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Print Article: KA-03367

How do I find specific gene expression studies at NCBI?

To find gene expression studies — and other studies on functional genomics — that utilized high-throughput technologies, search the GEO DataSets database:

  • Start your search by entering text terms that represent your topic of interest:
    • At first, try broad search terms (for example: breast cancer).  Replace these with more specific terms if you obtain too many irrelevant entries in your search results.
  • On the search results page (example), the Entry type facet on the left side of the screen will sort the results by the entry (record) type:
    • Series, Samples, and Platforms: After researchers conclude a high-throughput study that generates big data, they submit their information to Gene Expression Omnibus (GEO) repository as a family of records. The family usually consists of (1) a single Series record that describes the overall design of the study, (2) one or more Platform records that describe the technology/platform that was used in the experiment(s), and (3) one or more Sample records with experimental data for each sample. (You can regard the number of Series records as the number of individual studies in the database, although this is not a strict rule, as there are Superseries that consists of several Series.)
    • DataSets entry type refers to the curated studies in which GEO curators process individual submitted studies (individual families of records) so that the data — such as individual gene expression — and their analysis are more readily accessible on the web. Note that only a small portion (about 4%) of all archived studies are curated. For most GEO studies that you locate, you will need to conduct your own analysis with either the provided GEO2R tool or your own approach.
  • To narrow your search results, you can utilize customizable facets such as Study type, Organism, and Publication dates, and more:
    • To customize the Study type facet click on the Customize... link and select from the menu that lists all available technologies. Once the individual filter is added, you will still need to check it to have that set of records displayed. (You will also notice that once you select a study type, only Series and DataSets records will be displayed as they contain the study type information.)
    • To customize other facets click on the Customize... link and start typing your own term. If your term (for example "age" as an Attribute name) was frequently used in characterizing the submitted sample records it will appear as a term in an auto-complete dictionary. Otherwise, enter the term and press the return key to have it added to the facet.

Tip: Once you locate a study to use, the Similar studies link that is located at the bottom of the DataSets and Series summaries may help you locate additional studies of interest. This link is also useful to relate the submitted Series with their curated DataSet counterparts as they will be considered as most closely related. Likewise, the link will group Superseries with its Series members.