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Identifying tissue specific RNA markers

  Sample User Question
Step By Step Guide

Sample User Question back to top

Using the DDD from Unigene, identify RNA markers unique to mouse testis vs. mouse brain and determine the potential roles these markers may have in a mouse disease or defect. Can you verify the result using the SAGE anatomic Viewer?

Step By Step Guide back to top

  1. Go to UniGene ( and select the DDD

  2. Select "Begin DDD for" with "mus musculus"

  3. Select Whole Brain and Testis samples for comparison

  4. Examine the generated list to identify genes highly expressed in Testis vs. Brain-specifically note that Protamine 2 is the most highly expressed mRNA in Testis, followed by Protamine 1.

  5. Go to the UniGene Summary Pages for either Protamine 1 or 2 by clicking on the link next to the Gene Index next to the Gene Description

  6. On the Summary Page, click on the "Link" at the top right and select "Gene" or "OMIM"

  7. Note that both "Gene" or "OMIM" describe mutations in both protamines that cause steritity in both mouse and human males

  8. Go to the SAGE Anatomic Viewer ( and enter the UniGene Cluster number for Protamine 1 from the GeneSifter oneclick summary—select the resulting Best Tags and view their abundances in the viewer.

  9. Note that there is no data for Protamine 1 or Protamine 2 in the SAGE Anatomic Viewer as there is no data for testis tissue in the Viewer—driving home the point that there may not always be comparable tissues for comparisons between the SAGE data and the GEO data.

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Revised 07/24/2007