Identification of direction in gene networks from expression and methylation

BMC Systems Biology

Donald Geman²  Martin J Aryee³  Laurent Younes¹  David M Simcha⁴ 

[1] Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21218, USA;Department of Applied Mathematics and Statistics and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA;Department of Pathology, Massachusetts General Hospital, Charlestown, MA 02129, USA;Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA

关键词: Bayesian networks;    Microarrays;    Methylation;    Gene regulation;   

Others  :  1141821
DOI  :  10.1186/1752-0509-7-118

 received in 2012-09-17, accepted in 2013-10-17,  发布年份 2013

【 摘 要 】

Background

Reverse-engineering gene regulatory networks from expression data is difficult, especially without temporal measurements or interventional experiments. In particular, the causal direction of an edge is generally not statistically identifiable, i.e., cannot be inferred as a statistical parameter, even from an unlimited amount of non-time series observational mRNA expression data. Some additional evidence is required and high-throughput methylation data can viewed as a natural multifactorial gene perturbation experiment.

Results

We introduce IDEM (Identifying Direction from Expression and Methylation), a method for identifying the causal direction of edges by combining DNA methylation and mRNA transcription data. We describe the circumstances under which edge directions become identifiable and experiments with both real and synthetic data demonstrate that the accuracy of IDEM for inferring both edge placement and edge direction in gene regulatory networks is significantly improved relative to other methods.

Conclusion

Reverse-engineering directed gene regulatory networks from static observational data becomes feasible by exploiting the context provided by high-throughput DNA methylation data.

An implementation of the algorithm described is available at http://code.google.com/p/idem/ webcite.

【 授权许可】

   
2013 Simcha et al.; licensee BioMed Central Ltd.

【 图 表 】

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