Design of Yeast Genomic Expression Experiments

A. Duplicate experiments as identically as possible

1. Maintain as many experimental details (such as starting OD₆₀₀, culture shaker

speed, timing of experiment, etc.) as possible

2. The most common differences between experiments seem to be differences in

the expression of metabolic genes

V. The practical art of data Analysis

A. Remember all of the experimental details when analyzing the data

1. Be aware of:

a. Pleiotropic conditions during the experiment

b. Potential diauxic shift problems

c. Strain background (auxotrophic markers, mating type)

d. Cell cycle progression or arrest

e. Secondary effects of the primary stimulus

B. Keep an open mind when interpreting the results!

C. To identify responses that are specific to your conditions, compare the data to other

datasets of unrelated conditions … remember that many of the observed responses

may not be specific to your conditions.

D. Remember that whatever analytical method used to analyze the data (hierarchical

clustering, Self Organizing Maps, K-means clustering, Singular Value

Decomposition), these are methods of Organizing the data

1. Which analysis method is the best: NONE!

a. Different methods have different strengths and weaknesses which make