GEOGeneExpressionOmnibus：GEO基因表达数据库课件

1、Gene Expression Omnibus (GEO) /第1页，共24页。Microarrays in gene expressionA typical gene expression analysis experiment:Differential systems e.g. cancer vs. normal, drug vs. no drugChoose/prepare the microarrayExtract total mRNA (transcriptome)Reverse transcription/dye labeling Combine equal amountsHybr

2、idizeScanANALYSE AND INTERPRET THE RESULTS this is the tricky part第2页，共24页。Gene Expression Omnibus (GEO): Gene Expression and Molecular Abundance Data RepositoryRelated samples and seriesThis brings up an Entrez GEO DataSets results formPlatform Accession PageA typical gene expression analysis exper

3、iment:GEO ArchitectureQuerying GEO DataSetsGEO Links in PubMed Search ResultsSample details:Curated, online resource for gene expression data browsing, query, analysis and retrieval.Design summaryGEO DataSet RecordGrouping ofMicroarrays in gene expression第3页，共24页。SPOTS第4页，共24页。Hybridization第5页，共24页。

4、SCAN第6页，共24页。A public repository for the archiving and distribution of gene expression data submitted by the scientific community.Curated, online resource for gene expression data browsing, query, analysis and retrieval. Convenient for deposition of gene expression data, as required by funding agenc

5、ies and journals.Gene Expression Omnibus (GEO): Gene Expression and Molecular Abundance Data Repository第7页，共24页。GEO ArchitecturePlatform (GPL) = the technology used and the features detected.Sample (GSM) = preparation and description of the sample.Series (GSE) defines a set of samples and how they a

6、re related.DataSets (GDS) sample data collections assembled by GEO staff.GEO has four kinds of data records第8页，共24页。GPLPlatformdescriptionsGSMRaw/processedspot intensitiesfrom a singleslide/chipGSEGrouping ofslide/chip data“a single experiment”GDSGrouping ofexperimentsCurated byNCBISubmitted byExper

7、imentalistsSubmitted byManufacturerGEO Architecture第9页，共24页。GEO Home PageSimple interface to: show status find documentation query data browse data 第10页，共24页。Platform Accession Page Platform details:DescriptionTypeOrganismManufacturerRelated samples and seriesNOTE THE TOP BAR (SCOPE)第11页，共24页。Sample

8、 Accession PageSample details:DescriptionTypeOrganismSourceRelated platforms and series第12页，共24页。Sample File Data TableData table field descriptionsTruncated data table from Quick viewTotal data rows and file size 第13页，共24页。Series Accession PageBiological sample summaryDesign summaryPublication info

9、rmationRelated platforms and samples第14页，共24页。DATASET or GENE PROFILE searchGEO data can be queried as: Datasets: experiment-centric view using Entrez GEO DataSets Gene profiles: gene-centric view using Entrez GEO ProfilesSelecting either takes you to a similar Entrez introduction page第15页，共24页。Quer

10、ying GEO DataSetsStart a GEO DataSets search with the QueryDataSets text boxThis brings up an Entrez GEO DataSets results form第16页，共24页。DataSet Search Results第17页，共24页。GEO DataSet Record第18页，共24页。GENE PROFILE search第19页，共24页。GEO Gene Profiles第20页，共24页。GEO Gene Profiles第21页，共24页。GENE PROFILE searchDa

11、tasets: experiment-centric view using Entrez GEO DataSetsSubmitted byANALYSE AND INTERPRET THE RESULTS this is the tricky partGEO Links in PubMed Search ResultsExtract total mRNA (transcriptome)Series Accession PageRelated samples and seriesPlatform Accession Pagecancer vs.Querying GEO DataSetsGroup

12、ing ofA public repository for the archiving and distribution of gene expression data submitted by the scientific community.GEO has four kinds of data records“a single experiment”GEO ArchitectureQuerying GEO with IDs from Papers A common way to access GEO data is through accessions from papers.Online journals include hyperlinks to the GEO accession page.Or, at the GEO home page enter the accession into the QueryGEO accession text box第22页，共24页。GEO