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Visualizing Pathways and Networks in Cytoscape

You can visualize pathways and network neighborhoods that you find in Pathway Commons using the free Cytoscape software. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes.

Step-by-step instructions are provided below.

Getting Started

Sample Screenshot Cytoscape Link To load a pathway or network neighborhood, click on any of the "View in Cytoscape" links found throughout Pathway Commons.

 

These Cytoscape links are found on search results pages, pathway pages and physical entity pages.

 

A screenshot of the mTOR Pathway page, with a Cytoscape link is shown at right.

 

Sample Screenshot of mTOR Pathway, as visualized within Cytoscape The first time you click on a Cytoscape link, a Java Web Start version of Cytoscape will be launched, which takes a few moments.

 

Once launched, your chosen pathway or network neighborhood will be displayed within Cytoscape.

 

A screenshot of the mTOR pathway, as visualized within Cytoscape, is shown at right.

Loading additional data from Pathway Commons

Once Cytoscape is running, you have two options for loading additional data from Pathway Commons:
  • Click on additional "View in Cytoscape" links in the Pathway Commons web site; or
  • Search Pathway Commons directly from within Cytoscape. See the next section for details.

Accessing Pathway Commons Data from within Cytoscape

To search Pathway Commons directly from within Cytoscape:
  • Select: File → Import → Network from web services...
  • From the pull-down menu, select the Pathway Commons Web Service Client.

Importing networks via the Cytoscape web services framework

Then, follow the three steps outlined below:

Three-step process for searching Pathway Commons

  • Step 1: Enter your search term and organism filter; for example: BRCA1 [All Organisms].
  • Step 2: Select the protein or small molecule of interest. Full details regarding each molecule is shown in the bottom left panel.
  • Step 3: Download a specific pathway or interaction network.
In Step 3, you can simply double-click on a pathway of interest, or click on the "Interaction Networks" tab. This tab enables you to filter interactions by data source and/or interaction type. For example, you can choose to restrict your network to direct physical interactions from HPRD and MINT only:

Interaction Filters

Retrieval Options

You can configure access options from the Options tab. There are two retrieval options:
  • Simplified Binary Model: Retrieve a simplified binary network, as inferred from the original BioPAX representation. In this representation, nodes within a network refer to physical entities only, and edges refer to inferred interactions.
  • Full Model: Retrieve the full model, as stored in the original BioPAX representation. In this representation, nodes within a network can refer to physical entities and interactions.
By default, the simplified binary model is selected. Note, however, that all pathways and networks loaded via the Cytoscape links on the Pathway Commons web site will automatically be retrieved and displayed in the full BioPAX model.

Expanding a Network

If you download a network in the Simplified Binary Mode, you can choose to expand the network by retrieving neighbors of existing nodes within your network. To do so:
  • Right click on a node of interest.
  • From the pull-down menu, select: Use Web Services → Pathway Commons Web Service Client → Get Neighbors.

How to expand a network

Understanding and Using Cytoscape

You can click on molecules and their interactions in the Cytoscape view to get more details about them. Molecules can be moved around by clicking and dragging on them. You can zoom in and out using buttons on the toolbar and pan around the network view using the small overview window in the bottom left hand panel of Cytoscape. For further details, please refer to the Cytoscape web site and user manual (available in HTML and PDF formats).

Full BioPAX Mode: The Meaning of the Symbols in a Network View

By default, nodes and edges in the full BioPAX mode are displayed as follows:

Entity Visual Shape
Proteins, small molecules, complexes and other physical entities (as defined in the BioPAX pathway format). Ellipse Shape
Conversions, biochemical reactions, modulations and other interaction entities (as defined in the BioPAX pathway format). Square Shape
Interaction Type Arrow Shape
Inhibition Black inhibition arrow type
Containment, e.g. a complex can contain one or more proteins. Black circle arrow type
All other interaction types, e.g. activation, left, right, etc. Black arrow type
Labels for Physical Entities
All physical entities will be labeled as follows:

[NAME] [-CHEMICAL_MODIFICATION_ABBR] [(CELLULAR_LOCATION_ABBR)]

where [NAME] is determined by the following order of precedence: NAME, SHORT NAME, or Shortest Synonym, and [CHEMICAL_MODIFICATION_ABBR] and [CELLULAR_LOCATION_ABBR] are one of the abbreviations described below.
Examples:
MITF: MITF
MITF Phosphorylated: MITF-P
MITF Phosphorylated, in the cytoplasm: MITF-P (CP)
Abbreviations for Chemical Modifications
acetylation site A
glycosylation site G
phosphorylation site P
proteolytic cleavage site PCS
sumoylation site S
ubiquitination site U
[All others] No Abbreviation Provided.
Abbreviations for Cellular Locations
cellular component unknown No Abbreviation will be provided.
centrosome CE
cytoplasm CY
endoplasmic reticulum ER
endosome EN
extracellular EM
golgi apparatus GA
mitochondrion MI
nucleus NU
plasma membrane PM
ribosome RI
[All others] No Abbreviation Provided.

Bug Reporting

If you encounter a bug with this plugin, please use our feedback form, or log a bug directly to the Cytoscape Bug Tracker.

Contacts

Ethan Cerami
Benjamin Gross
Sander Group, Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York City

For any questions or feedback concerning this plugin, please use our feedback form.

Release Notes / Current Limitations

Version: 2.0

  • Date: April 1, 2008
  • Features:
    • Now supports full BioPAX mode and simplified binary model.
    • Now supports direct query of Pathway Commons from within Cytoscape.
    • Additional merge features for merging two or more networks.

Version: 0.2

  • Date: June 25, 2007
  • Features:
    • Enables the automatic download and visualization of network neighborhoods directly from PathwayCommons.org.

Version: 0.1

  • Date: May 15, 2007
  • Features:
    • Enables the automatic download and visualization of pathways directly from PathwayCommons.org.

License / Credits

This software is made available under the LGPL (Lesser General Public License).

This product includes software developed by the Apache Software Foundation