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ALIFE
2008

Exploring the Operational Characteristics of Inference Algorithms for Transcriptional Networks by Means of Synthetic Data

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Exploring the Operational Characteristics of Inference Algorithms for Transcriptional Networks by Means of Synthetic Data
The development of structure-learning algorithms for gene regulatory networks depends heavily on the availability of synthetic data sets that contain both the original network and associated expression data. This article reports the application of SynTReN, an existing network generator that samples topologies from existing biological networks and uses Michaelis-Menten and Hill enzyme kinetics to simulate gene interactions. We illustrate the effects of different aspects of the expression data on the quality of the inferred network. The tested expression data parameters are network size, network topology, type and degree of noise, quantity of expression data, and interaction types between genes. This is done by applying three well-known inference algorithms to SynTReN data sets. The results show the power of synthetic data in revealing operational characteristics of inference algorithms that are unlikely to be discovered by means of biological microarray data only.
Koenraad Van Leemput, Tim Van den Bulcke, Thomas D
Added 24 Dec 2010
Updated 24 Dec 2010
Type Journal
Year 2008
Where ALIFE
Authors Koenraad Van Leemput, Tim Van den Bulcke, Thomas Dhollander, Bart De Moor, Kathleen Marchal, Piet van Remortel
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