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Problem Definition

In this problem, you will learn how to use microarray data to judge which type of tumor a patient has. This method of diagnosis is currently one of the most cutting-edge ways to diagnose a patient with a specific type of cancer. You gather about 20 patients with ALL and 20 patients with AML. You take tumor samples from these patients and extract mRNA samples from the tumors. You allow the mRNAs from the tumors to hybridize to DNA chips, on which each spot contains a probe for a different human gene. What you find is that some genes are expressed at very high or very low levels in ALL tumors as compared to AML tumors. Other genes are expressed at very high or very low levels in AML tumors as compared to ALL tumors. This means that each type of tumor can be assigned a signature pattern of expression of genes, and then unknown tumors can be diagnosed by examining their signature patterns.

Viewing the Original Data

Use the instruction sheet to view the original data used in the following exercises.

MicroArray Data QuesCtions

a) What do genes shown in green indicate?

b) What do genes shown in orange indicate?

c) What are the four genes that show the best correlation with presence of ALL? (List them by their descriptions.)

d) What are the four genes that show the best correlation with presence of AML? (List them by their descriptions.)

e) Is the gene session pattern of U18271_cds3_s_at strongly correlated with the presence of AML or ALL? (see “how to answer question e)” on page 2 of the instruction sheet)

f) What is the name of the gene product encoded by U18271_cds3_s_at? (see “how to answer question f) and g)” on page 3 of the instruction sheet)

g) What chromosome arm and position does the gene U18271_cds3_s_at occupy? (see “how to answer question f) and g)” on page 3 of the instruction sheet)

HeatMap Data Questions

h) Look in the list of gene descriptions for “terminal transferase”. With respect to only the expression of terminal transferase mRNA, which tumor sample behaves the least like the other tumors in its class? (see “how to answer question h)” on page 4 of the instruction sheet)

Clustering Data Questions

i) Which AML sample is least like the other AML samples? (see “how to answer questions i) and j)” on page 4 of the instruction sheet)

j) Which ALL sample is least like the other ALL samples? (see “how to answer questions i) and j)” on page 4 of the instruction sheet)

k) A patient comes in with a tumor. After taking samples of the patient's tumor and running the appropriate tests you find that the tumor had high levels of expression of Nek3, and low levels of LPAP and CAMK4. Given this information and the clustering data, which type of tumor would you most likely diagnose it as? (see “how to answer question k)” on page 4 of the instruction sheet)