Understanding ArrayExpress archive browse results
1. Information displayed about each experiment
1.1 Table of results
Searches for experiments in the ArrayExpress archive will produce a table of experiments matching the searched terms e.g. cancer and human. For help on searches see the query help page.
1.1.1 Search term matches
- Matches to exact terms (e.g. 'cancer', 'human') are highlighted in yellow.
- Matches to synonyms are highlighted in green. E.g. 'Homo sapiens' is a synonym for 'human'.
- Matches to child terms in the Experimental Factor Ontology are highlighted in pink. E.g. osteosarcoma is a child term of cancer
There is a mouse-over for highlighted terms to tell you which type of matched term it is.
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1.1.2 Table column headings
- ID - the unique ArrayExpress accession number of the experiment.
- Title - the curated title for the experiment
- Assays - the total number of assays (hybridizations) in the experiment
- Species - the species of the samples used (can be multiple)
- Date - the date that the data were loaded into ArrayExpress
- Processed - direct link to the processed data as a zip file (icon indicates that this exists)
- Raw - a direct link to the raw data (icon indicates that this exists). An angled icon indicates Affymetrix .CEL files
- Atlas - a tick if the experiment is in the ArrayExpress Atlas of gene expression
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1.1 Sorting and filtering results
Results can be sorted by clicking on column titles. Results can be further filtered by sample species, array design used, molecule type (DNA, RNA, metabolite, protein) or technology (array, high-throughput sequencing, mass spectrometry) . Select the filter term and then press the ''Query' button.
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1.2 Starting a new search
To start a new search, enter a new term in the search box in the top left hand corner and click on the 'Query' button
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2. Getting more details about experiments
Click on the '+' icon in the left hand column to expand the view of the experiment and see where the term you searched for appears. Click on the icon again to hide the detailed information. To show detailed information about all the experiments in your search result check the ''detailed view' box in the top right hand corner of the page.
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2.1 Information provided in the detailed view
- Title - curated title of the experiment
- Description - a description of the experiment supplied by the submitter
- MIAME score - this is a score to indicate how close to full MIAME-compliance an experiment is, with a score of 5 being the highest. One point each is given for
- sufficient annotation of the associated array design
- essential laboratory and data processing protocols
- essential sample annotation including at least one experimental factor and the species of all samples
- final processed (normalized) data for the hybridizations in the experiment
- raw data files for each hybridization
- Contact - the name and email address of the submitter
- Citations - details about any publications that relate to the data, including links to the online article and to the PubMed entry where available
- Links to
- Files - this section provides links to
- data archives - the raw and processed data files in zip archives - see file downloads help page for more information
- the MAGE-TAB investigation description file (IDF) which provides top level information about the experiment
- the MAGE-TAB sample and data relationship file (SDRF) which provides information about samples, extracts, labeled extracts, hybridizations and the data files associated with them
- experiment design images - links to a diagram of the sample relationships in .png and .svg format. The graph represents the processing steps for each sample, each edge represents a protocol that has been applied. Typically the graph shows, from left to right: BioSource-> BioSample-> Extract-> LabeledExtract->Hybridization->Raw Data. If you click the .png it will open in any browser but is only an image, it is not clickable. For the svg (scaleable vector graphics) diagram you may need a plug in for IE or Firefox but using right click you can zoom in and out of the svg image and each object is clickable taking you to a page with further information about the object.
- the MAGE-TAB array design files (ADF) - describing the array designs used in the experiment
- "Browse all available files" link takes you to a web page listing all the files relating to the experiment that are available to download. E.g.
- More information about these files can be found on the file downloads help page.
- Experiment types - terms describing design types of the experiment. These can include biological, methodological and technology types e.g. disease state, strain or line, compound treatment, in-vivo, dye swap, co-expression, binding site identification.
- Experiment factors - a list of the experimental factor values in the experiment
- Sample attributes - a list of the attributes used to describe the samples. More information about the sample attributes can be found by viewing the experiment in the advanced query interface.
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3. Saving search results
The list of experiments obtained from searching the ArrayExpress archive can be saved for future reference by either saving as a text file, saving as an Microsoft Excel file. Use the icons in the bottom left hand corner of the search result window to do this. The search criteria can also be saved for a RSS feed.
Any further questions, please see our FAQ.
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