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Which genes are expressed in multiple regions? | GUDMAP
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Which genes are expressed in multiple regions?

Using the Boolean Anatomy Search, you can choose multiple anatomical regions and then query for expression of one or more genes. In this example, we’ll be using the Boolean Anatomy Search to answer the question:

Which genes are expressed in the renal medullary interstitium, outer medullary interstitium and inner medullary interstitium?

On this page:

Step 1: Go to the Boolean Anatomy Search app

In the top-level menu choose BROWSE DATA > Anatomy > Boolean Anatomy Search.

Which opens the Boolean Anatomy Search app:

screenshot of the Boolean Anatomy Search app

Step 2: Set up a Boolean query

You can find the full documentation page here, but on this page we’ll be demonstrating a particular query.

We will set up three different conditions - each for one of the anatomical regions where we want to know if expression strength is present: the renal medullary interstitium, outer medullary interstitium and inner medullary interstitium.

  • In the left hand section, in the search field above the tree, type renal medullary interstitium. When you see the term appear in the tree, click the term to populate the condition box on the right side.

    Make sure the “Strength” field is set to “present”

  • Click the plus (+) sign to add another condition.

  • Repeat this step with the terms outer medullary interstitium and inner medullary interstitium. You should now have three condition on the right side of the screen:

Note: If you see no results for an anatomical region, make sure you are using the appropriate developmental stage in the dropdown box at the top of the anatomy tree.

screenshot of the boolean conditions

Step 3: Search Specimen records

Now click the “Search Specimen” button to search all gene records that show expression present in those regions.

screenshot of the specimen search results from the query

In the search results, you’ll see in the Genes facet in the left sidebar the following genes, which indicate we have data that shows the expression of these genes in all three regions: Crym, Wnt4, Ptch1.

Video demonstration

Here is a video demonstrating the above steps: