Within a region, which structure expresses a particular gene?
In this GUDMAP Use Case, we will describe how to find which anatomical structures express a particular gene. In this example, we’ll show you how to answer the question:
Within the mouse testis, which structure expresses the gene Dppa5a (developmental pluripotency associated 5A)?
On this page:
- Step 1: Search by gene
- Step 2: Look for the anatomical structure in the Specimen section of the Gene page
- Step 3: Read the Specimen Expression table of the Specimen page
Step 1: Search by gene
On the home page of www.gudmap.org, use the search box, making sure the “GENE” radio button is selected, and enter the desired NCBI gene symbol, in this case “Dppa5a”.
If you’re not sure of the NCBI gene symbol, we also include most common synonyms in our gene search.
Or go to BROWSE DATA > Gene in the menu bar at the top of any page and enter “Dppa5a”
Then click the “View” icon for the row in the search results that most closely matches “Dppa5a” for mouse.
Note in this example, there is only one result. But there may be more results to browse or filter through depending on how the gene symbol matches other related gene records. In that case, use the filtering sidebar to narrow your search.
The following is a screenshot of the Dppa5a gene record page:
Step 2: Look for the anatomical structure in the Specimen section of the Gene page
On the Gene page, scroll down to the Specimen table (or click Specimen in the left hand “Sections” sidebar).
Look through the “Anatomical Sources” column to see if there is available data for your desired region. In this case, the first row is specific to “male reproductive system”.
Click the “View” icon for that row to view that Specimen page.
Step 3: Read the Specimen Expression table of the Specimen page
On the Specimen page, scroll down to the Specimen Expression table (or click Specimen Expression in the left hand “Sections” sidebar).
Browse through the anatomy tree to the desired region and look for icons that represent strength of expression (use the legend on the left of the tree).
You’ll find that “primary sex cord” indicates expression is present but does not indicate a regional pattern (click the image below to view larger size).