Searching ArrayExpress

2. all experiments where your term is found in any of these fields will be returned:
   1. ArrayExpress accession number e.g. E-MEXP-568
   2. secondary accession numbers e.g. GEO series accession GSE5389, ENA study accession number ERP000054
   3. experiment name
   4. submitter's experiment description
   5. sample and experimental factor attribute classifiers and values, including species (e.g. GeneticModification, Mus musculus, DREB2C over-expression)
   6. publication title, authors and journal name, PubMed ID
   7. array design name and accession

3. synonyms for terms are always included in searches e.g. 'human' and 'Homo sapiens'
4. a drop down menu will show matching terms in the Experimental Factor Ontology (marked EFO) or terms that exist in any record. The Experimental Factor Ontology is an application-focused ontology modelling the experimental factors in ArrayExpress. The Experimental Factor Ontology expansion affects values that are experiment types, sample attributes, experimental factor values and species. In the search results exact matches are highlighted yellow, synonyms green and child terms pink. See the search results help page here: Understanding archive browse/search results.

5. use * as a wildcard for 0 or more characters and ? for single characters e.g. embryo* will retrieve results with matches to embryo and embyronic, te?t will search for test and text. Wildcards will not work within phrases (see below)
6. put quotes around phrases where you want to search for more than one word together e.g. "bone marrow"
7. US spelling conventions are used e.g. leukemia not leukaemia, although common terms are searched for in both UK and US spellings
8. ArrayExpress uses latin names for species e.g Homo sapiens. For some species a search for the common name will bring up results but search for the latin name to be sure you find all relevant experiments.
9. Non-standard character sets are not supported, e.g. greek symbols
10. To browse all experiments in ArrayExpress click on the 'Browse experiments' link.

The search results page is described here: Understanding archive browse/search results.

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1.2. Advanced searches

1.2.1 Filter experiments to show data directly submitted to ArrayExpress only (not GEO-imported data)

We import data from the Gene Expression Omnibus (GEO, www.ncbi.nlm.nih.gov/geo/). To limit the search to only the experiments submitted directly to ArrayExpress and not imported from GEO check the box under the search box. For more information about how we import data from GEO see the GEO data help page.

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1.2.2 Filter experiments by species, array design, molecule or technology

Experiments can be filtered by species, array design, molecule (DNA, RNA, metabolite, protein) or technology (array, high-throughput sequencing, mass spectrometry) using the drop down menus in the centre of the top search option bar. After selecting a filter, click on the 'Query' box on the right hand side to filter experiments. To remove a filter, either re-select the top option from the list, or click on the '[reset]' link, and then click on the 'Query' box again to requery ArrayExpress.

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1.2.3. Combining search terms

Enter two or more keywords in the search box with the operators AND, OR or NOT. AND is the default search term; a search for 'prostate breast' will return hits with a match to 'prostate' AND 'breast'.

Search terms of more than one word must be entered inside quotes otherwise only the first word will be searched for. E.g. transcription AND Rattus norvegicus will effectively be a search for transcription AND Rattus.

If a field is not specified (see below) then the term is search in any of the experiment fields (experiment description, sample annotation, citation etc).

Operator	Searches	Example
AND	Experiments with more than one term. This is the default term
OR	Experiments with either term.
NOT	Experiments without a term

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1.2.4. Specifying fields for searches

Particular fields for searching can also be specified in the format of fieldname:value. Again, phrases of more than one word must be entered in quotes otherwise only the first word will be searched for. The fields that can be searched are shown in the table below.

Field name	Searches	Example
accession	Experiment primary or secondary accession
array	Array design accession or name
ef	Experimental factor, the name of the main variables in an experiment.
efv	Experimental factor value. Has EFO expansion.
expdesign	Experiment design type
exptype	Experiment type. Has EFO expansion.
gxa	Presence in the Gene Expression Atlas. Only value is gxa:true.
pmid	PubMed identifier
sa	Sample attribute values. Has EFO expansion.
species	Species of the samples. Has EFO expansion.

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1.2.5. Filtering experiments by counts of a particular attribute

Experiments fulfilling certain count critera can also be searched for e.g. having more than 10 assays (hybridizations). These searches use the following syntax:

Examples

1.3 Login to view private data

Data can be kept private in ArrayExpress until an associated paper is published. After a custom array design or experiment is loaded into ArrayExpress the submitter is sent details of login accounts for themselves, and for journal editors and reviewers so that they can the view data before it is publicly available. Data is made public when the submitter gives us permission to do so, or if we find that the data has been referenced in a published article.

Submitters and reviewers can login to view their private experiments and array designs by clicking on the 'Submitter/reviewer login' link in the browse interface (www.ebi.ac.uk/arrayexpress) . This will take you to a login box. Enter the login details we have provided you with.

If the 'Remember me' box is not checked, then you will remain logged in until the browser is closed.

If you have forgotten your ArrayExpress login and password, email the curation team at miamexpress@ebi.ac.uk to get your login details by email. Please specify the accession number of the experiment or array design you wish view.

If you are a reviewer and have not been provided with an ArrayExpress login to access private data connected to a publication please contact the data submitter, via the journal, to request this information. We cannot provide access to private data to anyone without first getting authorization from the submitter or journal.

If you have submitted data using our MIAMExpress or MAGE-TAB submission tools please note that your submitter login account cannot be used to login to ArrayExpress. You will be sent a separate ArrayExpress reviewer login account when the processing of your submission is complete.

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1.4 RSS feed

We provide an RSS service listing experiments as they become public in the ArrayExpress archive so that you can be aware of new experiments that may be of interest to you. The URL for the RSS feed is http://www.ebi.ac.uk/arrayexpress/rss/v2/experiments or you can click on the orange RSS icon on the ArrayExpress home page.

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1.5 Downloading data and programmatic access for the archive and atlas

All data, experiment descriptions and array annotation in the ArrayExpress experiment archive can be downloaded from our FTP site in MAGE-TAB formats. See the following help pages:

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1.6 Understanding Archive search results

See the Search Results page for help about the information displayed about each experiment.

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See the Atlas-specific help page for information about searching the Atlas of Gene Expression

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Any further questions, please see our FAQ.