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EpiExplorer live exploration and global analysis of large epigenomic datasets.doc

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EpiExplorer live exploration and global analysis of large epigenomic datasets

Halachevetal.GenomeBiology2012,13:R96 /2012/13/10/R96 SOFTWARE OpenAccess EpiExplorer:liveexplorationandglobalanalysis oflargeepigenomicdatasets KonstantinHalachev1*,HannahBast2,FelipeAlbrecht1,ThomasLengauer1andChristophBock1,3,4* Abstract Epigenomemappingconsortiaaregeneratingresourcesoftremendousvalueforstudyingepigeneticregulation. Tomaximizetheirutilityandimpact,newtoolsareneededthatfacilitateinteractiveanalysisofepigenome datasets.HerewedescribeEpiExplorer,awebtoolforexploringgenomeandepigenomedataonagenomicscale. WedemonstrateEpiExplorer’sutilitybydescribingahypothesis-generatinganalysisofDNAhydroxymethylationin relationtopublicreferencemapsofthehumanepigenome.AllEpiExploreranalysesareperformeddynamically withinseconds,usinganefficientandversatiletextindexingschemethatweintroducetobioinformatics. EpiExplorerisavailableathttp://epiexplorer.mpi-inf.mpg.de. Rationale [11], Ensembl [12]andtheWashUHumanEpigenome Understandinggeneregulationisanimportantgoalinbio- Browser[13]liesintheirintuitiveinterface,whichallows medical research. Historically, much ofwhat weknow userstobrowsethroughthegenomebyrepresentingitas about regulatory mechanisms has been discovered by aone-dimensional mapwithvarious annotation tracks. mechanism-focusedstudiesonasmallsetofmodelgenes Thisapproachispowerfulforvisualizingindividualgene [1,2]. High-throughput genomic mapping technologies loci, but the key concept of genomics - investigating haverecentlyemergedasacomplementaryapproach[3]; many genomic regions in concert - tends to get lost andlarge-scale communityprojectsarenowgenerating when working with genome browsers only. Therefore, comprehensivemapsofgeneticandepigeneticregulation complementary tools areneeded that handle thecom- for the human and mouse genomes [4-7]. Substantial plexity oflargegenomicdatasets whilemaintaining the potentialfordiscoveryliesinbetterconnectingmechan- interactive and user-friendly character of genome ism-focusedstudiestothe