01936nas a2200265   4500008004100000022001400041245005600055210005500111260001300166300001200179490000600191520117600197100002001373700001901393700002101412700001501433700001601448700001801464700001801482700002001500700001801520700002501538710002201563856008501585       2012                        eng d  a1548-710500aWisdom of crowds for robust gene network inference.0 aWisdom of crowds for robust gene network inference  c2012 Aug  a796-8040 v93 a<p>Reconstructing gene regulatory networks from high-throughput data is a long-standing challenge. Through the Dialogue on Reverse Engineering Assessment and Methods (DREAM) project, we performed a comprehensive blind assessment of over 30 network inference methods on Escherichia coli, Staphylococcus aureus, Saccharomyces cerevisiae and in silico microarray data. We characterize the performance, data requirements and inherent biases of different inference approaches, and we provide guidelines for algorithm application and development. We observed that no single inference method performs optimally across all data sets. In contrast, integration of predictions from multiple inference methods shows robust and high performance across diverse data sets. We thereby constructed high-confidence networks for E. coli and S. aureus, each comprising ~1,700 transcriptional interactions at a precision of ~50%. We experimentally tested 53 previously unobserved regulatory interactions in E. coli, of which 23 (43%) were supported. Our results establish community-based methods as a powerful and robust tool for the inference of transcriptional gene regulatory networks.</p>1 aMarbach, Daniel1 aCostello, J.C.1 aKüffner, Robert1 aVega, N.M.1 aPrill, R.J.1 aCamacho, D.M.1 aAllison, K.R.1 aKellis, Manolis1 aCollins, J.J.1 aStolovitzky, Gustavo1 aDREAM5 Consortium  uhttps://kdd.isti.cnr.it/publications/wisdom-crowds-robust-gene-network-inference