1. IBGP705 GEO—Gene Expression Omnibus
TA: Lee Cooper
February 25, 2009

2. answers by 6pm
Look up GDS3217. What disease does this dataset study? What tissue (cell) type is used in the study? What is the species of the sample? How many samples are there? What are the factors in the experiment? What is the microarray type (e.g., Affymetrix Mouse 430) and how many probes are on it?
Using the data analysis tool:
Select compare 2 sets of samples, in step1 select “One-tailed t-test (A>B)” and significance level “0.001”
In step 2, select “control, 12h” as group A and “estradiol, 12h” as group B, click OK. Click on Step 3.
For the output, sort by “Subgroup effect”. Change your display to show “100” items per screen.
Click on “Download Profile Data”, change the file name to “GDS3217_Down_12h.txt”.
Answer the following: how many probes are selected from this analysis, list the first 10 genes.
Repeat the above 5 steps but change to “One-tailed t-test (A<B)” in step 1 and save the file as “GDS3217_Up_12h.txt”, you need to answer the same question.
Repeat the above steps but change the selection in step 2 such that “control, 48h” is group A and “estradiol, 48h” is group B. When save to files, change “12h” to “48h” in the file names. Answer the same question.
Keep the saved files to yourself by copying it to a jumpdrive or to yourself. We will need them for the next two lab sessions for gene ontology and pathway analysis.