pathwaysKEGG

Extract pathways from KEGG database using EC entries.

Input files

Input files contain interaction information in three columns:

1. RHMR#### : reaction name
2. v#### : edge name

3. .#.#.#: EC number, enzyme nomenclature number

   Source of data

   Information source are from:

Tissue: Breast, Lung, Kidney or Renal, and Urothelial

Condition: Cancer, Healthy

Set: MDS, nonMDS, where MDS means Minimum Dominanting Set

Example of file name:

EC_BreastCancer_MDS,

EC_UrothelialHealthy_nonDMS

Functions in the scripts

First_KEGGPathways.R

In this script you have three functions:

function Pathways

This function is for extracting the list of pathways set by set and save two results:

• List of raw pathways
• List of pathways with the number of counts of that pathway.

• Two options are available, run for all datasets or run files one by one

function statistical_test

This function is to calculate the p-value for proportions differences using prop.test() or fisher.test(). It is recomended to use Fisher test. The results of this function are:

• Files with the p-value for compared sets (120 in total)

• Two options are available run all combinations or run for a single pair of sets.

function join-function

This function joins the results of proportional test or Fisher exact test, and returns three results.

• A raw file with all the combination name, list of pathways and the p-value,
• A file with a list pathways whose p-values were less than 0.05,
• A file with the count of the number of pathways significantly different on any of the set combinations.
  Join functios allows to entre “pt” or “ft” to run it.

Running Time

1. MDS files: aproximately 10 minutes (08’-15’) by file
2. nonMDS files: aproximately 42 minutes (38’-55’) by file

Second_fisherTest.R

This script is to calculate the Fisher exact test p-value for the comparison of healthy and cancer pathways.

Third_Plots.R

This script is to plot the figures used in this project report. It uses a tidy data file manipulated in excel with the raw results of pathways lists.

Fourth_KEGGDisease

This script allows to extract the name of the diseases to which our list of pathways are associated. The input data in this script is a list of codes in KEGG format. For example: map01100 is the KEGG code for purine metabolism.

Fifth_KEGGPathways_shorther

This is a shorter version and time saving pathway extraction script. This version is still in developing, but so far it extracts the list of all pathways, unlisting the list is not working correctly.