Integrating external biological knowledge in the construction of regulatory networks from time-series expression data.
BACKGROUND
Inference about regulatory networks from high-throughput genomics data is of great interest in systems biology. We present a Bayesian approach to infer gene regulatory networks from time series expression data by integrating various types of biological knowledge.


RESULTS
We formulate network construction as a series of variable selection problems and use linear regression to model the data. Our method summarizes additional data sources with an informative prior probability distribution over candidate regression models. We extend the Bayesian model averaging (BMA) variable selection method to select regulators in the regression framework. We summarize the external biological knowledge by an informative prior probability distribution over the candidate regression models.


CONCLUSIONS
We demonstrate our method on simulated data and a set of time-series microarray experiments measuring the effect of a drug perturbation on gene expression levels, and show that it outperforms leading regression-based methods in the literature.
Department of Microbiology, University of Washington, Box 358070, Seattle, WA 98195, USA.
Kenneth
K
Lo
Adrian E
AE
Raftery
Kenneth M
KM
Dombek
Jun
J
Zhu
Eric E
EE
Schadt
Roger E
RE
Bumgarner
Ka Yee
KY
Yeung
D001185:Artificial Intelligence; D001499:Bayes Theorem; D001665:Binding Sites; D025461:Feedback, Physiological; D053263:Gene Regulatory Networks; D011336:Probability; D049490:Systems Biology / Q000379:methods*; D013997:Time Factors; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome
D014157:Transcription Factors