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Bioinformatics Advance Access originally published online on September 27, 2006
Bioinformatics 2006 22(23):2952-2954; doi:10.1093/bioinformatics/btl491
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network

Xiaohui Chen 1, Ming Chen 1,2,* and Kaida Ning 1

1 Department of Bioinformatics Zhejiang University, Hangzhou 310058, China
2 The National Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences Zhejiang University, Hangzhou 310058, China

*To whom correspondence should be addressed.

Summary: BNArray is a systemized tool developed in R. It facilitates the construction of gene regulatory networks from DNA microarray data by using Bayesian network. Significant sub-modules of regulatory networks with high confidence are reconstructed by using our extended sub-network mining algorithm of directed graphs. BNArray can handle microarray datasets with missing data. To evaluate the statistical features of generated Bayesian networks, re-sampling procedures are utilized to yield collections of candidate 1st-order network sets for mining dense coherent sub-networks.

Availability: The R package and the supplementary documentation are available at http://www.cls.zju.edu.cn/binfo/BNArray/.

Contact: mchen{at}zju.edu.cn

Received on June 14, 2006; revised on August 28, 2006; accepted on September 18, 2006

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