Projects per year
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.
|Number of pages||8|
|Publication status||Published - 15 Sep 2008|
- CHAIN MONTE-CARLO
FingerprintDive into the research topics of 'Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler'. Together they form a unique fingerprint.
- 2 Finished
SynthSys; formerly CSBE: Centre for Systems Biology at Edinburgh
Millar, A., Beggs, J., Ghazal, P., Goryanin, I., Hillston, J., Plotkin, G., Tollervey, D., Walton, A. & Robertson, K.
8/01/07 → 31/12/12
Modelling circadian gene regulation in Arabidopsis thaliana
1/03/05 → 30/09/06
Circadian expression of genes: modelling the Arabidopsis circadian clock
Edwards, K. D. (Creator) & Millar, A. (Creator), University of Edinburgh, 2005
http://affymetrix.arabidopsis.info/narrays/experimentpage.pl?experimentid=108 and one more link, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5612 (show fewer)
Circadian gene expression under different light treatments by transcriptome profiling on microarrays
Edwards, K. D. (Creator) & Millar, A. (Creator), University of Edinburgh, 2007