Reference : Combining tree-based and dynamical systems for the inference of gene regulatory networks
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
Engineering, computing & technology : Computer science
http://hdl.handle.net/2268/181826
Combining tree-based and dynamical systems for the inference of gene regulatory networks
English
Huynh-Thu, Vân Anh mailto [Université de Liège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation >]
Sanguinetti, Guido [University of Edinburgh > School of Informatics > > >]
2015
Bioinformatics
Oxford University Press - Journals Department
31
10
1614-1622
Yes (verified by ORBi)
1367-4803
1460-2059
Oxford
United Kingdom
[en] Motivation: Reconstructing the topology of gene regulatory networks (GRNs) from time series of gene expression data remains an important open problem in computational systems biology. Existing GRN inference algorithms face one of two limitations: model-free methods are scalable but suffer from a lack of interpretability and cannot in general be used for out of sample predictions. On the other hand, model-based methods focus on identifying a dynamical model of the system. These are clearly interpretable and can be used for predictions; however, they rely on strong assumptions and are typically very demanding computationally.
Results: Here, we propose a new hybrid approach for GRN inference, called Jump3, exploiting time series of expression data. Jump3 is based on a formal on/off model of gene expression but uses a non-parametric procedure based on decision trees (called "jump trees") to reconstruct the GRN topology, allowing the inference of networks of hundreds of genes. We show the good performance of Jump3 on in silico and synthetic networks and applied the approach to identify regulatory interactions activated in the presence of interferon gamma.
Availability and implementation: Our MATLAB implementation of Jump3 is available at http:// homepages.inf.ed.ac.uk/vhuynht/software.html.
http://hdl.handle.net/2268/181826
10.1093/bioinformatics/btu863

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