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Integrating Biological Networks and Microarray Expression data
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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 sachromyeces cerevisea. 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.

 

 

 

 Figure 1: Screen shot to impor the network

 

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

 

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

 

  1. Click on select button and choose the network file where it is located locally as sjown in Figure 2.

 

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

 

 Figure 3: Screenshot of the loaded network

 

Importing the expression data

 

To download or to get gene expression data please go to simulator tab. 

 

  1. 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

 

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

 

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

 

Figure 5: Scrrenshot to select the expression data file  

 

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

 

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

 

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

 

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

 

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

 

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

 

 Figure 7: Screenshot to change the column names 

 

 

 

We have successfully loaded the data and integrated with the existing network, to see the data attributes go to the data panel and select “Node Attribute Browser”  and then choose “Select Attributes” where you can see the different attributes loaded.

 

Select few nodes from the network cascade and observe the values of attributes in the data panel.

 

 Figure 8: Screenshot of the nodeattribute browser

 

 

To visulalize the expression level change in the network model, set the visual properties to the network model by changing the node color or node size. 

 

Go to “VizMapper” in the controlpanel, by clicking on the icon shown in figure 9 " Create a new visual style"  by specifying a new name.

 

 Figure 9:Screenshot to create a visualisation style of a network

 

 

In the Visual mappping browser  select "Node Color" by double clicking, activate the node color.

 

 Figure 10: Screenshot cor color maping the network 

 

In the map, attribute pull down menu select “gal1RGexp” and select continuous mapping, thus you can see the color mapping graphics below that, click on the icon seen, set minimum and maximum values with color change.

 

Figure 11: Screenshot to set minimum and maximum values for colour gradients

 

Add the gradient and set the value to zero.

 

The network visualized as in the figure 12

 

 

 Figure 12: Screenshot of the network with expressison values 

 

Thus by integrating expression data with the network, one can observe the changes in the expression level of change in the genes at stretch in the network for complete analysis.

 

 

 

 

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.

 

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