Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods

被引:296
|
作者
Marbach, Daniel [1 ]
Schaffter, Thomas [1 ]
Mattiussi, Claudio [1 ]
Floreano, Dario [1 ]
机构
[1] Ecole Polytech Fed Lausanne, Lab Intelligent Syst, I2S LIS, Stn 11, CH-1015 Lausanne, Switzerland
基金
瑞士国家科学基金会;
关键词
DREAM challenge; gene regulatory networks; modularity; network motifs; reverse engineering; TRANSCRIPTIONAL REGULATORY NETWORK; EXPRESSION; PERTURBATIONS; SIMULATION; MOTIFS;
D O I
10.1089/cmb.2008.09TT
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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).
引用
收藏
页码:229 / 239
页数:11
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