How do I find genes expressed in one tissue but not another?

Overview
You can use the Gene Expression Data Query Form to query for genes expressed in some anatomical structures and/or developmental stages but not in others.
Accessing the Gene Expression Data Query Form
On most MGI pages, you can access the Gene Expression Data Query form from the Search drop down menu as shown in the image at right.

For this tutorial, open the Gene Expression Data Query form in a new window. Scroll down this page for further instructions.

Search Menu GXD data query

Example 1. Finding genes expressed in the endocrine system but not in the pineal gland
  1. Select the Differential Expression Search tab from the Gene Expression Data Query landing page.

  2. Use the triangular toggles (circled) to select an Anatomical, Developmental Stage or combined query. For this example, remain on the Anatomical Structures ribbon.

  3. Begin typing endocrine system into the upper box in the Anatomical Structures section of the form and select the term when it appears in the drop down menu.

  4. Type pineal gland into the lower text box and select the term when it appears in the drop down menu.

  5. Click Search.

    This search will return genes with expression present in the endocrine system whose expression was either:

    • analyzed and not detected (absent) in the pineal gland, or
    • not analyzed or annotated to the pineal gland
Search Menu GXD EQF Anatomical Structure Screen Shot

  1. The Results table indicates the genes for which data is returned, assays (independent experiments with references), assay results and images in the tabs along the top.

  2. Apply filters to refine your results if desired.

  3. Sort the table by clicking on the arrows in the headers. To change the search parameters, use the Click to modify search button at the top of the page.

  4. On the Genes tab, use the export buttons to download the gene list in either text or Excel formats, or forward to MGI Batch Query for further analysis.
GXD Summary Screen Shot

  1. Use the Click to modify search button at the top of the page to expand the Batch Query search options.

  2. The gene list from the previous search will be automatically loaded into the Input. Select Gene Attributes and/or Additional Information to add new data columns to the output.
Batch query