PPI network pipeline

These commands will create a network based on a set of genes you should provide as "seeds.txt".

Download this pipeline

• With git:

    git clone git@github.com:lelimat/PPI_network_pipeline.git
    cd PPI_network_pipeline
  

• Or directly downloading the zip file:

    wget https://github.com/lelimat/PPI_network_pipeline/archive/master.zip
    unzip master.zip
    cd PPI_network_pipeline-master
  

Download PPI database (iRefIndex)

Usage: R --slave --file=get_PPI_data_iRefIndex.R --args [min_evidence] [database_dir].

• [min_evidence] is the minimum number times the interaction is being reported. I usually choose 2.

• [database_dir] is the directory where the iRefIndex file will be saved.

    R --slave --file=get_PPI_data_iRefIndex.R --args 2 databases
  

Download gene information

wget ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz
gunzip Homo_sapiens.gene_info.gz

Create network from seed genes (initial set of interest)

python create_net_irefindex.py --database=iRefIndex_human.txt --seeds=seeds.txt --output=. --distance=1

The distance is the number of levels of neighbors added to the network starting from the seeds. If you only need to see how the seeds connect. Choose distance=0. For seeds + first neighbors, choose distance=1, and so on.

Output:

• edges.txt: File with edges created for the network.
• genes_not_found.txt: List of genes (from the seeds) whose names were not found in the PPI database.

Calculate network topology

echo -e "node_1\tnode_2" > edges_attributes.txt
cat edges.txt >> edges_attributes.txt
python network_topology.py edges_attributes.txt Homo_sapiens.gene_info
rm edges.txt

Create plots for brokers, bridges and bottlenecks

R --slave --file=get_network_info.R --args nodes_attributes.txt

Getting nodes in the initial list

grep Yes nodes_attributes.txt | cut -f1 > in_list_Yes.txt

Separating the gene symbols in the network

cut -f1 nodes_attributes.txt | grep -v node > all_genes.txt

Creating Cytoscape file

python net_cytoscape.py

The command above will generate a file "network.xgmml" to be open with Cytoscape.