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NCBI Resources: GEO Profiles

Contains information about the NCBI databases to be used as a teaching tool.

GEO Profiles Unique Identifiers

  • ID: 8 digit number for the profile record
  • Gene ID: from the gene database
  • RefSeq ID: for the transcript from GenBank
  • ID_REF: probe used to detect the transcript
  • GPL: platform used to generate the data
  • GDS: GEO DataSet the data were derived from

Boolean Operators

Boolean operators allow you to combine search terms: 

  • AND: Finds documents that contain both terms.
  • OR: Finds documents that contain either term. 
  • NOT: Finds documents that contain the term on the left but not the term on the right.

Advanced Search

By default, Entrez searches your text in "All fields", which looks for the text anywhere in the entry. So if you're getting irrelevant results, try limiting your text to a particular field.

Don't know what fields you can search for? Use the Advanced search

1. Click on advanced beneath the search bar. 

2. Click the drop down menu under Builder to see what fields are stored in gene records.

This is a comprehensive list of all fields you can search for. Fields will vary by database. Example shown here is for the Gene database. 

Need help? Ask Wlad

Search GEO Profiles

You can Search GEO Profiles by...

To see all available options, use the Advanced Search

Available fields are listed in the drop down menus on the resulting page, and you can see what values are in these fields by clicking Show index list to the right of the search box.

 

GEO Profiles Search Results

Below is an image of what GEO Profiles search results look like.

After submitting your search, a list of results will appear with gene records that match your query. The results page is divided into 3 columns:

  1. Filters: more ways to limit your search by things like genome location
  2. Results: a list of the Gene records that match your query with basic information
  3. Discovery Column: links to other databases and Search details

To limit to a specific gene, you can enter the gene symbol (blue box). You can choose the organism (red box). 

The center column contains the records that meet your search criteria. Each record includes a title, including the gene name and description, its annotation, the unique identifiers associated with the record (orange box), links to external databases, and a graphic depicting the differences in expression level of this gene in the sample groups included in the experiment. 

The right hand column is the discovery column, which contains links to external databases and your search strategy.

To view an individual record, click on the graph on the right side of the record. Clicking the title will bring up a new search results page with only that record.

GEO Profiles Records

Each individual record contains a labled graph that shows differences in expression between two condidtions. In the case below, they are comparing control cells with those expressing a particular microarray in humans. The red bars show the expression level, and the blue squares indicate the expression percentile among all other genes in the sample.

Additionally, the table at the bottom provides links to information about each individual sample, and numeric expression values.