https://github.com/erictleung/bmi667-tcga-network

Network analyses on 127 significantly mutated genes from well-known and emerging cellular processes in cancer using Python and Shell scripting.
https://github.com/erictleung/bmi667-tcga-network

Last synced: 17 days ago
JSON representation

Network analyses on 127 significantly mutated genes from well-known and emerging cellular processes in cancer using Python and Shell scripting.

• Host: GitHub
• URL: https://github.com/erictleung/bmi667-tcga-network
• Owner: erictleung
• Created: 2015-11-09T02:39:08.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2015-12-07T09:40:34.000Z (about 9 years ago)
• Last Synced: 2024-05-02T05:11:54.365Z (8 months ago)
• Language: Python
• Size: 22.5 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# BMI667 TCGA Gene Network Analysis

Network analyses on 127 significantly mutated genes from well-known and emerging

cellular processes in cancer using Python and Shell scripting. The paper

[Mutational landscape and significance across 12 major cancer

types](http://www.ncbi.nlm.nih.gov/pubmed/24132290) by Kandoth et. al. published

about the 127 significantly mutated genes.

## Execute Analysis

```shell

$ bash extract_and_save.sh

$ python network_analysis.py

$ python distance_and_paths.py

```

## Analysis Instructions

### Part 1

- Download Reactome interaction files in PSI-MITAB format from

  http://www.reactome.org/download with the link: `Human protein-protein

  interaction pairs in PSI-MITAB format`. 

- Extract interactions into pair-wise gene symbols: one interaction per line

  (e.g. NFS1\tITGA7). 

- Map the 127 TCGA PanCancer genes to create a sub-network. 

- Calculate four centralities (degree, eigenvector, PageRank, Katz) each gene in

  the sub-network.

### Part 2

- Implement breadth first search (BFS) algorithm and apply it to the sub-network

  for 127 cancer genes you have generated.

- Find how many components.

- Calculate pair-wise distances.

- Calculate average shortest path and the diameter of the sub-network.

### Part 3

- Try to develop a random permutation method to check whether or not the average

  shortest path obtained from last week's assignment is significant.

## Contents

- `bin`: scripts directory

- `data`: data repository

- `report`: written report for the analysis

## Scripts

TBD

## Data

TBD