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Revealing strengths and weaknesses of methods for gene network inference


Marbach, D; Prill, R; Schaffter, T; Mattiussi, C; Floreano, D; Stolovitzky, G (2010). Revealing strengths and weaknesses of methods for gene network inference. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 107(14):6286-6291.

Abstract

Numerous methods have been developed for inferring gene regulatory networks from expression data, however, both their absolute and comparative performance remain poorly understood. In this paper, we introduce a framework for critical performance assessment of methods for gene network inference. We present an in silico benchmark suite that we provided as a blinded, community-wide challenge within the context of the DREAM (Dialogue on Reverse Engineering Assessment and Methods) project. We assess the performance of 29 gene-network-inference methods, which have been applied independently by participating teams. Performance profiling reveals that current inference methods are affected, to various degrees, by different types of systematic prediction errors. In particular, all but the best-performing method failed to accurately infer multiple regulatory inputs (combinatorial regulation) of genes. The results of this community-wide experiment show that reliable network inference from gene expression data remains an unsolved problem, and they indicate potential ways of network reconstruction improvements.

Numerous methods have been developed for inferring gene regulatory networks from expression data, however, both their absolute and comparative performance remain poorly understood. In this paper, we introduce a framework for critical performance assessment of methods for gene network inference. We present an in silico benchmark suite that we provided as a blinded, community-wide challenge within the context of the DREAM (Dialogue on Reverse Engineering Assessment and Methods) project. We assess the performance of 29 gene-network-inference methods, which have been applied independently by participating teams. Performance profiling reveals that current inference methods are affected, to various degrees, by different types of systematic prediction errors. In particular, all but the best-performing method failed to accurately infer multiple regulatory inputs (combinatorial regulation) of genes. The results of this community-wide experiment show that reliable network inference from gene expression data remains an unsolved problem, and they indicate potential ways of network reconstruction improvements.

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233 citations in Web of Science®
278 citations in Scopus®
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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
Language:English
Date:2010
Deposited On:26 Nov 2010 16:08
Last Modified:05 Apr 2016 14:26
Publisher:National Academy of Sciences
ISSN:0027-8424
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:10.1073/pnas.0913357107
PubMed ID:20308593
Permanent URL: http://doi.org/10.5167/uzh-39548

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