Gene Expression Atlas user interface
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The document describes the ArrayExpress database, detailing its three main components: the experiment archive, the gene expression profile data warehouse, and the new atlas of gene expression, which offers meta-analysis statistics. It discusses the complex infrastructure and usability limitations while highlighting features such as condition-specific gene expression patterns and various visualization methods for data presentation and exploration. Overall, it emphasizes the goal of facilitating access to gene expression data and enhancing user experience in identifying differential expression patterns.
Gene Expression Atlas user interface
- 1. From ArrayExpress WarehouseToGene Expression AtlasIbrahim Emam
- 2. ArrayExpress DatabasesArrayExpress 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
- 5. RNA extraction protocol
- 6. Labeling protocol Hybridization protocol Array design information
- 7. Location of each element
- 8. Description of each element
- 9. Image
- 14. Control array elements
- 15. Normalization methodExperimentHybridizationSampleArrayRaw dataNormalized data
- 16. ArrayExpress WarehouseGene-centric databaseBased on BioMartLimitations:Complex infrastructureUI not very friendlyBuilt without meta-analysis in mindProof of concept
- 17. Gene Expression AtlasDual centricGene / ConditionProvides meta-analytical summary statistics (gene-expression-condition)Based on lightweight lucene indexConditions (sample annotations)GenesGene expression levels
- 18. AEW GEAtlasPlotsSearch results with thumbnails (List view)Gene viewExperiment viewSimilarity searchesDownload results
- 19. PlotsAEW plotsJava generated PNG files (v. slow!)StaticIn many cases difficult to interpretVariable in size depending on experiment size Atlas plotsBased on javascript library flot (v. fast!)Dynamic images (zoom, display info over plot…)Clearer presentation of dataFixed size
- 20. PlotsAEW Thumbnail plots: (E-GEOD-15460)Only part of the plot
- 21. PlotsAEW Thumbnail plots: (E-GEOD-15460)Full plot!
- 22. PlotsAEW Thumbnail plots: (E-GEOD-15460)Atlas thumbnails
- 25. PlotsAEW Experiment plotAtlas Experiment plot
- 26. PlotsAEW Experiment plotAtlas Experiment plot (zoomed in)
- 27. AEW search result viewsText search results
- 28. AEW search result viewsExperiment thumbnail view
- 29. Atlas list viewCombined experiment thumbnail and text results
- 30. Download search resultsKeep 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 summaryShows all conditions where this gene has been differentially expressed
- 33. Gene view plotsPurpose:To help identify condition-specific gene expression patternsFocus on groups of samplesFocus on differential expression patterns
- 34. Gene view plotsLiver samples are clearly showing a potential expression specificity to this gene
- 35. AEW experiment viewPlot 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 ViewKeep plot size fixed and compressed with the ability to zoom in/outShow top DE genes for this experiment and be able to plot them on spotSearch for gene(s) of interest to examine their behavior in this experimentSearch for similar expression pattersEasily identify sample properties
- 37. Experiment viewThree sections: Plot, Genes, SamplesSample Attributes selected highlight on plotSamples with selected attribute are highlighted on plot
- 38. Experiment viewHovering over a sample will display all its properties
- 39. Experiment viewAdd/Remove genes to plotAdd from list of top DE genes or genes with similar expression or your own gene queryRemove gene by clicking on little cross next to legend