Regulatory Pathway Analysis by High-Throughput In Situ Hybridization 英文参考文献.docVIP

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Regulatory Pathway Analysis by High-Throughput In Situ Hybridization 英文参考文献.doc

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Regulatory Pathway Analysis by High-Throughput In Situ Hybridization 英文参考文献

RegulatoryPathwayAnalysis byHigh-ThroughputInSituHybridization Axel Visel1,2,James Carson3,Judit Oldekamp1,Marei Warnecke1,Vladimira Jakubcakova1,Xunlei Zhou1,Chad A.Shaw4, Gonzalo Alvarez-Bolado1,Gregor Eichele1* 1DepartmentofGenesandBehavior,MaxPlanckInstituteofBiophysicalChemistry,Goettingen,Germany,2GenomicsDivision,LawrenceBerkeleyNationalLaboratory, Berkeley,California,UnitedStatesofAmerica,3BiologicalMonitoringandModelingDepartment,PacificNorthwestNationalLaboratory,Richland,Washington,UnitedStates ofAmerica,4DepartmentofMolecularandHumanGenetics,BaylorCollegeofMedicine,Houston,Texas,UnitedStatesofAmerica Automated in situ hybridization enables the construction of comprehensive atlases of gene expression patterns in mammals. Such atlases can become Web-searchable digital expression maps of individual genes and thus offer an entrywaytoelucidategeneticinteractionsandsignalingpathways.Towardsthisend,anatlashousing;1,000spatial geneexpressionpatternsofthemidgestationmouseembryowasgenerated.Patternsweretextuallyannotatedusing a controlled vocabulary comprising .90 anatomical features. Hierarchical clustering of annotations was carried out using distance scores calculated from the similarity between pairs of patterns across all anatomical structures. This processorderedhundredsofcomplexexpressionpatternsintoamatrixthatreflectstheembryonicarchitectureand therelatednessofpatternsofexpression.Clusteringyielded12distinctgroupsofexpressionpatterns.Becauseofthe similarityofexpressionpatternswithinagroup,membersofeachgroupmaybecomponentsofregulatorycascades. WefocusedonthegroupcontainingPax6,anevolutionaryconservedtranscriptionalmastermediatorofdevelopment. Seventeenofthe82genesinthisgroupshowedachangeofexpressioninthedevelopingneocortexofPax6-deficient embryos.ElectromobilityshiftassayswereusedtotestforthepresenceofPax6-paireddomainbindingsites.Thisled totheidentificationof12genesnotpreviouslyknownaspotentialtargetsofPax6regulation.Thesefindingssuggest that cluster a