Analysis of Functional Genomic Signals Using the XOR Gate 英文参考文献.docVIP

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Analysis of Functional Genomic Signals Using the XOR Gate 英文参考文献.doc

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Analysis of Functional Genomic Signals Using the XOR Gate 英文参考文献

AnalysisofFunctionalGenomicSignalsUsingtheXOR Gate MaheshYaragatti1*,QiWen2 1Biotechnology Program, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America, 2Department of Physics, University of Pennsylvania, Philadelphia,Pennsylvania,UnitedStatesofAmerica Abstract Modelinggeneregulatorynetworksrequiresrecognitionofactivetranscriptionalsitesinthegenome.Forthisreason,we presentanovelapproachforinferringactivetranscriptionalregulatorymodulesinagenomeusinganestablishedsystems modelofbitencodedDNAsequences.Ouranalysisshowedvariationsinseveralpropertiesbetweenrandomandfunctional sequences. Cross correlationwithin randomandfunctional groupsuncovered awave patternassociated withfunctional sequences. Using the exclusive-OR (XOR) logic gate, we formulated a scheme to threshold signals that may correlate to putativeactivetranscriptionalmodulesfromapopulationofrandomgenomicfragments.Itisourintenttousethisasa basisforidentifyingnovelregulatorysitesinthegenome. Citation:YaragattiM,WenQ(2009)AnalysisofFunctionalGenomicSignalsUsingtheXORGate.PLoSONE4(5):e5608.doi:10.1371/journal.pone.0005608 Editor:EshelBen-Jacob,TelAvivUniversity,Israel ReceivedFebruary4,2009;AcceptedApril17,2009;PublishedMay19,2009 Copyright: ? 2009 Yaragatti 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:Theauthorshavenosupportorfundingtoreport. CompetingInterests:Theauthorshavedeclaredthatnocompetinginterestsexist. *E-mail:myar@ Introduction a signal plot. The rationale for our approach was to evaluate the interactionofdiscretepropertiesbetweensequences. A digital transformation of genomic sequences has facilitated the biological discovery of regulatory regions in the genome through computational methods. Since 2003, the ENCODE Consortium has endeavored to identify all the regulatory sites in thehu