There are three methods we will use to explore Expression Connection.
A. First Method
1) Go to Expression Connection <http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl> and click on "Search I". Enter the gene name "tup1" (without quotation marks). Then click on every box next to an experiment with a searchable database.
2) Scroll down and you will see the results from all of the data sets you selected. Notice the columns that show the Max. and Min. data. These show the maximum fold induction and repression, respectively.
3) Find the diauxic shift DeRisi database. Click on the word "Enlarge" to see tup1's expression profile in this experiment.
4) On the left side, click on the Expression Graph to see a different display of these data. Describe in words what happens to this gene over time.
5) Click on the red dot under the column "Similarly Expressed Genes". What two genes are most similarly expressed with tup1? Do their cellular roles indicate that these three genes may have related functions and thus their similar transcription profiles are not coincidental?
6) Scroll down this list of genes with similar expression profiles until you find an "unknown" gene. Can you see any value in clustering genes that have no known function? Click on the blue text for the unknown genes and see what you can discover about them.
B. Second Method
1) Go to Expression Connection <http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl> and click on "Search II". Enter the gene name "tup1" (without quotation marks). For step 2, choose "Increase or Decrease" from the pull down menu. Then type in the number 2 in the blank box. Click on Submit.
2) The results give you only those experiments in which tup1 changed its expression by at least 2 fold (induced or repressed.
3) Find the experiment where tup1 was induced the most. How much was it induced?
4) Click on the icon that says "Reg". What gene is at the top of this regulatory cascade that lead to the strong induction of tup1?
5) Click on the icon that says "Stats" for this same data set. Look at the percentage of genes tha showed no change in expression after 5 minutes of heat shock in experiment #1. Scroll down a few more lines and compare this percentage with the value in experiment #2 at 5 minutes. What did you discover?
C. Third Method
1) Go to Expression Connection <http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl> and click on "Search III". Choose decrease from the pull down menu and then enter the value 70. Click on all of the boxes for the data sets and then hit "Submit".
2) Find the gene that was induced 205.1 fold and also repressed 99.7 fold. Click on the red dot for similarly expressed genes. What gene have you focused on?
3) This gene is induced under many conditions but it is repressed under four main treatments. What are those treatments?
This series of questions was intended to show you the information available for students to explore while discovering what DNA microarrays can do.
Genomics Course Page
Biology Department Main Page
© Copyright 2003 Department of Biology, Davidson College, Davidson, NC 28035