Reference : Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
Engineering, computing & technology : Computer science
http://hdl.handle.net/2268/73256
Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
English
Huynh-Thu, Vân Anh mailto [Université de Liège - ULg > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation >]
Irrthum, Alexandre mailto [Université de Liège - ULg > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation >]
Wehenkel, Louis mailto [Université de Liège - ULg > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation >]
Geurts, Pierre mailto [Université de Liège - ULg > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation >]
28-Sep-2010
PLoS ONE
Public Library of Science
5
9
e12776
Yes (verified by ORBi)
International
1932-6203
San Franscisco
CA
[en] bioinformatics ; Machine learning ; systems biology
[en] One of the pressing open problems of computational systems biology is the elucidation of the topology of genetic regulatory networks (GRNs) using high throughput genomic data, in particular microarray gene expression data. The Dialogue for Reverse Engineering Assessments and Methods (DREAM) challenge aims to evaluate the success of GRN inference algorithms on benchmarks of simulated data. In this article, we present GENIE3, a new algorithm for the inference of GRNs that was best performer in the DREAM4 In Silico Multifactorial challenge. GENIE3 decomposes the prediction of a regulatory network between p genes into p different regression problems. In each of the regression problems, the expression pattern of one of the genes (target gene) is predicted from the expression patterns of all the other genes (input genes), using tree-based ensemble methods Random Forests or Extra-Trees. The importance of an input gene in the prediction of the target gene expression pattern is taken as an indication of a putative regulatory link. Putative regulatory links are then aggregated over all genes to provide a ranking of interactions from which the whole network is reconstructed. In addition to performing well on the DREAM4 In Silico Multifactorial challenge simulated data, we show that GENIE3 compares favorably with existing algorithms to decipher the genetic regulatory network of Escherichia coli. It doesn't make any assumption about the nature of gene regulation, can deal with combinatorial and non-linear interactions, produces directed GRNs, and is fast and scalable. In conclusion, we propose a new algorithm for GRN inference that performs well on both synthetic and real gene expression data. The algorithm, based on feature selection with tree-based ensemble methods, is simple and generic, making it adaptable to other types of genomic data and interactions.
Systems and modeling (Dept. of EE and CS) and Bioinformatics and modeling (GIGA-R)
http://hdl.handle.net/2268/73256
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012776

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