Procedure

 

Follow the steps given to analyse the network and feature detection

 

Step1: Download and install cytoscape in your computer. Please go to simulator tab for detailed information about instalation.

 

Step 2: Launch cytoscape, make sure that you have internet in your computer. Go to plug-in options in the standard menu bar, check whether the network analyzer is installed or not, if not go to manage plug in and search for Network analyzer and install.

 

Figure 1: Screenshot of Cytoscape and to manage plugin menu

 

Step 3: Go to the required pathway database exaple IntAct, download the network in a suitable format like sif, sbml, xml, etc. One can download the network from external databases or can also import the network directly from the web services.

 

Step 4: Import the network into the cytoscape, by the standard menu "File" option as shown below.

 

Figure 2: Screenshot to import network files

 

Step 5: Once the network is loaded, change it into preferred layout.

 

Figure 3: Screen shot to manage with layouts

 

Step 6: Go to plug in menu, choose the option "Network Analysis", followed by choose "Analyze network".

 

Figure 4: Screenshot to analyze network

 

 

When one chooses to analyze network, the GUI appears asking the user to interpret network as undirected or directed network. Select according to the network one have downloaded.

 

Figure 5: screebshot to interpret the network

 

After one has chosen the network interpretation the network is analyzed with simple and complex parameters.

 

Figure 6: Scrrenshot of the results with simple parameters

 

The simple network parameters, analyze the network density, network radius, clustering coefficient, number of nodes and self loops, etc.

 

Complex network parameter shows the distribution of node, shortest path length, topological coefficient distribution etc.

 

Node Degree distribution:

Figure 7: screenshot of node degree distribution

 

Shows the distribution of the degree with number of nodes, there are different options to enlarge chart, to export the chart, and to fit a line.

The chart can be exported and can be saved as jpeg file.

 

 

 

 

 

 

 

 

This experiment uses : Cytoscape, www.cytoscape.org/ Michael Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Trey Ideker, Cytoscape 2.8: new features for data integration and network visualization Bioinformatics. 2011 February 1; 27(3): 431–432.Published online 2010 December 12.