Homework 2.1: A temperature controlled Gal4-UAS system (100 pts)
One of the students in a previous version of the class, Han Wang, published (Wang, H., …, Sternberg, P.W. (2017). cGAL, a temperature-robust GAL4-UAS system for Caenorhabditis elegans, Nat. Methods, 14(2), 145-148) an improved Gal4/UAS system in C. elegans. Briefly, the Gal4-UAS system was hijacked from budding yeast and incorporated into the genomes of other organisms, Drosophila being the first. The idea is to insert the Gal4 gene into the genome such that it is under control of a driver that is native to the organism. When Gal4 is expressed, it binds to UAS (upstream activation sequence) and it is activating, leading to expression of the UAS target gene.
In the paper, Han used the system with UAS activating production of green fluorescent protein (GFP). The Gal4 production is driven by Pmyo-2, which is only expressed in the pharynx of the worm.
The Gal4/UAS system typically works only at high temperatures. This does not work as well in worms that are stored at lower temperatures. Han therefore engineered a “cool” Gal4, which works at lower temperatures. To test how the new system worked, he measured the GFP fluorescence signal in the pharynx of worms.
He generously donated his data set for us to work with. He sent me a MS Excel file with the data, along with some comments via email. Here is what he said in that email about the data set (verbatim):
SC (orignal Gal4)
SK (cool Gal4)
m3 Pmyo-2::GFP fusion (control; measure of driver expression)
15 20 and 25 at the end for the name of each column shows the experimental temperature.
You can download the MS Excel file here: https://s3.amazonaws.com/bebi103.caltech.edu/data/wang_cool_gal4.xlsx.
a) Load and tidy the DataFrame. Be sure to remove any NaNs.
b) Do some exploratory data analysis of the data set. That is, make some instructive plots. Discuss why you chose to visualize the data set the way(s) you did. What can you say about Han’s cool Gal4 just by looking at the plots?