Wisdom of crowds for robust gene network inference

Marbach, D. et al. (2012) Wisdom of crowds for robust gene network inference. Nature Methods, 9(8), pp. 796-804. (doi: 10.1038/nmeth.2016)

Abstract

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.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Husmeier, Professor Dirk
• Authors: Marbach, D., Costello, J.C., Küffner, R., Vega, N.M., Prill, R.J., Camacho, D.M., Allison, K.R., Aderhold, A., Allison, K.R., Bonneau, R., Camacho, D.M., Chen, Y., Collins, J.J., Cordero, F., Costello, J.C., Crane, M., Dondelinger, F., Drton, M., Esposito, R., Foygel, R., de la Fuente, A., Gertheiss, J., Geurts, P., Greenfield, A., Grzegorczyk, M., Haury, A.-C., Holmes, B., Hothorn, T., Husmeier, D., Huynh-Thu, V.A., Irrthum, A., Kellis, M., Karlebach, G., Küffner, R., Lèbre, S., De Leo, V., Madar, A., Mani, S., Marbach, D., Mordelet, F., Ostrer, H., Ouyang, Z., Pandya, R., Petri, T., Pinna, A., Poultney, C.S., Prill, R.J., Rezny, S., Ruskin, H.J., Saeys, Y., Shamir, R., Sîrbu, A., Song, M., Soranzo, N., Statnikov, A., Stolovitzky, G., Vega, N., Vera-Licona, P., Vert, J.-P., Visconti, A., Wang, H., Wehenkel, L., Windhager, L., Zhang, Y., Zimmer, R., Kellis, M., Collins, J.J., and Stolovitzky, G.
• College/School: College of Science and Engineering > School of Mathematics and Statistics > Statistics
• Journal Name: Nature Methods
• ISSN: 1548-7091
• ISSN (Online): 1548-7105