Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data 英文参考文献.docVIP

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Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data 英文参考文献.doc

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Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data 英文参考文献

BayesianMarkovRandomFieldAnalysisforProtein FunctionPredictionBasedonNetworkData YiannisA.I.Kourmpetis1,AaltD.J.vanDijk2,MarcoC.A.M.Bink1,RoelandC.H.J.vanHam2,3,CajoJ.F. terBraak1* 1Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands, 2Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands,3LaboratoryofBioinformatics,WageningenUniversity,Wageningen,TheNetherlands Abstract Inferenceofproteinfunctionsisoneofthemostimportantaimsofmodernbiology.Tofullyexploitthelargevolumesof genomic data typically produced in modern-day genomic experiments, automated computational methods for protein functionpredictionareurgentlyneeded.Establishedmethodsusesequenceorstructuresimilarity toinferfunctionsbut those types of data do not suffice to determine the biological context in which proteins act. Current high-throughput biologicalexperimentsproducelargeamountsofdataontheinteractionsbetweenproteins.Suchdatacanbeusedtoinfer interactionnetworksandtopredictthebiologicalprocessthattheproteinisinvolvedin.Here,wedevelopaprobabilistic approachforproteinfunctionpredictionusingnetworkdata,suchasprotein-proteininteractionmeasurements.Wetakea Bayesian approach to an existing Markov Random Field method by performing simultaneous estimation of the model parametersandpredictionofproteinfunctions.WeuseanadaptiveMarkovChainMonteCarloalgorithmthatleadstomore accurate parameter estimates andconsequently toimproved prediction performance compared to thestandard Markov Random Fields method. We tested our method using a high quality S.cereviciae validation network with 1622 proteins against 90 Gene Ontology terms of different levels of abstraction. Compared to three other protein function prediction methods,ourapproachshowsverygoodpredictionperformance.Ourmethodcanbedirectlyappliedtoprotein-protein interaction or coexpression networks, but also can be extended to use multiple data sources. We apply our method to physicalproteininteractiondata