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Computational discovery of regulatory elements in acontinuous expression space
Lajoieetal.GenomeBiology2012,13:R109
/2012/13/11/R109
METHOD
OpenAccess
Computationaldiscoveryofregulatoryelements
inacontinuousexpressionspace
MathieuLajoie*,OlivierGascuel,VincentLefortandLaurentBréhélin
Abstract
Approachesforregulatoryelementdiscoveryfromgeneexpressiondatausuallyrelyonclusteringalgorithmsto
partitionthedataintoclustersofco-expressedgenes.Generegulatorysequencesarethenminedtofind
overrepresentedmotifsineachcluster.However,thisadhocpartitionrarelyfitsthebiologicalreality.Weproposea
novelmethodcalledRED2thatavoidsdataclusteringbyestimatingmotifdensitieslocallyaroundeachgene.
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