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Gene Expression Omnibus (GEO)

Gene Expression Omnibus (GEO) . http://www.ncbi.nlm.nih.gov/geo /. teachline.ls.huji.ac.il/72351/2008/talks/GEO%202008. ppt. Microarray in general. SPOTS. Hybridization. SCAN. G ene E xpression O mnibus (GEO): Gene Expression and Molecular Abundance Data Repository.

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Gene Expression Omnibus (GEO)

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  1. Gene Expression Omnibus (GEO) http://www.ncbi.nlm.nih.gov/geo/ teachline.ls.huji.ac.il/72351/2008/talks/GEO%202008.ppt

  2. Microarray in general

  3. SPOTS

  4. Hybridization

  5. SCAN

  6. GeneExpressionOmnibus(GEO): Gene Expression and Molecular Abundance Data Repository • A public repository for the archiving and distribution of gene expression data submitted by the scientific community. • MIAME compliant data. • Minimum Information About a Microarray Experiment http://www.mged.org/Workgroups/MIAME/miame.html • Convenient for deposition of gene expression data, as required by funding agencies and journals. • Curated, online resource for gene expression data browsing, query, analysis and retrieval.

  7. GEO Architecture GEO has four kinds of data records • Platform (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 are related. • DataSets (GDS) sample data collections assembled by GEO staff. • Submitters may provide raw data • Original microarray scans • Raw quantification data

  8. GEO Architecture Submitted by Experimentalists Curated by NCBI Submitted by Manufacturer* GDS Grouping of experiments GSE Grouping of slide/chip data “a single experiment” GPL Platform descriptions GSM Raw/processed spot intensities from a single slide/chip

  9. GEO Home Page • Simple interface to: • show status • find documentation • query data • browse data • submit data

  10. Basic Search: Repository Browser Selecting the total public data or Repository Browser links on the GEO home page, takes you to the Repository Browser, listing: • number of each type of submitted file, both public and unreleased • the total number of each technology type under Platforms • the total number of each Sample type

  11. Basic Search: Browse Platforms • All 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 manufacturer.

  12. Basic Search: Browse Platforms The table can be sorted on any field except organism by clicking on the header. Specific platform files can be found using the ‘Find Platform’ option. Accession:GEO ID Title: brief description of platform Samples: number of samples in GEO associated with platform ID Contact: submitter Technology: platform type Release date: when file is publicly accessible

  13. Basic Search: Find Platforms • Select ‘Find Platform’ • Select company • Select distribution • Select species • Enter title keyword

  14. Basic Search: Find Platforms (continued) • Start the platform search • Select the accession for the U133 plus 2.0 array • Scroll down to find data table information

  15. Data Retrieval: Browse Series • Data is submitted to GEO as a Series, which represents the experiment design. • Selecting Browse>Series brings up a list sorted by release date. • Selecting a Series ID brings up the Series file summary.

  16. Data Retrieval: Series Accession Page

  17. GEO Accession Results Display Options All GEO accession results pages have the same header that allows different views and formats for the data to be displayed • Scope controls what information is displayed: • Self • Platform, Samples or Series • Family • Format controls how information is displayed: • HTML • SOFT (Simple Omnibus Format in Text) • MINiML (MIAME Notation in Markup Language) • Amount controls how much information is displayed: • Brief Quick • Full Data

  18. Data Retrieval: Series Accession Page Biological sample summary Design summary Publication information Platform (total) Samples (total)

  19. Data Retrieval: Sample File Summary Sample preparation Hybridization and data processing Platform Series

  20. Data Retrieval: Sample File Data Table Data table field descriptions Truncated data table from Quick view Total data rows and file size Supplementary raw data file

  21. Querying 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 Query>GEO accession text box

  22. GEO Links in PubMed Search Results • One option for displaying PubMed search results is GEO DataSet links. • When present, the results page is actually from Entrez GEO DataSets.

  23. Advanced Searches GEO data can be queried as: • Datasets: experiment-centric view using Entrez GEO DataSets • Gene profiles: gene-centric view using Entrez GEO Profiles Selecting either takes you to a similar Entrez introduction page

  24. Querying GEO DataSets • Start a GEO DataSets search with the Query>DataSets text box • This brings up an Entrez GEO DataSets results form Total results Number of DataSets Number of Platforms Number of Series

  25. DataSet Search Result DataSet ID Description Platform Reference Series Supplementary files Number of Samples and truncated list Cluster image Select the DataSet ID or click on the cluster image to go to the DataSet record.

  26. GEO DataSet Record Experiment design and DataSet information. Sample and analysis information. Data retrieval. Selecting analysis takes you to the data clustering interface. Selecting the cluster image takes you to the clustering page

  27. GEO Gene Profiles GEO DataSet ID Platform ID, Platform Feature ID Gene description Target sequence accession Expression profile • GEO Gene Profiles use gene IDs from Platform files to show the expression of a gene across DataSets. • Entering a gene ID into the Query>Gene profiles text box takes you to the Entrez results page.

  28. GEO BLAST • On the GEO BLAST page enter sequences in fasta format, GenBank accessions or select sequence files on local disks for blastn comparisons. • These are compared to GenBank sequences listed in Platform files associated with GEO DataSets • From the Blast result page select the ‘E’ option to the right of an alignment to show GEO Gene Profiles for that sequence in GEO DataSets E button

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