Analysis of Protein Complexes in Cancer

This directory includes code and files for the analysis of the role of disrupted protein complexes in cancer.

Jupyter Notebooks

Analysis_Functions.ipynb

Analysis and plotting functions used in other notebooks. Includes data and package imports, functions involved in performing statistical tests on ratios within protein complexes, and visualization functions.

Plotting_Functions.ipynb

Functions used to create various histograms and boxplots of the data as well as perform basic t-tests. Contains most of the functions used in pancancer analysis.

Data Files

proteinGroups_cleaned.txt

Output of Clean_Dataset.ipynb. This is the file we used in our analyses, and contains proteomics data for both tumor and normal samples, some of which are matched.

proteinGroups_simplified.txt

The original data file, before it was cleaned up.

allComplexes.txt

Data about protein complexes downloaded from CORUM (http://mips.helmholtz-muenchen.de/corum/#download)

trrust_rawdata.human.tsv.txt

Data on transcription factors and their target genes downloaded from TRRUST v.2 (https://www.grnpedia.org/trrust/downloadnetwork.php)

spliceosome_proteins.csv

Information on which version of the spliceosome (A complex, B complex, etc) each protein is in