These Discovery Questions assume you know how to read microarray data. If you do not, please review this page.
1) Go to the Molecular Portraits Histology web site that show tissue samples used in a multi-national DNA microarray study. Click on the images for Patients: New york 2, Norway 10 and Norway 112. These three biopses are at three different stages of breast cancer. Can you tell which was the most advanced stage? Do these look like simple tissues for DNA microarray analysis? Explain your answer.
2) Now go to GeneXplorer to analyze some microarray data. Click on the interactive version of figure 2 on this page.
3) Set the radar for 400% and then click on any region where you would like to see the genes in more detail. Do these genes have any features in common that you can detect?
4) Type ERB in the blank after the phrase "Search for____" located at the top left above the dendrogram and then hit the return key on your computer. You should see a list of four ERBB2 names; the human gene is located on chromosome 17.
5) Click on one of the brightest red boxes located in an ERBB2 row (note red indicates iduced genes).
6) You will get a new results page that shows genes coexpressed with ERBB2. Towards the bottom of this list, note the gene FLOT2. Click on the blue text FLOT2 to learn what this gene does. Any obvious roles that might lead to cancer?
7) Go to EntrezGene and search for ERBB2; notice its chromosomal location. You will have to scroll down some to find the human (Hs) gene. Go back and repeat this search for FLOT2.
8) What chromosomal event might cause ERBB2 and FLOT2 to be upregulated similarly?
9) In this area of chromosome 17 are two other interesting genes: MAP kinase kinase kinase and BRCA1. If this region of the genome were altered, do you think this might have in impact on breast cancer formation?
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