Procedure 

 

Information on downloading the software and installation instructions please go to simulator tab.

 

In this experiment, we used model of galactose utilization pathway, which is a biochemical pathway converts Galactose into glucose-6-phosphate in Saccharomyces cerevisiae . The model has taken from sample directory of cytoscape.

 

1. Go to the “File” option in the standard menu bar and select "import", from submenu choose “Network (multiple file types)” as shown in Figure 1 to import model in to cytoscape.

 

Figure 1: Screenshot to import the network

 

2. One can see, the dialog box opened to choose the network file.

 

Figure 2: Screen shot to load the network from local path

 

3. Click on select button and choose the network file where it is located locally.

 

4. Thus the network will be loaded as in the figure 3.

 

Figure 3: Screenshot of the loaded network

Importing the expression data

 

5. To import the expression data , go to “File” import and choose Attribute from table(Text/Ms Excel).

 

  Figure 4: Screenshot to import the expression data attributes

 

6. From the dialog box opened, make sure the Node radio button selected in data sources attributes.

 

7. Click on select file, select the expression data file from the system and click open in file chooser.

 

Figure 5: Screenshot to select the expression data file

 

8. In the advances section from the dialog box, select “show text file import options”.

 

9. From the delimiter section, select the checkbox “space”.

 

10. In the “Attributes name section”, select transfer first line attributes name.

 

Figure 6: Screenshot to choose parameters to import the expression data

 

11.  In addition, select Import everything from the “Advanced section” to load all the data, not just only records that match the currently loaded network.

 

12.  Make sure the names of all columns are unique , if not right click on the column name and change the column name.

 

Figure 7: Screenshot to change the column names

 

Sub Module Analysis

 

13. Install JactiveModules plugin in the cytoscape if not installed.

 

14. Go to “Plugins” menu and select “jActiveModules” plugin for sub module analysis

 

Figure 8:Screenshot to open the "jActiveModule" plugin 

 

15. Set the Module parameters “Number of Modules”, “Overlap Threshold”, “Searching parameters”

 

 Figure 9: Screenshot of the jActiveModule plugin to set parameters

16. Click on “Find Modules” to run the plugin.

 

Thus, one can see the plugin found the five significant sub modules or sub networks on the expression data.

 

 Figure 10: Screenshot of the results to find submodules 

 

From the module analysis results, we can found module 1 contains 16 nodes and the module is having the significant score of 4.514, than all other microarray conditions. That means the first module is more significant than the other modules. When one selects the sub network, the nodes of the module got selected and new network can be created.

 

 Figure 11: Screenshot showing the most significant submodule with the expression data

 

Through the sub module analysis one can identify most significant sub networks or sub modules based on expression data, and the sub modules can further analyzed for better understanding.

 

 

 

 

 

 

 

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.