GEOGeneExpressionOmnibus：GEO基因表達數(shù)據(jù)庫課件

1、Gene Expression Omnibus (GEO) /第1頁，共24頁。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頁，共24頁。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頁，共24頁。SPOTS第4頁，共24頁。Hybridization第5頁，共24頁。

4、SCAN第6頁，共24頁。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頁，共24頁。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頁，共24頁。GPLPlatformdescriptionsGSMRaw/processedspot intensitiesfrom a singleslide/chipGSEGrouping ofslide/chip data“a single experiment”GDSGrouping ofexperimentsCurated byNCBISubmitted byExper

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

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

9、rmationRelated platforms and samples第14頁，共24頁。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頁，共24頁。Quer

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