REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms 英文参考文献.docVIP

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REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms 英文参考文献.doc

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REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms 英文参考文献

REVIGOSummarizesandVisualizesLongListsofGene OntologyTerms FranSupek1,2*,MatkoBosˇnjak1,NivesSkuncaˇ 1,TomislavSmucˇ 1 1DivisionofElectronics,RudjerBoskovicInstitute,Zagreb,Croatia,2BioinformaticsandGenomicsProgramme,CentreforGenomicRegulation(CRG)andUPF,Barcelona, Spain Abstract Outcomes of high-throughput biological experiments are typically interpreted by statistical testing for enriched gene functional categories defined by the Gene Ontology (GO). The resulting lists of GO terms may be large and highly redundant,andthusdifficulttointerpret.REVIGOisaWebserverthatsummarizeslong,unintelligiblelistsofGOtermsby findingarepresentativesubsetofthetermsusingasimpleclusteringalgorithmthatreliesonsemanticsimilaritymeasures. Furthermore, REVIGO visualizes this non-redundant GO term set in multiple ways to assist in interpretation: multidimensionalscalingandgraph-basedvisualizationsaccuratelyrenderthesubdivisionsandthesemanticrelationships inthedata,whiletreemapsandtagcloudsarealsoofferedasalternativeviews.REVIGOisfreelyavailableathttp://revigo. irb.hr/. Citation: Supek F, Bosˇnjak M, Skuncaˇ N, Smucˇ T (2011) REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms. PLoS ONE 6(7): e21800. doi:10.1371/journal.pone.0021800 Editor:CynthiaGibas,UniversityofNorthCarolinaatCharlotte,UnitedStatesofAmerica ReceivedMarch2,2011;AcceptedJune7,2011;PublishedJuly18,2011 Copyright: ? 2011 Supek et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:Thisworkwassupportedbygrant098-0000000-3168andbyiProject2008-057oftheMinistryofScience,Education,andSportofCroatia.FSwasco- fundedbyMarieCurieActions.Thefundershadnoroleinstudydesign,datacollectionandanalysis,decisiontopublish,orpreparationofthemanuscript. CompetingInterests:Theauthorshavedeclaredthatnocompetinginterestsexist. *E-