Asap A Framework for Over-Representation Statistics for Transcription Factor Binding Sites 英文参考文献.docVIP
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Asap A Framework for Over-Representation Statistics for Transcription Factor Binding Sites 英文参考文献
Asap:AFrameworkforOver-RepresentationStatisticsfor
TranscriptionFactorBindingSites
TroelsT.Marstrand1*,JesFrellsen1,IdaMoltke1,MartinThiim1,EivindValen1,DorotaRetelska2 ,Anders
Krogh1
1BioinformaticsCentre,DepartmentofMolecularBiologyandBiotechResearchandInnovationCentre(BRIC),UniversityofCopenhagen,Copenhagen,Denmark,2Swiss
InstituteofBioinformatics,SwissInstituteforExperimentalCancerResearch(ISREC),Epalinges,Switzerland
Abstract
Background:Instudiesofgeneregulationtheefficientcomputationaldetectionofover-representedtranscriptionfactor
binding sites is an increasingly important aspect. Several published methods can be used for testing whether a set of
hypothesised co-regulated genes share a common regulatory regime based on the occurrence of the modelled
transcription factor binding sites. However there is little or no informationavailable for guiding the end users choice of
method.Furthermoreitwouldbenecessarytoobtainseveraldifferentsoftwareprogramsfromvarioussourcestomakea
well-foundedchoice.
Methodology:Weintroduceasoftwarepackage,Asap,forfastsearchingwithpositionweightmatricesthatincludeseveral
standard methods for assessing over-representation. We have compared the ability of these methods to detect over-
representedtranscriptionfactorbindingsitesinartificialpromotersequences.Controllingallaspectsofourinputdatawe
are able to identify the optimal statistics across multiple threshold values and for sequence sets containing different
distributionsoftranscriptionfactorbindingsites.
Conclusions:Weshowthatourimplementationissignificantlyfasterthanmorena?¨vescanningalgorithmswhensearching
withmanyweightmatricesinlargesequencesets.Whencomparingthevariousstatistics,weshowthatthosebasedon
binomialover-representationandFisher’sexacttestperformsalmostequallygoodandbetterthantheothers.Anonline
serverisavailableathttp://servers.binf.ku.dk/asap/.
Citation:MarstrandTT,FrellsenJ,MoltkeI,ThiimM,ValenE,etal(2008)Asap:AFrameworkforOver-RepresentationStatisticsforTranscriptionFa
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