Conclusion Questions 3.1.5.

1. When analyzing DNA microarray results, why are colors turned into ratios?

When analyzing DNA microarray results the red and green colors are turned into ratios based on the
intensities of the color. Depending on the number of cDNA tagged with red markers that are bound to the
microarray, the colors will be of different shades. In order to quantify these colors, scientists convert the
colors to number ratios.

2. Using the graph of log​2​ ratios shown below, which genes do you think are induced by tumor
formation? Which genes do you think are suppressed by tumor formation?

Based on the ratios in the graph I think genes 1 and 2 are induced by tumor formation. This is because the
ratios for these two genes are positive in all patients. Gene 3 is suppressed by tumor formation because
the ratio is a negative number.

3. What does the correlation coefficient indicate about the similarities between the gene
expression profile for Mike Smith and the gene expression profile for Patient 4? What does
this number indicate about how Mike Smith’s cancer might respond to drug 4?

The correlation coefficient between Mike Smith and patient for is -0.94422. The number is negative, and
therefore indicates that the gene expression behaves in a way opposite to Mike’s osteosarcoma. Mike
Smith’s cancer will most likely be unaffected by drug 4.

4. What if researchers followed a similar method used in this activity to calculate the
correlation coefficients for the gene expression patterns of every patient with osteosarcoma
and they found that all patients fell into two categories of gene expression patterns? What
would this tell you about the single disease we call osteosarcoma? How might this
information affect osteosarcoma cancer patient diagnosis and treatment in the future?

Doctors could classify patients with osteosarcoma into two categories; patients whose cancer has similar
gene expressions to and those whose cancer has opposite gene expressions in comparison to Mike’s
cancer. Doctors would be able to identify these two types of osteosarcomas and could go about creating
treatments that target varying genes for the patients in the two categories. In addition, by identifying the
pattern of the gene expression doctor’s can determine which drugs will be effective for that disease.