RBF-TSS Identification of Transcription Start Site in Human Using Radial Basis Functions Network and Oligonucleotide Positional Frequencies 英文参考文献.docVIP

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RBF-TSS Identification of Transcription Start Site in Human Using Radial Basis Functions Network and Oligonucleotide Positional Frequencies 英文参考文献.doc

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RBF-TSS Identification of Transcription Start Site in Human Using Radial Basis Functions Network and Oligonucleotide Positional Frequencies 英文参考文献

RBF-TSS:IdentificationofTranscriptionStartSite inHumanUsingRadialBasisFunctionsNetwork andOligonucleotidePositionalFrequencies RamiN.Mahdi,EricC.Rouchka* DepartmentofComputerEngineeringandComputerScience,UniversityofLouisville,Louisville,Kentucky,UnitedStatesofAmerica Abstract Accurateidentificationofpromoterregionsandtranscriptionstartsites(TSS)ingenomicDNAallowsforamorecomplete understandingofthestructureofgenesandgeneregulationwithinagivengenome.Manyrecentlypublishedmethods haveachievedhighidentificationaccuracyofTSS.However,modelsprovidingmoreaccuratemodelingofpromotersand TSS are needed. A novel identification method for identifying transcription start sites that improves the accuracy of TSS recognition for recently published methods is proposed. This method incorporates a metric feature based on oligonucleotide positional frequencies, taking into account the nature of promoters. A radial basis function neural networkforidentifyingtranscriptionstartsites(RBF-TSS)isproposedandemployedasaclassificationalgorithm.Usingnon- overlappingchunks(windows)ofsize50and500onthehumangenome,theproposedmethodachievesanareaunderthe ReceiverOperatorCharacteristiccurve(auROC)of94.75%and95.08%respectively,providingincreasedperformanceover existingTSSpredictionmethods. Citation:MahdiRN,RouchkaEC(2009)RBF-TSS:IdentificationofTranscriptionStartSiteinHumanUsingRadialBasisFunctionsNetworkandOligonucleotide PositionalFrequencies.PLoSONE4(3):e4878.doi:10.1371/journal.pone.0004878 Editor:DarrenP.Martin,InstituteofInfectiousDiseaseandMolecularMedicine,SouthAfrica ReceivedOctober23,2008;AcceptedFebruary20,2009;PublishedMarch16,2009 Copyright: ? 2009 Mahdi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:SupportprovidedbyNIHNCRRgrantP20RR16481andNIHNIEHSgrantP30ES014443.Itscontentsaresolelytheresponsibili