Reverse Engineering Time Discrete Finite Dynamical Systems A Feasible Undertaking 英文参考文献.docVIP

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Reverse Engineering Time Discrete Finite Dynamical Systems A Feasible Undertaking 英文参考文献.doc

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Reverse Engineering Time Discrete Finite Dynamical Systems A Feasible Undertaking 英文参考文献

ReverseEngineeringTimeDiscreteFiniteDynamical Systems:AFeasibleUndertaking? EdgarDelgado-Eckert1,2¤ * 1CentreforMathematicalSciences,TechnischeUniversita¨tMu¨nchen,Garching,Germany,2PathologyDepartment,TuftsUniversity,Boston,Massachusetts,UnitedStates ofAmerica Abstract With the advent of high-throughput profiling methods, interest in reverse engineering the structure and dynamics of biochemicalnetworksishigh.Recentlyanalgorithmforreverseengineeringofbiochemical networkswasdevelopedby LaubenbacherandStigler.Itisatop-downapproachusingtimediscretedynamicalsystems.Oneofitskeystepsincludes the choice ofa term order, atechnicality imposed by theuse of Gro¨bner-bases calculations. The aim of this paper is to identifyminimalrequirementsondatasetstobeusedwiththisalgorithmandtocharacterizeoptimaldatasets.Wefound minimalrequirementsonadatasetbasedonhowmanytermsthefunctionstobereverseengineereddisplay.Furthermore, weidentifiedoptimaldatasets,whichwecharacterizedusingageometricpropertycalled‘‘generalposition’’.Moreover,we developedaconstructivemethodtogenerateoptimaldatasets,providedacodimensionalconditionisfulfilled.Inaddition, wepresentageneralizationoftheiralgorithmthatdoesnotdependonthechoiceofatermorder.Forthismethodwe derivedaformulafortheprobabilityoffindingthecorrectmodel,providedthedatasetusedisoptimal.Weanalyzedthe asymptotic behavior of the probability formula for a growing number of variables n (i.e. interacting chemicals). Unfortunately,thisformulaconvergestozeroasfastasreq nT,whereq[Nand0v v1.Therefore,evenifanoptimaldataset r isusedandtherestrictionsinusingtermordersareovercome,thereverseengineeringproblemremainsunfeasible,unless prodigious amounts of data are available. Such large data sets are experimentally impossible to generate with today’s technologies. Citation: Delgado-Eckert E (2009) Reverse Engineering Time Discrete Finite Dynamical Systems: A Feasible Undertaking? PLoS ONE 4(3): e4939. doi:10.1371/ journal.pone.0004939 Editor:GustavoStolovitzk