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BBSI: Fundamentals of Microarrays
Michael F. Miles, M.D., Ph.D.
Depts. of Pharmacology/Toxicology and Neurology and
The Center for Study of Biological Complexity
Virginia Commonwealth University
e-mail: [email protected]
phone: 804-827-4054
Problem Set/Questions 1: 7/19/06
You have discovered a new species of primates, wookie starwarius. This species is prone to extreme hair
growth and you want to study the mechanisms of this in the hope of discovering a new treatment for
baldness in humans. After reading several reviews on DNA microarray technology, you decide that
performing microarray studies on skin biopsies from wookie starwarius would be your method of choice
for this work. However, these studies pose certain technical and theoretical problems:
1) Being a new species, wookie starwarius gene structure and expression has not been studied at all.
How would you propose conducting microarray studies on a new primate species? Name two alternate
2) Describe the pros and cons of using spotted cDNA arrays vs. short oligonucleotide microarrays for
your studies on wookie starwarius.
3) Using the dataset provided (BBSIarraydata7_06.xls), explore your primary data. Using scattergram
analysis (to be demonstrated in class), determine if any of the arrays appear “abnormal”. What are you
looking for in such a quality control step? Similarly, compare results of the two different primary
analysis methods that are provided (MAS5 vs. PDNN). Does either appear superior? Why?
4) The goal of these studies is to identify gene expression patterns that might be relevant for treatment of
human baldness. There might be many gene expression differences between wookies and humans using
the microarray platform utilized. Some (most?) of these may be unrelated to hair growth. Describe an
experimental design that might help identify those genes most closely related to hair growth.