Bayesian Network Expansion Identifies New ROS and Biofilm Regulators 英文参考文献.docVIP

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Bayesian Network Expansion Identifies New ROS and Biofilm Regulators 英文参考文献.doc

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Bayesian Network Expansion Identifies New ROS and Biofilm Regulators 英文参考文献

BayesianNetworkExpansionIdentifiesNewROSand BiofilmRegulators AndrewP.Hodges1.,DongjuanDai2.,ZuoshuangXiang3,PeterWoolf1,4,5,ChuanwuXi2 ,Yongqun He1,3,6 * 1CenterforComputationalMedicineandBioinformatics,UniversityofMichigan,AnnArbor,Michigan,UnitedStatesofAmerica,2DepartmentofEnvironmentalHealth Sciences,UniversityofMichigan, AnnArbor,Michigan,UnitedStatesofAmerica, 3UnitforLaboratoryAnimalMedicine,UniversityofMichigan, AnnArbor,Michigan, UnitedStatesofAmerica,4DepartmentofChemicalEngineering,UniversityofMichigan,AnnArbor,Michigan,UnitedStatesofAmerica,5DepartmentofBiomedical Engineering,UniversityofMichigan,AnnArbor,Michigan,UnitedStatesofAmerica,6DepartmentofMicrobiologyandImmunology,UniversityofMichigan,AnnArbor, Michigan,UnitedStatesofAmerica Abstract Signaling and regulatory pathways that guide gene expression have only been partially defined for most organisms. However,giventheincreasingnumberofmicroarraymeasurements,itmaybepossibletoreconstructsuchpathwaysand uncover missing connections directly from experimental data. Using a compendium of microarray gene expression data obtainedfromEscherichiacoli,weconstructedaseriesofBayesiannetworkmodelsforthereactiveoxygenspecies(ROS) pathwayasdefinedbyEcoCyc.AconsensusBayesiannetworkmodelwasgeneratedusingthosenetworkssharingthetop recovered score. This microarray-based network only partially agreed with the known ROS pathway curated from the literature and databases. A top network was then expanded to predict genes that could enhance the Bayesian network modelusinganalgorithmwetermed‘BN+1’.Thisexpansionprocedurepredictedmanystress-relatedgenes(e.g.,dusBand uspE),andtheirpossibleinteractionswithotherROSpathwaygenes.Atermenrichmentmethoddiscoveredthatbiofilm- associatedmicroarraydatausuallycontainedhighexpressionlevelsofbothuspEandgadX.Thepredictedinvolvementof gene uspE in the ROS pathway and interactions between uspE and gadX were confirmed experimentally using E. coli reporterstrains.GenesgadXanduspEshoweda