Meeting ReportSystems Biology

Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge

Science Signaling  06 Sep 2011:
Vol. 4, Issue 189, pp. mr7
DOI: 10.1126/scisignal.2002212

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Meeting Information: The DREAM4 Predictive Signaling Network Challenge took place in the summer of 2009. Results were presented at the DREAM4 conference, December 2009, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.

Abstract

Computational analyses of systematic measurements on the states and activities of signaling proteins (as captured by phosphoproteomic data, for example) have the potential to uncover uncharacterized protein-protein interactions and to identify the subset that are important for cellular response to specific biological stimuli. However, inferring mechanistically plausible protein signaling networks (PSNs) from phosphoproteomics data is a difficult task, owing in part to the lack of sufficiently comprehensive experimental measurements, the inherent limitations of network inference algorithms, and a lack of standards for assessing the accuracy of inferred PSNs. A case study in which 12 research groups inferred PSNs from a phosphoproteomics data set demonstrates an assessment of inferred PSNs on the basis of the accuracy of their predictions. The concurrent prediction of the same previously unreported signaling interactions by different participating teams suggests relevant validation experiments and establishes a framework for combining PSNs inferred by multiple research groups into a composite PSN. We conclude that crowdsourcing the construction of PSNs—that is, outsourcing the task to the interested community—may be an effective strategy for network inference.

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