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

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)

4. Sample treatments

5. RNA extraction protocol

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 methodExperiment Hybridization Sample Array Raw data Normalized data

16. ArrayExpress Warehouse Gene-centric database Based on BioMart Limitations: 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 (gene-expression-condition) Based on lightweight lucene index Conditions (sample annotations) Genes Gene expression levels

18. AEW GEAtlas Plots Search results with thumbnails (List view) Gene view Experiment view Similarity searches Download results

19. 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

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 Purpose: 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 thanks