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DNA microarray

You perform DNA microarray experiments on cancer cells at different time points
(0, 6, and 12 hours) following the addition of a novel anti-cancer drug. You obtain the following
normalized and scaled microarray data for the genes Myc, p53, and Ras.

Gene Name 0 hr 6 hr 12 hr
Myc 1.0 0.2 -1.2
P53 -1.1 0.4 0.7
Ras 1.3 -1.4 0.1

a. Use the Euclidean distance method to calculate the following distance matrix:
Gene Myc p53 Ras
Myc
P53
Ras

b. Which two genes would be clustered together first using the hierarchical clustering
method'?
c. If we are using the Complete Linkage cluster method, what is the new distance
between the remaining (unclustered) gene and the new gene cluster generated in part (b)?

Solution Preview

Please see attachment for better explanation.

Gene Name 0 hr 6 hr 12 hr
Myc 1.0 0.2 -1.2
P53 -1.1 0.4 0.7
Ras 1.3 -1.4 0.1

Use the Euclidean distance method to calculate the following distance matrix

Gene Myc P53 Ras
Myc
P53
Ras

How to do this?

For example
So the Euclidean distance is:

Gene Myc ( A) Exp 1 P53 (B )Exp 2 Ras (C ) Exp 3
Myc ( A ) 0 2.1 1.63
P53 ( B ) 2.1 0 ...

Solution Summary

DNA microarray is considered the most advanced and novel technologies in the field of genetic research. DNA microarray can be used to investigate everything from cancer to pest control. It is primarily used to investigate the gene expression or gene profile of different organisms. It can be used to identify genes that are expressed differently in cancer and normal individuals. In this experiment, one will perform DNA microarray experiments on cancer cells at different time points following the addition of a novel anti-cancer drug.

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