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. 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. Theiler stage ranges describing the developmental stages where this structure exists are also displayed alongside each anatomical structure.

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

  4. 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, images, tissue x stage matrix, and tissue x gene matrix in tabs along the top.

  2. To see more about each of these tabs, read on in How do I interpret the results of my expression search?

  3. Apply filters to refine your results if desired (applies to all tabs simultaneously), or sort individual tabs 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. Go to the Tissue x Genes matrix results tab, and scroll to find genes where filled cells appear blue (expression detected) in the desired tissue and red (expression examined, but not detected) in the other selected tissue. White cells indicate no data for a particular combination within the matrix view.

  5. Darker or lighter shades of blue and red are used to represent the number of supporting annotations underlying a combination, and do not denote higher or lower levels of gene expression. Please see the Legend for a more information
GXD Summary Screen Shot
Example 2. Finding genes expressed in the pineal gland but not anywhere else
  1. Select the Differential Expression Search tab from the Gene Expression Data Query landing page.

  2. Begin typing retina into the upper box in the anatomical structures section of the form and select the term when it appears in the drop down menu. Theiler stage ranges describing the developmental stages where this structure exists are also displayed alongside each anatomical structure.

  3. Select the anywhere else box under and NOT detected or analyzed.

  4. Click Search.

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

    • analyzed and not detected (absent) in other systems, or
    • not analyzed or annotated to other systems.
Search Menu GXD EQF Anatomical Structure Screen Shot2