Tup1 Microarray Data

Discovery Questions

The Tup1 database is located at two different sites. The interface uses a standard port and is located at Stanford University but the database itself is located at UCSF, has an IP address of, and uses a nonstandard port (591 instead of 80). If you attempt the database serches below and you do not get any meaningful results, then your institution probably has a firewall blocking your access to this database. Please contact your IT department to allow access to the IP address via the 591 port.

These Discovery Questions assume you know how to read microarray data. If you do not, please review this page.

1) Go to the Tup1 database. This database shows the gene expression patterns for a strain of yeast that had the transcriptional repressor Tup1 deleted from its genome.

2) Enter Tup1 into the gene name box and hit "start search". The red signal is from the deletion strain and green is from a wild-type strain. Was Tup1 expression reduced? By how much? Is this higher or lower than you expected? Explain your answer.

3) Go back to the Tup1 database to find genes in the Tup1 deletion strain that were repressed rather than induced. To perform this type of search, delete Tup1 from the gene box. Go down to the “Average fold induction in tup1 deletion” box and choose less than from the menu and enter the number “1”. Don’t sort the results for now. There will be over 3000 genes in this list, but only 25 on the first screen. From the list you get of the first 25, find the gene with the greatest average repression. Look at the variation in the two trials. Is it high or low?

4) From the list you have of 3000+ hits, go to record number 52 (click on next page a couple more times). Look at its average repression. Then look at the variation in the two trials. Is the variation high or low? What is the function of gene number 52 from this list?

5) Go back to search Tup1 database and find the gene with the greatest repression. To do this, have it sort by “average fold induction”. What gene was repressed the most by deleting a repressor? What gene was second?

6 ) Search Tup1 database again to find the gene that was induced the most. This time change the menu to “greater than” and sort by “average fold induction” and choose “descending” for the order of display. You will see a common gene family in the most induced genes. What is the family? Which gene was induced the most?
[Hint: you might want to have two browser windows open for the next series of questions. One for Function Junction and one to explore the tup1 database.]

7 ) Go the Saccharomyces Genome Database Function Junction web site and enter the name of the gene family (use Tir1) that describes the trend for question number 6above (but don’t add the “p’ which stands for protein). Describe the role this gene plays in the cell.

8) Based on your answer from number 7, is there a significant impact on the cell when one repressor is deleted?

Discovery Questions

Genomics Course Page

Biology Department Main Page

Send comments, questions, and suggestions to: macampbell@davidson.edu or (704) 894 - 2692

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