Below is a stylized representation of a small portion of a microarray grid. Dots

Question

Below is a stylized representation of a small portion of a microarray grid. Dots are indicated by row and column. The dots represent one of the 30,000 genes and regulatory RNAs present in the human genome. The array was hybridized with cDNA from normal liver cells (represented by red fluorescence) and with cDNA from liver tumor, hepato-cellular carcinoma, cells (represented by green fluorescence).

a.     What do the yellow dots represent in the microarray results?

b.     Which dots (give coordinates) represent genes that are associated with higher expression in hepatic cellular carcinoma cells?

c.     Which dots (give coordinates) represent genes that are associated with lower expression in hepatic cellular carcinoma cells?

d.     What can be determined about the gene at G3?

e.     One of the genes associated with higher expression in hepatic cellular carcinoma cells is IGFR2 – do some research and find out more about this gene. What is it? Where in the cell would you expect to find it? What is its role in the cell? Why is it or might it be associated with cancer?

f. Spot C1 has a gene that has been identified only as gene of unknown function. Provide a strategy to elucidate some more information about the potential function of the gene using the following questions as a guide: in what tissues is it expressed? Does it show changes in expression in response to any stimuli? Is the protein located in any specific part of the cell?

Explanation / Answer

a. Yellow color represents the equal expression of gene in normal and cancer cell.

b. Red dots (A3, C2, C4, C8, F2, and H1).

c. Green dots (B3, B5, C1, C7, F5, and H2).

d. G3 (clear dot) represents gene was expressed neither in normal nor cancer cell. It actually shows that CDMA was not hybridized with mRNA.

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