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Gene Expression Atlas user interface


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Ibrahim Emam from the EBI gave a talk to the Interfaces interest group about his work on the new Gene Expression Atlas, which replaces the ArrayExpress Warehouse

Ibrahim Emam from the EBI gave a talk to the Interfaces interest group about his work on the new Gene Expression Atlas, which replaces the ArrayExpress Warehouse

Published in: Design, Technology
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  • 1. From ArrayExpress WarehouseToGene Expression Atlas
    Ibrahim Emam
  • 2. ArrayExpress Databases
    ArrayExpress has three major components:
    ArrayExpress experiment archive - the main database containing complete data supporting publications
    ArrayExpress gene expression profile data warehouse - contains gene-indexed expression profiles from a curated subset of experiments from the archive
    ArrayExpress Atlas of Gene ExpressionNew! – provides meta-analysis based summary statistics over the entire ArrayExpress Data Warehouse, servicing queries for condition-specific gene expression patterns (e.g. genes over-expressed in a particular tissue or disease state)
  • 3. Components of a Microarray Experiment
    • Sample source
    • 4. Sample treatments
    • 5. RNA extraction protocol
    • 6. Labeling protocol
    Hybridization protocol
    • Array design information
    • 7. Location of each element
    • 8. Description of each element
    • 9. Image
    • 10. Scanning protocol
    • 11. Software specifications
    • 12. Quantification matrix
    • 13. Software specifications
    • 14. Control array elements
    • 15. Normalization method
    Raw data
    Normalized data
  • 16. ArrayExpress Warehouse
    Gene-centric database
    Based on BioMart
    Complex infrastructure
    UI not very friendly
    Built without meta-analysis in mind
    Proof of concept
  • 17. Gene Expression Atlas
    Dual centric
    Gene / Condition
    Provides meta-analytical
    summary statistics
    Based on lightweight lucene index
    Conditions (sample annotations)
    Gene expression levels
  • 18. AEW GEAtlas
    Search results with thumbnails (List view)
    Gene view
    Experiment view
    Similarity searches
    Download results
  • 19. Plots
    AEW plots
    Java generated PNG files (v. slow!)
    In many cases difficult to interpret
    Variable in size depending on experiment size
    Atlas plots
    Based on javascript library flot (v. fast!)
    Dynamic images (zoom, display info over plot…)
    Clearer presentation of data
    Fixed size
  • 20. Plots
    AEW Thumbnail plots: (E-GEOD-15460)
    Only part of the plot
  • 21. Plots
    AEW Thumbnail plots: (E-GEOD-15460)
    Full plot!
  • 22. Plots
    AEW Thumbnail plots: (E-GEOD-15460)
    Atlas thumbnails
  • 23. Plots
    AEW Experiment plot
  • 24. Plots
    AEW Experiment plot
  • 25. Plots
    AEW Experiment plot
    Atlas Experiment plot
  • 26. Plots
    AEW Experiment plot
    Atlas Experiment plot (zoomed in)
  • 27. AEW search result views
    Text search results
  • 28. AEW search result views
    Experiment thumbnail view
  • 29. Atlas list view
    Combined experiment thumbnail and text results
  • 30. Download search results
    Keep track of all downloads per session
  • 31. Gene view
    “A one stop shop for all you ever wanted to know about expression of your favorite gene”
  • 32. Gene view expression summary
    Shows all conditions where this gene has been differentially expressed
  • 33. Gene view plots
    To help identify condition-specific gene expression patterns
    Focus on groups of samples
    Focus on differential expression patterns
  • 34. Gene view plots
    Liver samples are clearly showing a potential expression specificity to this gene
  • 35. AEW experiment view
    Plot could expand dramatically you had to scroll left and right looking for any interesting peaks.
    Plot samples and their annotations linked by numbers.
  • 36. Atlas Experiment View
    Keep plot size fixed and compressed with the ability to zoom in/out
    Show top DE genes for this experiment and be able to plot them on spot
    Search for gene(s) of interest to examine their behavior in this experiment
    Search for similar expression patters
    Easily identify sample properties
  • 37. Experiment view
    Three sections: Plot, Genes, Samples
    Sample Attributes selected highlight on plot
    Samples with selected attribute are highlighted on plot
  • 38. Experiment view
    Hovering over a sample will display all its properties
  • 39. Experiment view
    Add/Remove genes to plot
    Add from list of top DE genes or genes with similar expression or your own gene query
    Remove gene by clicking on little cross next to legend
  • 40. That’s all folks