From ArrayExpress WarehouseToGene Expression AtlasIbrahim Emam

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)

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 protocolSoftware specifications Quantification matrix Software specifications Control array elements Normalization methodExperimentHybridizationSampleArrayRaw dataNormalized data

Sample source

Sample treatments

RNA extraction protocol

Labeling 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

ArrayExpress WarehouseGene-centric databaseBased on BioMartLimitations:Complex infrastructureUI not very friendlyBuilt without meta-analysis in mindProof of concept

Gene Expression AtlasDual centricGene / ConditionProvides meta-analytical summary statistics (gene-expression-condition)Based on lightweight lucene indexConditions (sample annotations)GenesGene expression levels

AEW GEAtlasPlotsSearch results with thumbnails (List view)Gene viewExperiment viewSimilarity searchesDownload results

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

PlotsAEW Thumbnail plots: (E-GEOD-15460)Only part of the plot

PlotsAEW Thumbnail plots: (E-GEOD-15460)Full plot!

PlotsAEW Thumbnail plots: (E-GEOD-15460)Atlas thumbnails

PlotsAEW Experiment plot

PlotsAEW Experiment plot

PlotsAEW Experiment plotAtlas Experiment plot

PlotsAEW Experiment plotAtlas Experiment plot (zoomed in)

AEW search result viewsText search results

AEW search result viewsExperiment thumbnail view

Atlas list viewCombined experiment thumbnail and text results

Download search resultsKeep 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 summaryShows all conditions where this gene has been differentially expressed

Gene view plotsPurpose:To help identify condition-specific gene expression patternsFocus on groups of samplesFocus on differential expression patterns

Gene view plotsLiver samples are clearly showing a potential expression specificity to this gene

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.

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

Experiment viewThree sections: Plot, Genes, SamplesSample Attributes selected highlight on plotSamples with selected attribute are highlighted on plot

Experiment viewHovering over a sample will display all its properties

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

That’s all folksthanks