醫(yī)學數(shù)據(jù)挖掘 Gene Expression Omnibus

1、Gene Expression Omnibus (GEO) A public repository for the archiving and distribution of gene expression data submitted by the scientific community.MIAME compliant data. （邁阿密協(xié)議）Minimum Information About a Microarray Experiment /Workgroups/MIAME/miame.htmlConvenient for deposition of gene expression d

2、ata, as required by funding agencies and journals.Curated, online resource for gene expression data browsing, query, analysis and retrieval. Gene Expression Omnibus (GEO): Gene Expression and Molecular Abundance Data RepositoryhomepageGEO ArchitecturePlatform (GPL) = the technology used and the feat

3、ures detected.Sample (GSM) = preparation and description of the sample.Series (GSE) defines a set of samples and how they are related.DataSets (GDS) sample data collections assembled by GEO staff.GEO has four kinds of data recordsSubmitters may provide raw dataOriginal microarray scansRaw quantifica

4、tion dataGPLPlatformdescriptionsGSMRaw/processedspot intensitiesfrom a singleslide/chipGSEGrouping ofslide/chip data“a single experiment”GDSGrouping ofexperimentsCurated byNCBISubmitted byExperimentalistsSubmitted byManufacturer*GEO Architectureshow statusfind documentationquery dataBasic Search: Br

5、owse PlatformsAll GEO submissions need to be associated with a platform file. These describe the features on a given platform, required to understand the data.A platform file must be submitted if one is not already present in GEO.Commercial array platform files are submitted to GEO by the manufactur

6、er.Basic Search: Browse PlatformsAccession:GEO IDTitle:brief description of platformContact:submitterdata in GEO associated with platform IDTechnology:platform typeRelease date:when file is publicly accessibleThe table can be sorted on any field except organism by clicking on the header.Specific pla

7、tform files can be found using the Find Platform anismSelect Find PlatformSelect companySelect distributionSelect speciesEnter title keywordData Retrieval: Browse SeriesData is submitted to GEO as a Series, which represents the experiment design.Selecting a Series ID brings up the Series f

8、ile summary.Data Retrieval: Series Accession PageGEO Accession Results Display OptionsScope controls what information is displayed:SelfPlatform, Samples or SeriesFamilyFormat controls how information is displayed:HTMLSOFT (Simple Omnibus Format in Text)MINiML (MIAME Notation in Markup Language)Amoun

9、t controls how much information is displayed:BriefQuickFullDataAll GEO accession results pages have the same header that allows different views and formats for the data to be displayedData Retrieval: Series Accession PageBiological sample summaryDesign summaryPublication informationPlatform (total)S

10、amples (total)Data Retrieval: Sample File SummarySample preparationHybridization and data processingPlatform Series Data Retrieval: Sample File Data TableData table field descriptionsTruncated data table from Quick viewTotal data rows and file size Supplementary raw data file Querying GEO with IDs from Papers A common way to access GEO data is through accessions from papers.O