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Bioinformatics Advance Access published online on September 27, 2006
Bioinformatics, 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
Received June 14, 2006
Revised August 28, 2006
Accepted September 18, 2006

Applications note

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

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

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

* To whom correspondence should be addressed.
Ming Chen, E-mail: mchen{at}zju.edu.cn


  Abstract

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 submodules of regulatory networks with high confidence are reconstructed by using our extended sub-network mining algorithm of directed graphs. BNArray can handle microarray data sets 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/.

Associate Editor: John Quackenbush
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