In this lab we will perform a differential expression analysis starting from scratch.
Doxorubicin is a commonly prescribed cancer drug, but one of its side effects is cardiotoxicity. This drug damages heart cells by binding to the protein topoisomerase-II beta, or Top2b.
A 2x2 factorial experiment will be performed: 1.Two types of mice in this case:
- genetically normal wild type (wt)
- Top2b knockout mice (mice that have had Top2b removed from heart cells) (top2b)
2.Two treatments:
- PBS control solution (pbs)
- Doxorubicin (dox)
If doxorubicin requires Top2b to exert its cardiotoxic effect, Top2b knockout mice should not be affected by doxorubicin treatment. This is the hypothesis to be tested. The data contains measurements from 29,532 genes and 12 mice, with three replicates for each factor combination.
https://alejandro2195.github.io/Differential-Expression-Analysis-in-R/