title: Exploring the operational characteristics of inference algorithms for transcriptional networks by means of synthetic data.
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.
authors.affiliation: ISLab (Intelligent Systems Lab), Universiteit Antwerpen, Antwerpen, Belgium. koen.vanleemput@ua.ac.be
authors.forename: Koenraad
authors.initials: K
authors.lastname: Van Leemput
authors.forename: Tim
authors.initials: T
authors.lastname: Van den Bulcke
authors.forename: Thomas
authors.initials: T
authors.lastname: Dhollander
authors.forename: Bart
authors.initials: B
authors.lastname: De Moor
authors.forename: Kathleen
authors.initials: K
authors.lastname: Marchal
authors.forename: Piet
authors.initials: P
authors.lastname: van Remortel
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D003198:Computer Simulation; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D008954:Models, Biological; D012984:Software; D014158:Transcription, Genetic