Andres Floto

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