Cardiff University | Prifysgol Caerdydd ORCA
Online Research @ Cardiff 
WelshClear Cookie - decide language by browser settings

Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler

Grzegorczyk, Marco, Husmeier, Dirk, Edwards, Kieron D., Ghazal, Peter ORCID: and Millar, Andrew J. 2008. Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler. Bioinformatics 24 (18) , pp. 2071-2078. 10.1093/bioinformatics/btn367

Full text not available from this repository.


Method: The objective of the present article is to propose and evaluate a probabilistic approach based on Bayesian networks for modelling non-homogeneous and non-linear gene regulatory processes. The method is based on a mixture model, using latent variables to assign individual measurements to different classes. The practical inference follows the Bayesian paradigm and samples the network structure, the number of classes and the assignment of latent variables from the posterior distribution with Markov Chain Monte Carlo (MCMC), using the recently proposed allocation sampler as an alternative to RJMCMC. Results: We have evaluated the method using three criteria: network reconstruction, statistical significance and biological plausibility. In terms of network reconstruction, we found improved results both for a synthetic network of known structure and for a small real regulatory network derived from the literature. We have assessed the statistical significance of the improvement on gene expression time series for two different systems (viral challenge of macrophages, and circadian rhythms in plants), where the proposed new scheme tends to outperform the classical BGe score. Regarding biological plausibility, we found that the inference results obtained with the proposed method were in excellent agreement with biological findings, predicting dichotomies that one would expect to find in the studied systems. Availability: Two supplementary papers on theoretical (T) and experi-mental (E) aspects and the datasets used in our study are available from,

Item Type: Article
Date Type: Publication
Status: Published
Schools: Medicine
Publisher: Oxford University Press (OUP): Policy B - Oxford Open Option B
ISSN: 1367-4803
Last Modified: 23 Oct 2022 14:17

Citation Data

Cited 58 times in Scopus. View in Scopus. Powered By Scopus® Data

Actions (repository staff only)

Edit Item Edit Item