Identifying tissue specific RNA markers
|Sample User Question
| 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
- Go to UniGene (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene) and select the DDD
- Select "Begin DDD for" with "mus musculus"
- Select Whole Brain and Testis samples for comparison
- 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.
- 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
- On the Summary Page, click on the "Link" at the top right and select "Gene" or "OMIM"
- Note that both "Gene" or "OMIM" describe mutations in both protamines that cause steritity in both mouse and human males
- 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.
- 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.