Minimum requirements
- Linux system with minimum 8GB of RAM and 20GB of storage space
- Python (v-2.7) & Python dependencies: zen, numpy, cython
- R (>= 3.4) and Bioconductor
Steps for analysis
-
Create node weight files with 2 comma separated columns with headers "Gene" and "NodeWt"
-
Compute edge weights using the Edgeweight.R code and HPPIN.txt file
-
Calculate top perturbed networks using the following:
python2.7 shortest_path.py edgeweightFileName 3 # 3 stands for minimum path length
./top50K.sh ShortestPathOutputFile #sorts all path by pathscore and outputs top 50K paths
Rscript Top_Perturbed_network.R 500 # 500 for the number of top nodes, this script runs for all the sorted top paths file at once
-
Use InnateDB (https://www.innatedb.com/redirect.do?go=batchPw) for pathway overepresentation analysis.
-
For binary scoring of enriched pathways and Consensus Clustering use binaryScoring_ConsensusClustering.R with IPLTB.csv and critical_genes.csv files