YETIYeast Exploration Tool Integrator

Summary: Yeast Exploration Tool Integrator (YETI) is a novel bioinformatics tool for the integrated visualization and analysis of functional genomic data sets from the budding yeast Saccharomyces cerevisiae. Availability: YETI is freely available for use o

BIOINFORMATICSAPPLICATIONSNOTE

Vol.20no.22004,pages284–285DOI:

10.1093/bioinformatics/btg408

YETI:YeastExplorationToolIntegrator

R.J.Orton1,W.I.Sellers2andD.L.Gerloff1,

1Institute

ofCellandMolecularBiology,UniversityofEdinburgh,Edinburgh,EH93JR,

UKandofHumanSciences,UniversityofLoughborough,Loughborough,LE113TU,UK

2Department

ReceivedonApril30,2003;revisedonJune25,2003;acceptedonJuly4,2003

ABSTRACT

Summary:YeastExplorationToolIntegrator(YETI)isanovelbioinformaticstoolfortheintegratedvisualizationandana-lysisoffunctionalgenomicdatasetsfromthebuddingyeastSaccharomycescerevisiae.

Availability:YETIisfreelyavailableforuseovertheWWW,ordownloadunderlicense,athttp://www.bru.ed.ac.uk/～orton/yeti.html

Contact:orton@bch.ed.ac.uk

ThebuddingyeastSaccharomycescerevisiaeisoneofthemostwidelystudiedeukaryoticorganismsduetoitsvalueasamodelorganisminbiologicalresearch.Itscompletegenomesequenceiswellannotated(Goffeauetal.,1996)andavarietyoflargefunctionalgenomicdatasetsarepubliclyavailable.TheSaccharomycesGenomeDatabase(SGD)(Cherryetal.,1998)containsawealthofgenomicandbiologicalinforma-tion,isregularlyupdatedandmakesalargeamountofitsdatapubliclyavailable.Therearealsoanumberofpubliclyavailableyeasttwo-hybridprotein–proteininteractiondatasetsavailablefromonlinedatabasesandindividualstudies(Mewesetal.,1997;Uetzetal.,2000;Itoetal.,2001).

listsbasedonGeneOntology(GO)annotations(Ashburneretal.,2000).Usersareabletoscrollalongchromosomes,zoominorout,clickongenesofinteresttoviewdatasheetsorselectregionsofinteresttoinvestigatefurther(Fig.1B).

(2)AProteomeSectionfortheeffectivevisualizationof

protein–proteininteractionsasinferredfromyeasttwo-hybridscreens(Fig.1C).Aproteininteractionmapisgeneratedbyinputtingthenameofaproteinofinterest;YETIthendynamicallydisplaysallrelevantinterac-tionsonagraphicalpanel,asinspiredbyMrowka(2001).Someadvancedfeaturesincludereorganizingthemap,interactiondirection,deselecting,expandingout,erscanalsoselectmultipleproteinsorinteractionclusterstoinvestigatefurther.(3)AnAnalysisSectionprovidesuserswithagraphical

interfacetothedatabase(Fig.1D).Oneofthelimita-tionswithonlinedatabasesisthattheprimaryandsometimesonlywayofsearchingisbyenteringasinglenameandthenviewingtheresultsoneatatime.YETIoffersamuchmoredynamicand exiblesearchsystemthatallowsforcomplexquerysearchesandprovidesaninteractivedatatabletocollectivelyviewresults.Allsectionsarecloselyinterlinkedenablinguserstomoveswiftlybetweensectionsandinvestigateallaspectsofanygenesorproteinsofinterest.Furthermoreaccesstotextualinformation,includingGOannotations,isprovidedatanypoint.

YETI

TheYeastExplorationToolIntegrator(YETI)isanovelbioin-formaticstoolfortheintegratedvisualizationandanalysisofS.cerevisiaefunctionalgenomicdatasets.YETIconsistsofaMySQLrelationaldatabaseforthestorageandmanagementofdataandaJavaprogramforvisualizationandanalysis.YETIusespubliclyavailabledatafromtheSGDandindi-vidualstudiestopopulateitsowndatabaseandscriptshavebeenwrittentokeepthedatabaseup-to-date.The rstreleaseofYETIconsistsofthreesections:

(1)AGenomeSectionfortheinformativedisplayofthe

S.cerevisiaechromosomes,knownandpredictedgenesandassociatedannotations.Thissectionallowsuserstoviewthelocationofgroupsofgenesonagenomicschematic(Fig.1A).Thesegroupscanbespeci edbytheusersthemselvesorselectedfromprede ned

To

DISCUSSION

YETIiswrittenintheJavaprogramminglanguageandshouldrunonanyoperatingsystemthathasaccesstoaJava1.4orhighervirtualmachine;ithasbeentestedunderWindows,LinuxandMacOS-X.YETIcanbeusedovertheWWWviaaJavaappletoritcanbedownloaded,underlicense,withtheMySQLdatabaseandinstalledlocally.OneofYETI’sstrengthsisitsuser-friendlinesstowardswet-laboratoryuserswhowilluseYETIasa‘workbench’toexplorethedata.Thisiscombinedwithasoliddatabasestructureenabling

whomcorrespondenceshouldbeaddressed.

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Bioinformatics20(2)©OxfordUniversityPress2004;allrightsreserved.

Summary: Yeast Exploration Tool Integrator (YETI) is a novel bioinformatics tool for the integrated visualization and analysis of functional genomic data sets from the budding yeast Saccharomyces cerevisiae. Availability: YETI is freely available for use o

YETI

Fig.1.YETIscreenshots:(A)genomeschematic;(B)chromosomescrolling;(C)proteininteractionmap;(D)interactivedatatable.

bioinformaticianstocarryoutcollectiveanalysesofthedatasets.Inaddition,twonewsectionsarecurrentlyunderdevel-opment.ATranscriptomeSectionwillprovideameansforeffectivelyvisualizingandanalysingdatafromgeneexpres-sionmicroarraysusingbothclusteringalgorithmsandprin-cipalcomponentanalysisandaCellSectionwillprovideaccesstometabolicpathways.AlthoughYETI’sdesignisspe-ci callyaimedatS.cerevisiae,theframeworkoftheprogramcouldbeappliedtootherorganismswithease.

ACKNOWLEDGEMENTS

WewouldliketothankProf.JeanBeggsandherlaboratoryattheUniversityofEdinburghfortheircontinuedsupportandadvice.R.J.O.issupportedbyaSpecialBioinformaticsStudentshipfromtheMedicalResearchCouncil.

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