On reverse engineering of gene interaction networks using time course data with repeated measurements.
BACKGROUND
Gene expression measurements are the most common data source for reverse engineering gene interaction networks. When dealing with destructive sampling in time course experiments, it is common to average any available measurements for each time point and to treat this as the actual time series data for fitting the network, neglecting the variability contained in the repeated measurements. Proceeding in such a way can affect the retrieved network topology.


RESULTS
We propose a fully Bayesian method for reverse engineering a gene interaction network, based on time course data with repeated measurements. The observations are treated as surrogate measurements of the underlying gene expression. As these measurements often contain outliers, we use a non-Gaussian specification for dealing with measurement error. The network interactions are assumed linear and an autoregressive model is specified, augmented with indicator variables that allow inference on the topology of the network. We analyse two in silico and one in vivo experiments, the latter dealing with the circadian clock in Arabidopsis thaliana. A systematic attenuation of the estimated regulation strengths and a concomitant overestimation of their precision is demonstrated when measurement error is disregarded. Thus, a clear improvement in the inferred topology for the synthetic datasets is demonstrated when this is included. Also, the influence of outliers in the retrieved network is demonstrated when using the in vivo data.


BACKGROUND
Matlab code and data used in the article are available from http://go.warwick.ac.uk/majuarez/home/materials.
Morrissey
E R
ER
Warwick Systems Biology Centre and Warwick HRI, University of Warwick, Coventry, UK.
Juárez
M A
MA
Denby
K J
KJ
Burroughs
N J
NJ
D000465:Algorithms; D017360:Arabidopsis / Q000502:physiology; D001499:Bayes Theorem; D002940:Circadian Rhythm; D003198:Computer Simulation; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D035501:Uncertainty