ucsc基因組瀏覽器Galaxy

UCSCGenomeBrowserandGalaxy

(BMEG5790)Prof.Tin-Lap,LEESchoolofBiomedicalSciences,CUHKCUHK-BGIInnovationInstitutesofTrans-omics622ALoKwee-SeongIntegratedBiomedicalSciencesBuildingleetl@.hkLearningesTounderstandkeyfeaturesofUCSCgenomebrowserToretrievegenomicdatainUCSCgenomebrowserTointroduceweb-basedgenomeanalysisplatform-GalaxyToperformbasicgenomicanalysisusingGalaxyHumanGenomeProject(HGP)Aninternational,collaborativeresearchprogramGoal:completemappingandunderstandingofallthegenesofhumanbeingsThefullsequencewascompletedandpublishedinApril2003WhyHGPissouseful?FrancisCollins,formerdirectorofNationalHumanGenomeResearchInstituteonHGP:“It'sahistorybook-anarrativeofthejourneyofourspeciesthroughtime.It'sashopmanual,withanincrediblydetailedblueprintforbuildingeveryhumancell.Andit'satransformativetextbookofmedicine,withinsightsthatwillgivehealthcareprovidersimmensenewpowerstotreat,preventandcuredisease.”WhatisbenefitedspecificallybyHGP?Improvementsinmedicine:improveddiagnosisofdisease.Microbialresearch:newenergysources,biofuels.DNAforensics:identifyingpotentialsuspectsatacrimescene.Agriculture:morenutritiousproducts.Evolutionandhumanmigration:studymigrationofdifferentpopulationgroupsbasedonfemalegeneticinheritance.Riskassessment:reducethelikelihoodofheritablemutations.InternationalHumanGenome

SequencingConsortiumCollaborationwouldbeopentocentersfromanynation20centersfrom6countriesUS,UK,China,France,Germany,JapanRapidandunrestricteddatareleaseAssembledsequences>2kbweredepositedwithin24hoursofassemblyHGPtimeline(1990-2003)HGPtimeline(1990-2003)UntiltodayHGPhasalreadyfueledthediscoveryofmorethan1,800diseasegenesAtleast350biotechnology-basedproductsresultingfromtheHGParecurrentlyinclinicaltrialsTherearenowmorethan2,000genetictestsforhumanconditionsEDGreen

etal.

Nature

470,204-213(2011)doi:10.1038/nature09764GenomicachievementssincetheHumanGenomeProjectBeyondHGP2003LaunchofENCODEproject2004NextGenerationSequencingavailable2005LaunchoftheInternationalHapMapPoject2006LaunchoftheHumanVariantProject2007ENCODEPilotPhasepublishedandPhaseIIstarted2008Launchofthe1000genomeproject2010HapMap3released2012ENCODElargedatareleasedUCSantaCruzgotinvolvedinHGPComputationalbiology(orBioinformatics)isaresearchfieldthatusescomputerstohelpsolvebiologicalproblemsBecauseoftheworkProfessorDavidHausslerwasdoinginthefieldofcomputationalbiology,UCSantaCruzwasinvitedtoparticipateintheHGPinlateof1999.AssemblygeneratedbyUCSCFreezeofsequencedatageneratedbyNCBIClonelayoutsgeneratedByWashingtonUniversityACCTTGGCCTGAATCTAGGCTTTGCATCCCTAGTCCTGATCGsequenceClonemapsWorkingdraftassemblyThe“WorkingDraft”ofthehumangenomeUCSCputthehumangenomesequenceon

thewebJuly7,2000UCSCputthehumangenomesequenceonCDinOctober2000,withvaryingresultsCybergeeksSearchedforhiddenMessages,and“GATTACA”

BigDataChallengesDatatransportationShippingexternalharddisksProcessingthedatawhileitisbeingtransferredFuture?Datawon’tbemoved!SecurityandprivacyIncreasedspaceforstorageCloud-basedcomputingIsthereanyquickwaytomakeuseofbigdata?VisualizethemHowdogeneralscientistsfindgenes?Althoughtheseprojectsprovideplentyofgenomicinformation,thegenomeissolargethatusefulinformationishardtofind.ResearchersatUCSCdecidedtomakeacomputationalmicroscopetohelpscientistssearchthegenomeandvisualizetheinformation.Justasyouwoulduse“google”tofindsomethingontheinternet,researcherscanusethe“UCSCGenomeBrowser”tofindinformationinthehumangenome.TheUCSCGenomeBrowserFeaturesofUCSCGenomeBrowserLargestandupdateddatabaseBroadtypesofgenomicinformationAnnotationsarealignedtogenomeShowmultipleannotationsatatimeGenesearchingbyname/ID/sequenceInteractiveinterfaceSameinterfacefordifferentspecies/genomesFlexiblescalefromsingle-basetowholechromosomeCustomtracks

34121.UCSCGenomeBrowserChoosingorganism,referencegenome,genomicregion,orgene.ViewofageneIntron,directionoftranscriptionIsoforms5’UTRCodingsequenceScalebarGenomiclocationandwidth(bp)ofcurrentviewGenomiclocationinchromosomeClicktomodifytracksettingsandgetextrainformationDatasourceExonGenome3’-UTRViabilityofgraphicdetailsSquishDenseFullSquishPackDenseFlexiblescaleofdisplayThewholechromosome55’-most30nucleotidesofGDNFTracksavailableforhumangenomeSomecommontracksGeneandnearbygene(s)CpGTFBSMicroarrayprobeExpressionPolyASNPHistoneClickthetracktoreadtheirmeaningClickinsometrack,likeUCSCGenes,

youmayfindextradataliketheseCustomtrackCustomtrackuploadWiderangeofdataformatsChoosingthecorrectgenomeUploadlocaldataorbyURL2.BLAT342Besidesgenenamesorlocations,wemayalsosearchagenebyit’sDNA/RNA/proteinsequenceinBLAT.2.BLAST-likealignmenttool(BLAT)ThesequencesearchingfunctionofUCSCgenomebrowserVeryfastersearching(MySQLdatabase)CanhandleintronsinRNA/DNAalignmentsEnteraDNA/proteinsequenceCompareandcontrast,BLASTvsBLATBLAST(BasicLocalAlignmentSearchTool)BLAT

(BLAST-likeAlignmentTool)BasicfunctionBothareforsearchingforaknownDNA/RNA/proteinsequencesimilartoaninputquerysequence.ResultpresentationBothofferdetailsofalignment,matchingscores,ofallmatchedresultsSearchingreliabilityE-value,matchingscoreandpercentage,coverageMatchingscoreandpercentage,coverageSearchprocessingtimeSlowerFasterFlexibilityWiderangeofsimilarities,fromsomewhattohighlysimilarExactmatchornearlyexactmatchonlySearchoptionsMoreLessDirectlinksinsearchresultsLinktoNCBI’spageaboutthegeneorproteinLinktoUCSCGenomeBrowserMultiple-speciessearchingOKJustonespeciesatatimeResultsofBLATsearchResultssortedbyscoreClicktoviewthealignedresultingenomebrowserTryto‘BLAT’thefollowingsequencegtgccgccgccggacgggactttaagatgaagttatgggatgtcgtggctgtctgcctggtgctgctccacaccgcgtccgccttcccgctgcccgccgggcacaggaagatgacttgatgatttaagagaagattgatgacggtcatttcaaatgtagccgagacattcagccaagagcaaatatgccagaggattatctgatcagttcgatgatgtcatggattttattcaagccaccattaaaagactgaaaaggtcaccagataaacaaatggcagtgcttcctagaagagagcggaatcggcaggctgcagctgccaacccagagaattccagaggaaaaggtcggagaggccagaggggcaaaaaccggggttgtgtcttaactgcaatacatttaaatgtcactgacttgggtctgggctatgaaaccaaggaggaactgatttttaggtactgcagcggctcttgcgatgcagctgagacaacgtacgacaaaatattgaaaaacttatccagaaatagaaggctggtgagtgacaaagtagggcaggcatgttgcaga3.TableBrowser34Besidesgenesearching,wemayalsodownloadthedatafromTableBrowserforfurtheranalysis.3.TableBrowserFordownloadingtheinformationofatrackAvailableincommondataformats:Otherthandownloadtolocalcomputer,theinformationcanalsobeoutputtoGalaxyandothertools3fileformatsrecordingthesamegeneGTFchr5hg38_refGenestop_codon37815651378156530-.gene_id"NM_000514";transcript_id"NM_000514";chr5hg38_refGeneCDS37815654378161350-2gene_id"NM_000514";transcript_id"NM_000514";chr5hg38_refGeneexon37812677378161350-.gene_id"NM_000514";transcript_id"NM_000514";chr5hg38_refGeneCDS37834646378347960-0gene_id"NM_000514";transcript_id"NM_000514";chr5hg38_refGenestart_codon37834794378347960-.gene_id"NM_000514";transcript_id"NM_000514";chr5hg38_refGeneexon37834646378348220-.gene_id"NM_000514";transcript_id"NM_000514";chr5hg38_refGeneexon37839507378396800-.gene_id"NM_000514";transcript_id"NM_000514";BEDchr5 37812676 37839680 NM_000514 0 - 37815650 37834796 0 3 3459,177,174, 0,21969,26830,FASTA>NM_000514ccgcctccagcgcgcccttgctgccccgcgcgaccccaggattgcgaactcttgcccctgacctgttgggcggggctccgcgctccagccatcagcccggatgggtctcctggctgggacttggggcacctggagttaatgtccaacctagggtctgcggagacccgatccgaggtgccgccgccggacgggactttaagatgaagttatgggatgtcgtggctgtctgcctggtgctgctccacaccgcgtccgccttcccgctgcccgccggtaagaggcctcccgaggcgcccgccgaagaccgctccctcggccgccgccgcgcgcccttcgcgctgagcagtgactcaaatatgccagaggattatcctgatcagttcgatgatgtcatggattttattcaagccaccattaaaagactgaaaaggtcaccagataaacaaatggcagtgcttcctagaagagagcggaatcggcaggctgcagctgccaaccca…….Howtomakeuseoftheseinformation?Let’suseTableBrowserandGalaxytosolvethefollowingqueriestogether.ListallhumanRefSeqgeneshaveCpGislandinpromoter(3kbupstreamtotranscriptionstartsite).FindouttheexonswithmostSNPinchromosome8.CpGislandpromoterregioni.e.RefSeqGeneAi.e.ExonCExonAExonBSNPs

Howtomakeuseoftheseinformation?Toanswerthetwoqueries,weneedthefollowingdatasets:LocationsofRefSeqgenepromotersandCpGislandsLocationsofexonsofRefSeqgenesandSNPsinchr8First,sendallrelevantgenomicdata

fromTableBrowsertoGalaxyPromotersofRefSeqgenes23456781Step1:SelecthumanRefSeqgenesandfileformatStep2:Selectthepromoters231Step3:Done!2.CpGislands23:MUSTthesamewithothers456781Step1:SelecthumanCpGislandsandfileformatStep3:Done!21Step2:Select‘WholeGene’,whichmeanstheCpGislandsperse3.RefSeqgenesonchr823456781Step1:SelectRefSeqgene,filterforchr810119Step3:Done!21Step2:Select‘Exons’4.SNPinchr823456781Step1:SelectcommonSNPs,filterforchr89Step3:Done!21Step2:Select‘WholeGene’4.Galaxy4GalaxyallowsbiologiststododifferentbioinformaticsanalyseswithUCSCandNGSdata.GalaxyTutorialCommunicationwithotherusersStartGalaxyGalaxy–aweb-basedplatformforbioinformaticsToperformbioinformaticswithoutknowledgeoncomputerprogramingIntegratesmanybioinformaticstoolswithinoneinterfaceDetaileddescriptionandusageavailableforeachtoolToolsforNGSanalysisKeepstrackofallthestepsperformedinananalysisRepeatableanalysisstepsknownasWorkflowsWorkflowsandHistoriescanbesharedamongusersGalaxyplatformHistorypanel–dataateverystepofanalysisFocuspanel–showsoptions,parameters,andcurrentdataToolbarWecanclickandtakealookateachdataDisplayinUCSCgenomebrowserViewdataBasicinfo.SaveacopyRename,changeformat/genome…Nowthedatasetshavebeenimported,let’s