341: Introduction to Bioinformatics

Tutorial on Protein Interaction Network Analysis using Cytoscape

(Sample Study)
Tools Used

Cytoscape, http://www.cytoscape.org , provides open source tools for the analysis and integration of
biological networks.
BiogridPlugin2 (version 2.1) for Cytoscape, http://wiki.thebiogrid.org/doku.php/biogridplugin2 ,
allows importing and filtering protein-protein interaction (PPI) networks from BioGrid Database.

Data Used

Prostate Cancer and Pancreatic Cancer Pathways extracted from KEGG Pathway Database,
http://www.genome.jp/kegg/pathway.html.
Human PPI Network extracted from BioGRID database, http://thebiogrid.org/.

Objectives

Extracting PPI networks from BioGRID database

Extracting pathways from KEGG database
Visualizing PPI networks using Cytoscape
Comparing two PPI networks using Cytoscape
Identifying graph-theoretic properties of PPI networks using Cytoscape

Tasks
1.
2.

3.
4.

5.

Download and install Cytoscape from Cytoscape web site. Alternatively, you can use the archived
distribution files that do not require installation, if you are using department computers.
Go to the BioGRID web site. Download the BiogridPlugin2 for Cytoscape (version 2.1) which is
provided under the downloads section. Put the downloaded jar file under C:\Program
Files\Cytoscape_v2.8.0\plugins folder of your computer and restart Cytoscape. (Provided path is for
Windows systems. It may differ depending on your computer)
From the downloads section of BioGRID web site, download the file named BIOGRID-ORGANISM3.1.73.tab2.zip. Get the Homo Sapiens (human) PPI network from this package.
Identify the genes associated with Pancreatic cancer and Prostate cancer from KEGG database.
You can use the Pathway Entry link to access all the information related to the selected pathway.
Copy the gene names to an excel file and create two .txt files containing gene names associated with
a pathway.
Open Cytoscape and import the following networks using the BioGRID tab under Control Panel:
The network containing all the physical interactions in the human PPI network
The subnetwork containing the physical interactions between the proteins associated with
Pancreatic Cancer pathway.
The subnetwork containing the physical interactions between the proteins associated with
Prostate Cancer pathway.
You should make use of the gene names identified in step 4 while importing the cancer related
subnetworks. Make sure that you have excluded interspecies interactions and self-loops from these
networks. Observe that the three networks you have imported exist under Network tab under
Control Panel. How many proteins and how many interactions do the subnetworks contain?

6.

Try different network visualization layouts using the list of layout algorithms listed under Layout tab
of the main panel. (You are advised to do this for subnetworks.) Export your favourite visualization as
an image file. You can use the button with the camera image which is located on the main panel for
exporting the visualization of the network.
7. You can zoom in/out on the visualization of the network using the scroll-wheel. You can also move
anywhere in the network by clicking middle mouse button. Left mouse button is used for selecting
nodes and edges. Right clicking on a node or edge provides a list of operations that you can perform
with the selected object. Experience it. What happens in the Data Panel when you select a list of
nodes and edges?
8. Select the proteins that exist in both Pancreatic Cancer and Prostate Cancer pathways on the
visualization of the subnetwork of Pancreatic Cancer. You can make use of the Nodes option
under the Select tab of the main panel. Click From File and provide the .txt file containing the list
of genes that are associated with the pathway. How many proteins are common between these
networks?
9. Find the network containing the nodes and interactions that exist in both Prostate Cancer and
Pancreatic Cancer pathways. You can make use of the Compare Two Networks functionality
defined under the Plugins tab of the main panel. Remember to change the visualization layout of
the intersection network if you find a single red node as the intersection. (Note: this functionality is
not provided by default before Cytoscape version 2.8. If you are using an older version of Cytoscape,
you might need to install Network Analyzer plug-in containing this functionality.)
10. Find the clustering coefficient, the number of connected components, radius, density, diameter of the
intersection network. Export the degree distribution of the network into a text file. You can make use
of the Analyze Network option under the Plugins tab of the main panel. Repeat the analysis for
the subnetworks of Pancreatic Cancer and Prostate Cancer and compare your results.
11. Export the subnetworks of Pancreatic Cancer and Prostate Cancer pathways as SIF files. You can
use the Export option under File tab of the main panel. Remove the second column from these
files (basically by replacing pp\t with using a text editor). You are going to use these files for the
GraphCRUNCH tutorial.

Notes
The guidelines above are only a short introduction to the main functionalities of Cytoscape. Cytoscape can be
extended with many different plugins. Detailed information about Cytoscape and existing plugins can be found
from Cytoscape web site. You can watch a demonstration of the main functionalities of Cytoscape from:
http://www.youtube.com/watch?v=KIJ6M1nvKoY
Also note that every PPI database has a different structure. Although there exist plugins for importing BioGRID
datasets, you have to write your own scripts while extracting networks from different databases.