Title
Exploring the operational characteristics of inference algorithms for transcriptional networks by means of synthetic data
Author
Faculty/Department
Faculty of Sciences. Biology
Faculty of Sciences. Mathematics and Computer Science
Publication type
article
Publication
Cambridge :Mit press ,
Subject
Computer. Automation
Source (journal)
Artificial life. - Cambridge, Mass.
Source (book)
8th European Conference on Artificial Life, SEP 05-09, 2005, Canterbury, ENGLAND
Volume/pages
14(2008) :1 , p. 49-63
ISSN
1064-5462
ISI
000252248700004
Carrier
E
Target language
English (eng)
Full text (Publishers DOI)
Affiliation
University of Antwerp
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.
E-info
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Handle