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1、AComparativeGenomicMappingResourceforGrainsGrameneisacurated,open-source,Web-accessibledataresourceforcomparativegenomeanalysisinthegrasses.Asaninformationresource,Gramenespurposeistoprovideaddedvaluetodatasetsavailablewithinthepublicsectortofacilitateresearchersabilitytoleveragethericegenomicsequen
2、cetoidentifyandunderstandcorrespondinggenes,pathwaysandphenotypesinthecropgrasses.Thisisachievedbybuildingautomatedandcuratedrelationshipsbetweenriceandothercerealsforbothsequenceandbiology.Extensiveworkoverthepasttwodecadeshasshownremarkablyconsistentconservationofgeneorderwithinlargesegmentsoflink
3、agegroupsinrice,maize,sorghum,barley,wheat,rye,sugarcaneandotheragriculturallyimportantgrasses.Asubstantialbodyofdatasupportsthenotionthatthericegenomeissignificantlycolinearatbothlargeandshortscaleswithothercropgrasses,openingthepossibilityofusingricesyntenyrelationshipstorapidlyisolateandcharacter
4、izehomologuesinmaize,wheat,barleyandsorghum.Gramene ModulesThebestplacetobeginasearchatGrameneisofteninthemoduleofwhatyouwant.Ifyouwantinformationonamarker,lookinthemarkersmodule,ifyouwanttolearnaboutaprotein,gototheproteinsmodule.AnothergoodplacetostartiswiththeQuickSearchonthehomepage,alsofoundatt
5、hetoprightofallotherpages.Eventually,youwillfindthatmostofthemodulesareinterconnected,andyoumaymovebetweenmodulesasyoursearchprogresses.AccessGramenemodulesthroughtheNavigationbar.Thisisthelistofcurrentmodulesavailable.NoteThepresentationofthemodulesisorganizedaccordingtotheirlocationonthenavigation
6、bar.Thisdoesnotindicatethatyoushouldbeginwiththefirstmodulepresented,norendwiththelastone.TogetherthemodulescomplementeachotherbyformingtheGrameneDatabase.Genome browser is a dynamic graphical display used to browse genomes. Use it to: Search for genes and other features identified from the Rice-Jap
7、onica, Maize and Arabidopsis genomes, as well as features from maize, sorghum, barley and wheat that were mapped on the rice genome. View the location of a particular feature on the rice genomeExamine neighboring genes and markers. View the gene model of a candidate gene of interest in order to desi
8、gn primers. Identify the genomic sequence to which a particular gene is mapped. Look for synteny. Compare the position of features from other species with the location of genes in the rice genome, such as sequenced genetic markers, ESTs, cDNAs, CDSs, genes, insertion and repeat elements.Gramene Geno
9、me BrowserAugust2005Link to maps and ontologies from the genome browser.Upload your data to view in a karyotype ideogram.Download genetic information Customize your results specifically for the information you need.Genome BrowserBrowse a Chromosome or View a Synteny MapCustomize options for Contig V
10、iewFeaturesESTsGSSsFSTsArraysMarkersDecorationsExportJump ToWidthIdentifythelocationofaparticulargene,trait,QTLormarker-andthegrassspeciestheyhavebeenmappedto-ongenetic,QTL,physical,sequence,anddeletionmaps.UsetheCMapviewertoexaminetheco-linearityofaparticularregioninonechromosomeorspeciestoanother;
11、orinferwhichlinkagegroupinonespeciesismostconservedwithalinkagegroupinanotherspecies.Determinewhichmapsarethebestformakingcomparisons.Maps and CMapCompare Maps and Customize OptionsThe two images here reflect the same map comparison with different options selected for display.Locateaspecificmarkerba
12、seduponname,typeorspecies.Viewmarkerinformation,includingID,germplasmandgenomepositioning.Getmarker-typespecificinformation.LinktotheMaps,LiteratureandOntologiesDatabases.Markers DatabaseMarker Search MapMarkersMarker NameSynonymsSpeciesMarker TypeGR_TaxOntologiesLiteratureOther DBMapsSearchMarkerID
13、MarkerNameSynonymsMarkerTypeSpeciesGermplasmLibraryDescriptionMappingsCorrespondencesCloneRepeatMotifForwardPrimerReversePrimerAnnealTemperatureExpectedPCRProductSizeRemarksSequenceSourceGenomePositionsDBcross-referencesImagesOntologies SearchOntology AccessionAspect (Ontology)SynonymsDefinitionOnto
14、logyTermAspectDefinitionExternal ReferencesDerivationAnnotationsOntology Term NameObjectObject AccessionObject SymbolObject NameObject SynonymObject SpeciesEvidenceLiterature DBGenomes DBMaps DBProteins DBGenes DBQTL DBMarker DBOntologies MapSearchProtein accessionNames/Symbols/SynonymsOrganism (Cul
15、tivar)Evidence CodesProtein NameSymbolSynonymEC #Gene NameLink to BLASTGen Bank AccessionTrembl AccessionSpecies & CultivarPhenotypeCommentOntology AssociationsReferencesEvidence CodesProtein SimilaritiesProtein FeaturesFASTA sequenceGramene BLAST BrowseOntology DBAssociated ProteinsOntologies DBNCB
16、I, ExPaSy, GRINIRIS, PFam,. PROSITE, ProtomapLiterature DBGenes DBDetailed Information from Proteins DatabaseQTL DatabaseQTL(QuantitativeTraitLoci) areastatisticalcreationthatidentifiesaparticularregionofthegenomeascontainingagene(orgenes)thatisassociatedwiththetraitbeingassayedormeasured.Learnwhich
17、traitisassociatedwithaQTL,findwhereitislocatedonamap,andconstructcomparisonswithothermaps.DeterminewhichmarkersdelimitaQTLDeterminewhatgenesarelocatedinthesameregionasothergenesTrait CategoriesTraits at Gramene are categorized according to:Abiotic stress: Traitsrelatedtostressesfromabioticenvironmen
18、t,e.g.,water,light,temperature,orchemical. Anatomy: Traitsdirectlymeasuringplantpartssuchasroot,stemorleaf. Biochemical: Biochemicalandphysiologicaltraits,e.g.,enzymeactivity.Biotic stress: Traitsrelatedtostressesfrompestsandpathogens. Development: Traitsrelatedtoplantandplantpartdevelopment.Alsoinc
19、ludesmaturityrelatedtraits. Quality: Traitsofeconomicimportancethatmayaffectproductquality. Sterility or fertility: Traitsrelatedtomaleandfemaleflowersterilityorfertility,includingincompatibility.Vigor: Traitsrelatedtogrowthanddormancy. Yield: Traitscontributingdirectlytoyieldbasedoneconomicvalue.Br
20、owse TraitsTrait NameTrait SymbolTO Accession# of QTLSpecies NameTrait NameTrait SynonymsLinkage GroupTrait CategoryTrait symbolPublished SymbolQTL AccessionMap set nameMap PositionQTL AccessionSpeciesPublished SymbolTrait SymbolTrait NameTO AccessionTrait SynonymsTrait CategoryLinkage GroupMap Posi
21、tionGenome PositionCommentsDBX ReferencesQTL SearchMaps DBLiterature DBOntology DBGenomes DB1123QTL Data MapDiversitySearchbyGermplasmPassport DataAccessiondataSynonymsHoldingInstituteStockSourceGermplasmTaxonomydtaCollection DataCollector,LocationExperiment DataTitleDesignPolymorphismtypeScoringPro
22、tocolProducerOriginatorCommentsAlleledataMarker and Allele DataAccession#AccessionnameLocusnameGenotypeAllgenotypesonamarker/germplasmsSearchbyMarkerLiteratureDBMarkersDBExternalgermplasmDBsDiversity Data MapRetrievedescriptionsofallelesassociatedwithmorphological,developmental,andagronomicallyimpor
23、tantphenotypesandvariantsofphysiologicalcharacters,biochemicalfunctionsandisozymes.Getagenesinformation,includinginformationonnameofthegene,genesymbol,relatedphenotypes(traits),images,alleleandgermplasm.LinktoLiteratureandOntologydatabases.Viewassociatedmapsandsequencingdata.Gene & Allele DatabaseCl
24、ickathumbnailtoenlargeimage.Selectdesireddetailedinfofrommenuandclick.Gene Detail Page Gene Data MapGene SymbolGene NameChromosomeSpeciesGene TypeOntology AssociationsSynonymsGene AccessionGene SymbolGene NameSynonymsSpeciesChromosomeGene TypeHas Phenotype?DescriptionPhenotypic imageCurator Comments
25、AlleleGermplasmSequence AssociationMapReferencesAllele AccessionAllele SymbolAllele NameDescriptionAllelic interactionStudyGermplasmGene nameOntology AssociationsStudy NameYearSeasonStudy LocationStudy TypeEnvironmental FactorsAllelesReferences Germplasm AccessionLocationWildtypeMutagenMutagenesis M
26、ethodGeneProteinNucleotide (DNA)Map set nameChromosomePositionsProtein DBMaps DBGenBank (NCBI)Literature DBGenomes DBOntologyDatabaseGene SearchOryzabaseMaizeGDBGene InformationGene SymbolGene NameChromosomeSpeciesGene TypeOntology AssociationsSynonymsGene AccessionGene SymbolGene NameSynonymsSpecie
27、sChromosomeGene TypeHas Phenotype?DescriptionPhenotypic imageCurator CommentsAlleleGermplasmSequence AssociationMapReferencesAllele AccessionAllele SymbolAllele NameDescriptionAllelic interactionStudyGermplasmGene nameOntology AssociationsStudy NameYearSeasonStudy LocationStudy TypeEnvironmental Fac
28、torsAllelesReferences Germplasm AccessionLocationWildtypeMutagenMutagenesis MethodGeneProteinNucleotide (DNA)Map set nameChromosomePositionsProtein DBMaps DBGenBank (NCBI)Literature DBGenomes DBOntologyDatabaseGene SearchOryzabaseMaizeGDBProteins DatabaseProvidescollectiveinformationonproteinsfromgr
29、asses(familyPoaceae/Gramineae), andareannotatedaccordingtoGeneOntologyandPlantOntology.GeneOntology(GO)Molecularfunctionofthegeneproduct.Biologicalprocessinwhichthegeneproductisinvolved.Cellularcomponentwherethegeneproductislocalized.PlantOntologyPlantstructurewherethegeneisexpressed(PO)Plantgrowths
30、tageatwhichthegeneisexpressed(GRO)* Only rice (Oryza) protein entries are manually curated.FindaproteinandconductaBLASTqueryonit.Determinethemolecularfunction,biologicalprocessorcellularlocationofaparticularriceprotein.Findproteinsequenceinformationandorthologsfromotherspecies.Findwhichproteinsareme
31、mbersofaproteinfamily(Pfam&PROSITE).Linktoontologyandliteraturedatabases.ProteinsGeneral Protein InfoA textual description of the proteinProtein Detail Page: General InformationCross references to GenBank and SWISSPROT protein entries.Selectinformationofinteresttoyou.SearchProtein accessionNames/Sym
32、bols/SynonymsOrganism (Cultivar)Evidence CodesProtein NameSymbolSynonymEC #Gene NameLink to BLASTGen Bank AccessionTrembl AccessionSpecies & CultivarPhenotypeCommentOntology AssociationsReferencesEvidence CodesProtein SimilaritiesProtein FeaturesFASTA sequenceGramene BLAST BrowseOntology DBAssociate
33、d ProteinsOntologies DBNCBI, ExPaSy, GRINIRIS, PFam,. PROSITE, ProtomapLiterature DBGenes DBProteins Data MapThisdatabaseisacollectiveresourceofstructuredcontrolledvocabularies(Ontologies)forknowledgedomainsandtheirassociations.PlantOntology(PO)PlantStructure(morphology,organs,tissueandcelltypes)*Gr
34、owthstages(plantgrowthanddevelopmentalstages)(GRO)TraitOntology(TO)PlanttraitsandphenotypesGeneOntology(GO)MolecularfunctionBiologicalprocessCellularcomponentEnvironmentOntology(EO)Gramenestaxonomyontology(GR_tax)Associations:FindEnsemblricegenes(fromTIGRsricegenomeassembly),proteinsfromSWISSPROT-Tr
35、EMBLrepresentingPoaceae(grass)family,ricegenes,QTLandmapsets.OntologiesNote: Remember that different ontologies are for different purposes and do not overlap with each other. For more information on each ontology type please visit the current ontologies section at Gramene OntologiesUsingontologieswi
36、llassistusersintheirsearches.AnOntologyisaglossaryofkeywordsarrangedinastructuredorder/networkbasedonthebiologicalconceptthatdescribesthekeywordsrelationshipinanontologytree.Researchersareworkingtowardsastandardizedontology,thusfacilitatingsearchingindifferentdatabases.The lineage of alpha-amylase a
37、ctivity as a molecular functionTerm-term relationshipi: IS A (type of)Number of database objects associated in the database with this term. Exact ontology termDefinition of the termOntology Term Accession DetailOntologies SearchOntology AccessionAspect (Ontology)SynonymsDefinitionOntologyTermAspectD
38、efinitionExternal ReferencesDerivationAnnotationsOntology Term NameObjectObject AccessionObject SymbolObject NameObject SynonymObject SpeciesEvidenceLiterature DBGenomes DBMaps DBProteins DBGenes DBQTL DBMarker DBOntologies Data MapPathways (RiceCyc)RiceCycallowsbiochemicalpathwaystobeanalyzedandvis
39、ualized.ThistutorialhasbeendevelopedforfirsttimeandcasualusersofRiceCyc.ToaccessamoredetailedoverviewoftheprogramsfeaturesandthedatacontainedwithinpleaserefertothePathwayslinksavailablefromthePathwayshomepage.FormoreinformationonPathwaystools,seehere.RiceCyc allows biochemical pathways to be analyze
40、dandvisualized.GramenehasincorporatedthelatestTIGR4genomeintothis release to create an Oryza sativa specific pathwaydataset.Dataisunderdevelopmentandsubjecttochange.IfyoudoseeanyerrorsinthedatasetpleasefeelfreetocontactusthroughthefeedbackprovidedatthetopofGramenewebpages.IntroductionTheflowofthepat
41、hwayisfromthetopofthepagetothebottomBiosyntheticpathwaysTCACycleCatabolicOrphanMetabolic Map Overview Level4Pathway DetailLevel5Movebetweenlevelswith“moredetail”and“lessdetail”buttons.LiteraturesearchesareagoodoptionforbeginningyourGramenesearch.Searchforcitationsonrice,aswellasotherspecies.Literatu
42、researchresultsprovidelinkstopublicationsourcesandotherGramenedatabaseswhereavailable.LiteratureLiteratureFindarticlesaboutgenes,proteins,QTL,markers,orontology.Linktomapsdescribedinthegivencitations,aswellasthegene,QTL,proteinandmarkerdatabases.Literature DetailClickheretolinktocross-referenced res
43、ources.GramenesIDfor that referenceLiterature Data MapLiteratureRice Genetics NewsletterAuthorPublicationTitleAbstractReference IDCross ReferencesAssociated DataSource WebsiteQTLGenesMarkersProteinsMapsBLASTBLASTisatool.SearchforsequencesimilaritymatchesintheGramenedatabase.Selectthebesttargetdataba
44、seforyoursearch.Choosethebestalgorithmforyoursearch.Fine-tunesearchparameters.Displaymatchresults.August2005BLAST Data MapBLASTticket IDHigh Scoring PairsLocations vs. KaryotypeLocations vs QueryChromosomeStartStopCloneAlignmentSequenceGenomic SequenceContigviewRaw ScorePercent IDLengthP-valueE-valu
45、eGenome BrowserGrameneMartBatchDataSequenceRetrievalSelectaGramenedatasettosearchagainst.Addfilterstothedatasettoincreaseitsspecificity.Choosethefieldstoincludeinthereport.Generateabatchreportinaformatthatcanbeimportedintolocaltools,suchasExcel.GrameneMartisbaseduponBiomart.Martisparticularlysuitedforprovidingthedatamininglikesearchesofcomplexdescriptive(e.g.biological)data,andisoptimizedforlargedatabases,suchasgenomicsequenceormicroarrayexperiments.BioMartsoftwareiscompletelyOpenSource,licensedundertheLGPL,andfreelyavailabletoanyonewithoutrestrictions
