Article (Scientific journals)
Wisdom of crowds for robust gene network inference
Marbach, Daniel; Costello, James C.; Küffner, Robert et al.
2012In Nature Methods, 9, p. 796-804
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Abstract :
[en] 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.
Disciplines :
Computer science
Biochemistry, biophysics & molecular biology
Author, co-author :
Marbach, Daniel
Costello, James C.
Küffner, Robert
Vega, Nicole M.
Prill, Robert J.
Camacho, Diogo M.
Allison, Kyle R.
Aderhold, Andrej
Bonneau, Richard
Chen, Yukun
Cordero, Francesca
Crane, Martin
Dondelinger, Frank
Drton, Mathias
Esposito, Roberto
Foygel, Rina
de la Fuente, Alberto
Gertheiss, Jan
Geurts, Pierre ;  Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation
Greenfield, Alex
Grzegorczyk, Marco
Haury, Anne-Claire
Holmes, Benjamin
Hothorn, Torsten
Husmeier, Dirk
Huynh-Thu, Vân Anh ;  Université de Liège - ULiège > GIGA-Management : Coordination ALMA-GRID
Irrthum, Alexandre ;  Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation
Karlebach, Guy
Lèbre, Sophie
De Leo, Vincenzo
Madar, Aviv
Mani, Subramani
Mordelet, Fantine
Ostrer, Harry
Ouyang, Zhengyu
Pandya, Ravi
Petri, Tobias
Pinna, Andrea
Poultney, Christopher S.
Rezny, Serena
Ruskin, Heather J.
Saeys, Yvan
Shamir, Ron
Sîrbu, Alina
Song, Mingzhou
Soranzo, Nicola
Statnikov, Alexander
Vega, Nicci
Vera-Licona, Paola
Vert, Jean-Philippe
Visconti, Alessia
Wang, Haizhou
Wehenkel, Louis  ;  Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation
Windhager, Lukas
Zhang, Yang
Zimmer, Ralf
Kellis, Manolis
Collins, James J.
Stolovitzky, Gustavo
More authors (49 more) Less
Language :
English
Title :
Wisdom of crowds for robust gene network inference
Publication date :
15 July 2012
Journal title :
Nature Methods
ISSN :
1548-7091
eISSN :
1548-7105
Publisher :
Nature Publishing Group
Volume :
9
Pages :
796-804
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 20 July 2012

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