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Commun Integr Biol. 2010 Nov;3(6):549-54. doi: 10.4161/cib.3.6.12845. Epub 2010 Nov 1.

BN+1 Bayesian network expansion for identifying molecular pathway elements.

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1
Center for Computational Medicine and Bioinformatics; University of Michigan Medical School; University of Michigan; Michigan USA.

Abstract

A Bayesian network expansion algorithm called BN+1 was developed to identify undocumented gene interactions in a known pathway using microarray gene expression data. In our recent paper, the BN+1 algorithm has been successfully used to identify key regulators including uspE in the E. coli ROS pathway and biofilm formation.18 In this report, a synthetic network was designed to further evaluate this algorithm. The BN+1 method was found to identify both linear and nonlinear relationships and correctly identify variables near the starting network. Using experimentally derived data, the BN+1 method identifies the gene fdhE as a potentially new ROS regulator. Finally, a range of possible score cutoff methods are explored to identify a set of criteria for selecting BN+1 calls.

KEYWORDS:

BN+1; E. coli; ROS; bayesian network; biofilm; gene interaction; microarray data analysis; network expansion; reactive oxygen species; synthetic network

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