This repository contains the files for the final project in BMI 656.
This script will perform an odds ratio calculation to identify pathways containing a larger number of differentially expressed genes than would be expected by chance.
This script will assume you have the following text files in the current directory:
- H5N1_VN1203_DE_Probes.txt
- H5N1_VN1203_UNIVERSE_Probes.txt
- KEGG_Pathway_Genes.txt
The script will parse through each of them and find KEGG pathways which have an odds ratio greater than 1.5. A KEGG pathway will be chose out of the ones with an odds ratio greater than 1.5 to study further in the next section.
- (60 points) Write Part I and Part II as separate python programs that are both called from a linux bash script. This script should check for the existence of relevant files and check that Part I has successfully completed before running Part II. Turn in both python programs and the bash script.
- (10 points) Screen shot of pathway with highlighted differentially expressed genes
- (10 points) Boxplot labeled with p-value of Mann-Whitney statistic
- (20 points) 1-2 page write-up summarizing your findings. This should be a word document that includes at least 2 figures corresponding to your pathway and boxplot. Discuss the limitations of the study and any obstacles/problems you experienced. Discuss the relevance of the pathway to H5N1 infection. Discuss why the conservation of the affected pathway might be important for the study of H5N1 (Hint: think about our use of model organisms to study infectious diseases).
