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Generating realistic in silico gene networks for performance assessment of reverse engineering methods.


Marbach, Daniel; Schaffter, Thomas; Mattiussi, Claudio; Floreano, Dario (2009). Generating realistic in silico gene networks for performance assessment of reverse engineering methods. Journal of Computational Biology, 16(2):229-39.

Abstract

Reverse engineering methods are typically first tested on simulated data from in silico networks, for systematic and efficient performance assessment, before an application to real biological networks. In this paper, we present a method for generating biologically plausible in silico networks, which allow realistic performance assessment of network inference algorithms. Instead of using random graph models, which are known to only partly capture the structural properties of biological networks, we generate network structures by extracting modules from known biological interaction networks. Using the yeast transcriptional regulatory network as a test case, we show that extracted modules have a biologically plausible connectivity because they preserve functional and structural properties of the original network. Our method was selected to generate the "gold standard" networks for the gene network reverse engineering challenge of the third DREAM conference (Dialogue on Reverse Engineering Assessment and Methods 2008, Cambridge, MA).

Reverse engineering methods are typically first tested on simulated data from in silico networks, for systematic and efficient performance assessment, before an application to real biological networks. In this paper, we present a method for generating biologically plausible in silico networks, which allow realistic performance assessment of network inference algorithms. Instead of using random graph models, which are known to only partly capture the structural properties of biological networks, we generate network structures by extracting modules from known biological interaction networks. Using the yeast transcriptional regulatory network as a test case, we show that extracted modules have a biologically plausible connectivity because they preserve functional and structural properties of the original network. Our method was selected to generate the "gold standard" networks for the gene network reverse engineering challenge of the third DREAM conference (Dialogue on Reverse Engineering Assessment and Methods 2008, Cambridge, MA).

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119 citations in Web of Science®
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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:Special Collections > SystemsX.ch
Special Collections > SystemsX.ch > Research, Technology and Development Projects > WingX
Dewey Decimal Classification:570 Life sciences; biology
Date:2009
Deposited On:08 Dec 2010 13:09
Last Modified:05 Apr 2016 14:27
Publisher:Mary Ann Liebert
ISSN:1066-5277
Publisher DOI:10.1089/cmb.2008.09TT
PubMed ID:19183003
Permanent URL: http://doi.org/10.5167/uzh-39863

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