Bagging statistical network inference from large-scale gene expression data.

Ricardo de Matos Simoes, Frank Emmert-Streib

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Abstract

Modern biology and medicine aim at hunting molecular and cellular causes of biological functions and diseases. Gene regulatory networks (GRN) inferred from gene expression data are considered an important aid for this research by providing a map of molecular interactions. Hence, GRNs have the potential enabling and enhancing basic as well as applied research in the life sciences. In this paper, we introduce a new method called BC3NET for inferring causal gene regulatory networks from large-scale gene expression data. BC3NET is an ensemble method that is based on bagging the C3NET algorithm, which means it corresponds to a Bayesian approach with noninformative priors. In this study we demonstrate for a variety of simulated and biological gene expression data from S. cerevisiae that BC3NET is an important enhancement over other inference methods that is capable of capturing biochemical interactions from transcription regulation and protein-protein interaction sensibly. An implementation of BC3NET is freely available as an R package from the CRAN repository. © 2012 de Matos Simoes, Emmert-Streib.
Original languageEnglish
Article number e33624
Pages (from-to)1-11
Number of pages11
JournalPLoS ONE
Volume7
Issue number3
DOIs
Publication statusPublished - 30 Mar 2012

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Gene expression
Gene Regulatory Networks
Gene Expression
gene expression
Genes
Modern 1601-history
Bayes Theorem
Molecular interactions
Biological Science Disciplines
protein-protein interactions
Transcription
Research
Medicine
Saccharomyces cerevisiae
medicine
Proteins
transcription (genetics)
methodology
Biological Sciences
gene regulatory networks

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de Matos Simoes, Ricardo ; Emmert-Streib, Frank. / Bagging statistical network inference from large-scale gene expression data. In: PLoS ONE. 2012 ; Vol. 7, No. 3. pp. 1-11.
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Bagging statistical network inference from large-scale gene expression data. / de Matos Simoes, Ricardo; Emmert-Streib, Frank.

In: PLoS ONE, Vol. 7, No. 3, e33624, 30.03.2012, p. 1-11.

Research output: Contribution to journalArticle

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