"This web page was produced as an assignment for an undergraduate course at Davidson College."

My Favorite Yeast Expression

For the previous assignment, I chose to investigate the following Saccharomyces cerevisiae genes that are located on chromosome XVI :

FHL1, an annotated gene that encodes a fork head protein involved in rRNA processing and YPR098C, a non-annotated gene upstream of FHL1 with a small hypothetical ORF and characteristics suggesting that it is a membrane protein.

To find out more about these genes, click here to see my other webpage.

Using DNA microarray databases that we recently discussed in Genomics class, I will now attempt to analyze the expression patterns of both genes, and hopefully gain useful information that I can use to predict a possible role for the non-annotated gene, YPR098C.

DNA microarrays are a fairly new technology that allow researchers to perform high-throughput experiments testing the transcription of specific genes in different experimental conditions . Previously, these types of experiments were performed using Southern blots. A DNA microarray is made by first spotting PCR products onto a slide, with each spot on the slide representing a different gene. Then, some cells are placed in normal conditions while others are placed in an experimental environment. After a specified amount of time, mRNA is extracted from both sets of cells. Flourescently labeled cDNA is made from this mRNA with the experimental cDNA labeled red and the control cDNA labeled green. After the data is analyzed by a computer, the data is converted to a color scale where black means no change in gene expression (transcription) between experimental and control conditions, red indicates induction of gene expression during experimental conditions, and green indicates repression during experimental conditions. This information is informative because the response of almost every gene in a genome can to an experimental condition can be simultaneously tested and because software programs allow the expression ratios to be compared so that genes with similar expression patterns can be clustered together. From this information, hypotheses about the role of genes with unknown functions can be made and tested. Inferring function from genes with similar expression patterns is termed "guilt by association."

To see an animation explaining the procedure for performing DNA microarray experiments, click here.


Microarray analysis of FHL1

Microarray analysis of YPR098C



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Send comments, questions, and suggestions to: sahenry@davidson.edu