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Uncovering gene regulatory networks from time-series microarray data with variational Bayesian structural expectation maximization.
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MedLine Citation:
PMID:  18309364     Owner:  NLM     Status:  PubMed-not-MEDLINE    
Abstract/OtherAbstract:
We investigate in this paper reverse engineering of gene regulatory networks from time-series microarray data. We apply dynamic Bayesian networks (DBNs) for modeling cell cycle regulations. In developing a network inference algorithm, we focus on soft solutions that can provide a posteriori probability (APP) of network topology. In particular, we propose a variational Bayesian structural expectation maximization algorithm that can learn the posterior distribution of the network model parameters and topology jointly. We also show how the obtained APPs of the network topology can be used in a Bayesian data integration strategy to integrate two different microarray data sets. The proposed VBSEM algorithm has been tested on yeast cell cycle data sets. To evaluate the confidence of the inferred networks, we apply a moving block bootstrap method. The inferred network is validated by comparing it to the KEGG pathway map.
Authors:
Isabel Tienda Luna; Yufei Huang; Yufang Yin; Diego P Ruiz Padillo; M Carmen Carrion Perez
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  EURASIP journal on bioinformatics & systems biology     Volume:  -     ISSN:  1687-4145     ISO Abbreviation:  EURASIP J Bioinform Syst Biol     Publication Date:  2007  
Date Detail:
Created Date:  2008-02-29     Completed Date:  2010-06-28     Revised Date:  2011-09-15    
Medline Journal Info:
Nlm Unique ID:  101263720     Medline TA:  EURASIP J Bioinform Syst Biol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  71312     Citation Subset:  -    
Affiliation:
Department of Applied Physics, University of Granada, Granada, Spain.
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ID/Acronym/Agency:
R21 AI067543-01A1/AI/NIAID NIH HHS
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

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Journal Information
Journal ID (nlm-ta): EURASIP J Bioinform Syst Biol
ISSN: 1687-4145
ISSN: 1687-4153
Publisher: BioMed Central
Article Information
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Copyright ©2007 Isabel Tienda Luna et al.
open-access:
Received Day: 1 Month: 7 Year: 2006
Revision Received Day: 4 Month: 12 Year: 2006
Accepted Day: 11 Month: 5 Year: 2007
Print publication date: Year: 2007
Electronic publication date: Day: 27 Month: 6 Year: 2007
Volume: 2007 Issue: 1
First Page: 71312 Last Page: 71312
ID: 3171349
Publisher Id: 1687-4153-2007-71312
PubMed Id: 18309364
DOI: 10.1155/2007/71312

Uncovering Gene Regulatory Networks from Time-Series Microarray Data with Variational Bayesian Structural Expectation Maximization
Isabel Tienda Luna1 Email: isabelt@ugr.es
Yufei Huang2 Email: yufei.huang@utsa.edu
Yufang Yin2 Email: yyin@lonestar.utsa.edu
Diego P Ruiz Padillo1 Email: druiz@ugr.es
M Carmen Carrion Perez1 Email: mcarrion@ugr.es
1Department of Applied Physics, University of Granada, Granada 18071, Spain
2Department of Electrical and Computer Engineering, University of Texas at San Antonio (UTSA), San Antonio, TX 78249-0669, USA

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