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 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. AEWGEAtlas
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 ofyour 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. Thats all folks
thanks