MP Biopath Reactome Ten Pathway Tests

These are tests used to test MP-BioPath results with Reactome Pathways

Dependencies (Docker Engine)

To run this program you will need to have access to command line and also have Docker installed. If docker is not installed please see https://docs.docker.com/engine/install/.

Resources

The version of MP-BioPath used to run this analysis is 1.0.4.

A precompiled MP-BioPath version 1.0.4 container has been uploaded to DockerHub here: oicr/mpbiopath:1.0.4

If for some reason you are not able to access the docker container on docker hub you can download the 1.0.4 and from the root of the repository run the following commands:

make build-env
make build-app

Pathways

The following Ten Pathways were run with the main Analysis:

• Cell Cycle Checkpoints
• HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)
• Mitotic G1-G1/S phases
• Mitotic Prophase
• RAF/MAP kinase cascade
• S Phase
• Signaling by ERBB2
• Signaling by WNT
• Transcriptional Regulation by TP53
• PIP3 activates AKT signaling

Another 73 pathways were run for to generate the ROC curves

Contents of Repository

Folders

input_data

This folder contains a single file per pathway containing the input values for each of the tests

pathways

This folder contains each of the Reactome pathways in the form of pairwise interaction files.

configs

This folder contains a config file per pathway that provides the inputs/parameters to MP-BioPath when running the tests.

results/tests and results/tests-roc

This folder contains the results that were generated by running the tests in this repository

Files

db_id_to_name_mapping.txt

This file allows us to make intupts based on node name/identifiers to Reactome IDs

expression/E-MTAB-2836.tsv

These Ensembl expression values are used in the analysis for determining the relative amount of expression of members in input sets. For the purpoese of these tests we used the tissue type.

Running tests

In order to run the tests for the ten pathways you have to do is have docker installed and run the following command from the root of this project:

bash run_tests.sh

To run the tests for the 73 ROC pathways run the following command

bash run_tests_roc.sh

Test Results

The results from running these tests will be located in "results/tests-new" and "results/tests-roc-new"

Previously run results from these are located in folders "results/tests" and "results/tests-roc"

Input and Result file Format

Both the input and result file formats follow the same conventions. both files are organized into a tab-delimited files where there is a column for each test and a row for each of the nodes. The input files only contain rows for nodes where the input value is being specified. The user can specify the nodes based on Reactome IDs or other IDs found in the db_id_to_name_mapping file including UNIPROT gene names.

Results files contain a row for every node in the pathway and are specified with Reactome IDs.

The values themselves range from 0.01 to 100. Where "1" is unchanged, "0.01" is 1/100th of the amount, and "100" is 100 times the amount relative to normal.