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Genome sequencing projects have limited impact until their results can be used to answer biological ques-
tions. Raw genome sequence data can be used, in conjunction with EST databases, to predict which genes exist.
Tags representing each of those genes can by synthesized or spotted at different locations on a glass plate, and the
resulting microarray can be used to simultaneously measure the net rate of transcription of all of the ORFs in the
array. In this exercise, you will work with data generated in microarray assays of transcription, and use the results
to answer questions about global regulation of gene expression.
1) Review microarray construction, and think about
Beginning in Chapter 4 of your Campbell and
how data from these experiments is acquired and pro-
Heyer text, read pages 107 - 117, including the three
sections on mathematical treatment of microarray data,
before coming to class. Note that several of the figures
2) Use the data from microarray experiments to an-
you will need for this section are on the CD-ROM that
swer questions about gene expression.
came with your text. Make sure you view and under-
stand them. Remember to bring the CD to lab. You
may also want to bring a biochemistry or general biol-
ogy text that treats the enzymes and pathways of gly-
colysis, fermentation, and the TCA cycle. An overview
Microarray datasets provide researchers with of these pathways is provided in Figure 4.17 on your
huge amounts of information on the levels of expression CD but you will probably want a reference with more
of large numbers of genes under many different condi- detailed explanations. Answer Discovery Questions 5-
tions. Before you can think about the data, though, you 7, and bring them to class with you.
need to review how microarrays are constructed and
probed. Once the data has been acquired, expression
In class, begin with Figure 4.11 on your CD,
data are transformed into log space and clustered ac- and answer Discovery Questions 8-12, accessing the
cording to similarities in the pattern of expression. Af- Functional databases at SGD from the course website.
ter these automated data manipulations, the datasets are Do you think any of the links on the Function Junc-
often made available to the research community. We tion site could help you with your protein family lab
will use two datasets, along with several other tools, report?
to think about the regulation of the entire genome in
Then, think about the promoter sequences and
regulatory proteins that might cause genes to be coreg-
You may complete this exercise with a lab part- ulated. Read pages 120 and 121, answering Discovery
ner if you would like. No one should work in a group Questions 13 and 14.
of more than two people. Answers to the questions in
this assignment can be turned in at the end of lab, or
Finally, read through page 124, and use the
Friday 26 March, in lecture at the latest.
microarray expression datasets to answer questions 17-
Copyright 2004, University of Evansville Department of Biology
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