Gene Expression Atlas user interface
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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

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    Gene Expression Atlas user interface Gene Expression Atlas user interface Presentation Transcript

    • From ArrayExpress WarehouseToGene Expression Atlas
      Ibrahim Emam
    • 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)
    • Components of a Microarray Experiment
      • Sample source
      • Sample treatments
      • RNA extraction protocol
      • Labeling protocol
      Hybridization protocol
      • Array design information
      • Location of each element
      • Description of each element
      • Image
      • Scanning protocol
      • Software specifications
      • Quantification matrix
      • Software specifications
      • Control array elements
      • Normalization method
      Experiment
      Hybridization
      Sample
      Array
      Raw data
      Normalized data
    • ArrayExpress Warehouse
      Gene-centric database
      Based on BioMart
      Limitations:
      Complex infrastructure
      UI not very friendly
      Built without meta-analysis in mind
      Proof of concept
    • Gene Expression Atlas
      Dual centric
      Gene / Condition
      Provides meta-analytical
      summary statistics
      (gene-expression-condition)
      Based on lightweight lucene index
      Conditions (sample annotations)
      Genes
      Gene expression levels
    • AEW GEAtlas
      Plots
      Search results with thumbnails (List view)
      Gene view
      Experiment view
      Similarity searches
      Download results
    • Plots
      AEW plots
      Java generated PNG files (v. slow!)
      Static
      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
    • Plots
      AEW Thumbnail plots: (E-GEOD-15460)
      Only part of the plot
    • Plots
      AEW Thumbnail plots: (E-GEOD-15460)
      Full plot!
    • Plots
      AEW Thumbnail plots: (E-GEOD-15460)
      Atlas thumbnails
    • Plots
      AEW Experiment plot
    • Plots
      AEW Experiment plot
    • Plots
      AEW Experiment plot
      Atlas Experiment plot
    • Plots
      AEW Experiment plot
      Atlas Experiment plot (zoomed in)
    • AEW search result views
      Text search results
    • AEW search result views
      Experiment thumbnail view
    • Atlas list view
      Combined experiment thumbnail and text results
    • Download search results
      Keep track of all downloads per session
    • Gene view
      “A one stop shop for all you ever wanted to know about expression of your favorite gene”
    • Gene view expression summary
      Shows all conditions where this gene has been differentially expressed
    • Gene view plots
      Purpose:
      To help identify condition-specific gene expression patterns
      Focus on groups of samples
      Focus on differential expression patterns
    • Gene view plots
      Liver samples are clearly showing a potential expression specificity to this gene
    • 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.
    • 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
    • Experiment view
      Three sections: Plot, Genes, Samples
      Sample Attributes selected highlight on plot
      Samples with selected attribute are highlighted on plot
    • Experiment view
      Hovering over a sample will display all its properties
    • 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
    • That’s all folks
      thanks