Corresponding lecture

Lecture 8 – Differential gene expression

Image credit: Khrystyna Kozyuk


You’re tasked with studying gene expression in Plasmodium falciparum, a single-celled protozoan parasite that infects human red blood cells (RBCs) and is the causative agent of malaria, one of the deadliest infectious diseases on the planet. After invading an RBC, parasites progress through a 48 hour developmental cycle before rupturing the cell and invading a new one. To understand how parasite gene expression changes during this cycle, you infect RBCs in vitro and isolate RNA every 8 hours for 48 hours straight. As you’re finishing the experiment (and very much looking forward to sleeping), your PI asks if you can put together a figure for a last-minute grant submission. You have ~2hrs to produce a publication-quality figure. The team that produces the best figure (as judged by the TAs) will win this challenge.

Before you start


  • Don’t worry about annotations or summarizing data to gene-level, just read the data into R at the transcript-level
  • There are different ways that you could set-up the model matrix, so you’ll have to choose an approach and move forward
  • You’ll use the Steps 1, 2, 3, 5 and 6 for challenge. Don’t worry about trying to do any functional enrichment analysis.
  • Think about what makes a good figure and use your data to tell a story!
  • Feel free to include illustrations/schematics if useful.


Part 1 – A brief overview of the challenge, as well as first steps for importing, filtering and normalizing

Part 2 - Walking through PCA, differential transcript analysis, and module identification for this hackdash