Gene Expression Atlas user interface

From ArrayExpress WarehouseToGene Expression Atlas
Ibrahim Emam

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)

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 protocol
Software specifications
Quantification matrix
Software specifications
Control array elements
Normalization method
Experiment
Hybridization
Sample
Array
Raw data
Normalized data

ArrayExpress Warehouse
Gene-centric database
Based on BioMart
Limitations:
Complex infrastructure
UI not very friendly
Built without meta-analysis in mind
Proof of concept

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

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

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

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

Plots
Full plot!

Plots
Atlas thumbnails

Plots
AEW Experiment plot

Plots
AEW Experiment plot
Atlas Experiment plot

Plots
AEW Experiment plot
Atlas Experiment plot (zoomed in)

AEW search result views
Text search results

AEW search result views
Experiment thumbnail view

Atlas list view
Combined experiment thumbnail and text results

Download search results
Keep 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 summary
Shows all conditions where this gene has been differentially expressed

Gene view plots
Purpose:
To help identify condition-specific gene expression patterns
Focus on groups of samples
Focus on differential expression patterns

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

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.

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

Experiment view
Three sections: Plot, Genes, Samples
Sample Attributes selected highlight on plot
Samples with selected attribute are highlighted on plot

Experiment view
Hovering over a sample will display all its properties

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

That’s all folks
thanks

Gene Expression Atlas user interface

by Francis Rowland

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