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Exploring the operational characteristics of inference algorithms for transcriptional networks by means of synthetic data

(2008) ARTIFICIAL LIFE. 14(1). p.49-63
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Abstract
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.
Keywords
gene regulatory network, simulated data, network inference, gene expression data, GENE-EXPRESSION DATA, REGULATORY NETWORKS

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Chicago
Van Leemput, Koenraad, Tim Van den Bulcke, Thomas Dhollander, Bart De Moor, Kathleen Marchal, and Piet van Remortel. 2008. “Exploring the Operational Characteristics of Inference Algorithms for Transcriptional Networks by Means of Synthetic Data.” Artificial Life 14 (1): 49–63.
APA
Van Leemput, K., Van den Bulcke, T., Dhollander, T., De Moor, B., Marchal, K., & van Remortel, P. (2008). Exploring the operational characteristics of inference algorithms for transcriptional networks by means of synthetic data. ARTIFICIAL LIFE, 14(1), 49–63. Presented at the 8th European conference on Artificial Life.
Vancouver
1.
Van Leemput K, Van den Bulcke T, Dhollander T, De Moor B, Marchal K, van Remortel P. Exploring the operational characteristics of inference algorithms for transcriptional networks by means of synthetic data. ARTIFICIAL LIFE. 2008;14(1):49–63.
MLA
Van Leemput, Koenraad, Tim Van den Bulcke, Thomas Dhollander, et al. “Exploring the Operational Characteristics of Inference Algorithms for Transcriptional Networks by Means of Synthetic Data.” ARTIFICIAL LIFE 14.1 (2008): 49–63. Print.
@article{3187211,
  abstract     = {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.},
  author       = {Van Leemput, Koenraad and Van den Bulcke, Tim and Dhollander, Thomas and De Moor, Bart and Marchal, Kathleen and van Remortel, Piet},
  issn         = {1064-5462},
  journal      = {ARTIFICIAL LIFE},
  keyword      = {gene regulatory network,simulated data,network inference,gene expression data,GENE-EXPRESSION DATA,REGULATORY NETWORKS},
  language     = {eng},
  location     = {Canterbury, UK},
  number       = {1},
  pages        = {49--63},
  title        = {Exploring the operational characteristics of inference algorithms for transcriptional networks by means of synthetic data},
  url          = {http://dx.doi.org/10.1162/artl.2008.14.1.49},
  volume       = {14},
  year         = {2008},
}

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