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ArrayExpress and Atlas practical: querying and exporting gene
expression data at the EBI
This practical will introduce you to the database data content and query functionality of ArrayExpress
Archive and Atlas. We suggest using Firefox for this tutorial.
Exercise 1: Searching experiments, understanding experiment display and data download
1.
Go to http://www.ebi.ac.uk/arrayexpress/
2.
In the ‘Experiments’ box, on the left-hand side of the page, query for ‘ataxia’. How many
experiments are retrieved?
3.
Click on the + sign to the left of E-MEXP-886 to expand the experiment view and answer
the following questions
4.
How many assays does the experiment have? What type of data is available for download? Is
the experiment available in the Atlas of Gene Expression?
5.
Which experimental factor was investigated in this experiment? Which are its values?
6.
How many biological replicates there are for each experimental factor value? View the
SDRF file to answer this question.
7.
Finally, what array platform was used for this experiment?
Exercise 2: Querying the Atlas of Gene Expression – Single gene query
1.
Open http://www.ebi.ac.uk/gxa/
2.
In the ‘genes’ box type mat1a (use suggestion: Mat1a ENSMUSG00000037798 Mus
musculus). Leave all other fields as default and search the Atlas.
3.
In which condition (or EF) is mat1a mostly up-regulated? In which condition (or EF) is
mat1a mostly down-regulated?
4.
In how many experiments was mat1a observed up-regulated, in liver? Can you find out more
information about these experiments? In which experiment is mat1a up-regulation
statistically more significant?
5.
What other genes have a similar expression profile to mat1a in experiment E-GEOD-4262?
Exercise 3: Querying the Atlas of Gene Expression
1.
Open http://www.ebi.ac.uk/gxa/
2.
In the ‘genes’ box type neuropeptide signalling pathway (use suggestion: ‘goterm:
neuropeptide signalling pathway’).
3.
Select Organism ‘Mus musculus’
4.
In the ‘conditions’ box type brain (use suggestion ‘brain EFO_0000302’) and search the
Atlas
5.
How many genes, matching all these criteria, are retrieved? How many of the genes retrieved
carry a ‘GPS protein’ domain?
Answers
Exercise 1: Searching experiments, understanding experiment display and data download
1.
How many experiments are retrieved? 20 experiments, 545 assays
2.
How many assays does the experiment E-MEXP-886 have? 10 hybridizations
1
What type of data is available for download? Raw and processed data are available
Is the experiment available in the Atlas of Gene Expression? Yes
3.
Which experimental factor was investigated in this experiment? Genotype
Which are its values? ataxin 1 -/-, wild_type
4.
How many biological replicates there are for each experimental factor value? 5 replicas for
genotype ataxin 1 -/-, 5 replicas for genotype wild_type. The ‘Sample and Data
Relationship’ file can also help you to find this out.
5.
What array platform was used for this experiment? Affymetrix GeneChip Mouse
Expression Array MOE430A
Exercise 2: Querying the Atlas of Gene Expression – Single gene query
1.
In which condition is mat1a mostly up-regulated? Liver
In which condition is mat1a mostly down-regulated? Kidney
2.
In how many experiments was mat1a observed up-regulated, in liver? 12 experiments
Can you find out more information about these experiments? Yes; by clicking anywhere on
the row corresponding to condition liver, you will display information about the
selected
12 experiments only, on the right hand side of the gene summary page
In which experiment is mat1a up-regulation statistically more significant? E-GEOD-4262;
experiments are ranked by p-value
3.
What other genes have a similar expression profile to mat1a in experiment E-GEOD-4262?
To answer this question, go to the experiment page and run a similarity search. The
similarity search returned Pah, Cyp4a10, Fgb and Ugt2b1
Exercise 3: Querying the Atlas of Gene Expression
1.
How many genes, matching all these criteria, are retrieved? 70 genes
2.
How many of the genes retrieved carry a GPS protein domain? 27 genes; you can find this
out by utilizing the ‘refine your query’ option and select the ‘GPS domain’ from the
list of enriched InterPro terms
2