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  Reconstruction of gene networks using prior knowledge

Ganbari, M., Lasserre, J., & Vingron, M. (2015). Reconstruction of gene networks using prior knowledge. BMC Systems Biology, 9: 9:84. doi:10.1186/s12918-015-0233-4.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-3B25-0 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-3B26-E
Genre: Journal Article

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© 2015 Ghanbari et al. Published by BioMed Central Ltd.
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 Creators:
Ganbari, M.1, Author              
Lasserre, Julia1, Author              
Vingron, M.2, Author              
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              
2Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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Free keywords: Gene regulatory networks; Network reconstruction; Prior knowledge; Bayesian networks
 Abstract: BACKGROUND: Reconstructing gene regulatory networks (GRNs) from expression data is a challenging task that has become essential to the understanding of complex regulatory mechanisms in cells. The major issues are the usually very high ratio of number of genes to sample size, and the noise in the available data. Integrating biological prior knowledge to the learning process is a natural and promising way to partially compensate for the lack of reliable expression data and to increase the accuracy of network reconstruction algorithms. RESULTS: In this manuscript, we present PriorPC, a new algorithm based on the PC algorithm. PC algorithm is one of the most popular methods for Bayesian network reconstruction. The result of PC is known to depend on the order in which conditional independence tests are processed, especially for large networks. PriorPC uses prior knowledge to exclude unlikely edges from network estimation and introduces a particular ordering for the conditional independence tests. We show on synthetic data that the structural accuracy of networks obtained with PriorPC is greatly improved compared to PC. CONCLUSION: PriorPC improves structural accuracy of inferred gene networks by using soft priors which assign to edges a probability of existence. It is robust to false prior which is not avoidable in the context of biological data. PriorPC is also fast and scales well for large networks which is important for its applicability to real data.

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Language(s): eng - English
 Dates: 2015-11-20
 Publication Status: Published online
 Pages: -
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 Identifiers: DOI: 10.1186/s12918-015-0233-4
ISSN: 1752-0509 (Electronic)
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Title: BMC Systems Biology
Source Genre: Journal
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Pages: - Volume / Issue: 9 Sequence Number: 9:84 Start / End Page: - Identifier: ISSN: 1752-0509
CoNE: /journals/resource/1000000000225260