DriveWays: A Method for Identifying Possibly Overlapping Driver Pathways in Cancer

This is the original repository for the DriveWays paper

Installing the dependencies

pip install -r requirements.txt

Input

1. The PPI network file:

The file is located at data/intAct_PPI.txt

gene1 gene2 confidence value
MDM2  TP53  0.99
APP APP 0.99
MYC MAX 0.98
...

Note: this network contains the edges with confidence value > 0.35

2. Mutation data

The file contains the list of mutated genes. Each line consists of a gene and the list of patients where that gene is mutated

The file is located at data/gene_patients.txt

RNF14 TCGA-BH-A0BR TCGA-A5-A0GJ ...
UBE2Q1 TCGA-B0-5709 TCGA-AA-3549 ...
RNF17 TCGA-CN-4731 TCGA-D1-A0ZQ ...
....

This file is needed for calculating the mutex and coverage scores

3. The Ranked seed list

The file is located at data/intAct_seeds.txt

TP53
CUL9
NMT1
...

Note: this list is generated based on the network provided above and the pancancer mutation data

Seed list generation

To generate the ranked seed list for a given network and patients mutation data, the following script should be run first

cd src/seed_generation/
python generate_seed_file.py

Modify the appropriate parameters in the script to change the network, the mutation data, and the output files path

Run

To run DriveWays on the given input files:

cd src
python driveways.py

src/config.py contains different parameters for the input files paths and the functions used for scoring

Evlauation

ODMSS and MMR evaluations included in the paper can be found in src/Evaluation.ipynb