From ArrayExpress WarehouseToGene Expression Atlas<br />Ibrahim Emam<br />
ArrayExpress Databases<br />ArrayExpress has three major components:<br />ArrayExpress experiment archive - the main datab...
Components of a Microarray Experiment<br /><ul><li> Sample source
 Sample treatments
 RNA extraction protocol
 Labeling protocol </li></ul>Hybridization protocol<br /><ul><li> 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</li></ul>Experiment<br />Hybridization<br />Sample<br />Array<br />Raw data<br />Normalized data<br />
ArrayExpress Warehouse<br />Gene-centric database<br />Based on BioMart<br />Limitations:<br />Complex infrastructure<br /...
Gene Expression Atlas<br />Dual centric<br />Gene / Condition<br />Provides meta-analytical <br />   summary statistics <b...
AEW          GEAtlas<br />Plots<br />Search results with thumbnails (List view)<br />Gene view<br />Experiment view<br />S...
Plots<br />AEW plots<br />Java generated PNG files (v. slow!)<br />Static<br />In many cases difficult to interpret<br />V...
Plots<br />AEW Thumbnail plots: (E-GEOD-15460)<br />Only part of the plot<br />
Plots<br />AEW Thumbnail plots: (E-GEOD-15460)<br />Full plot!<br />
Plots<br />AEW Thumbnail plots: (E-GEOD-15460)<br />Atlas thumbnails<br />
Plots<br />AEW Experiment plot<br />
Plots<br />AEW Experiment plot<br />
Plots<br />AEW Experiment plot<br />Atlas Experiment plot<br />
Plots<br />AEW Experiment plot<br />Atlas Experiment plot (zoomed in)<br />
AEW search result views<br />Text search results<br />
AEW search result views<br />Experiment thumbnail view<br />
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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

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Gene Expression Atlas user interface

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