Building a pathway with Cytoscape and WikiPathways

Thomas Kelder

Maastricht University

Biological Use Case: Building and extending biological pathway diagrams using Cytoscape. This demo shows you how to use Cytoscape and WikiPathways to create a visually annotated pathway diagram based on a very simple pathway or a list of genes.


Cytoscape version: Version number (2.6)

Plugins to Load: GPML plugin (0.4, yet to be added to the plugin manager), Agilent Literature Search plugin, BubbleRouter plugin

Other software: WikiPathways or PathVisio 1.1.

GUI steps:

Describe each step (story), the GUI action to take, and probable remarks




A pathway diagram can be a good medium to create an overview of relevant knowledge for your research topic. Here we start with a very basic draft pathway, e.g. based on conference notes or an image in a review paper.

Open and edit circadian_start.gpml at or in PathVisio.

TODO: Prepare this pathway on wikipathways and reset after every demo

We want to extend the pathway with related genes, proteins and interactions. We are going to use Cytoscape to extract the relevant information from literature.

Copy the draft pathway to Cytoscape: (1) Select all objects. (2) Press CTRL-C or the copy button on the toolbar. (3) Switch to Cytoscape. (4) Press CTRL-V or "edit->Paste GPML", the pathway should appear as Cytoscape network.

Note the visual annotations, you can hide them using CTRL-H or "view->Hide GPML annotations"

Now use Agilent Literature Search to find genes or proteins that are associated with Clock/Arntl.

(1) Start Agilent Literature Search. (2) Search for Clock and Arntl in context of Mus Musculus and "circadian", setting "Max Engine Matches" to 50.

We want to filter out the most relevant associations to include in our pathway.

(1) Use a filter to select edges with "numberOfSources >= 4". (2) Select all nodes that are connected by the edges (CTRL-7). (3) Create a child network from selected nodes and edges (CTRL-SHIFT-N).

You should end up with a network containing Clock, Arntl, Per1, Per2, Cry 1, Cry2, Npas2 and Dbp. Per1,2 and Cry1,2 are part of a negative feedback loop. Npas2 can act as substitute for Arntl. Dbp is a downstream gene, transcription is controlled by Clock/Arntl.

Now we can update the GPML pathway with the new genes. After we studied the associated publications, we can create a mechanistic diagram and add visual annotations.

Select the nodes/edges in the filtered network and press CTRL-C to copy them to the clipboard. Switch to the WikiPathways editor and paste using CTRL-V. Now rearrange the genes and interactions and annotate the pathway using shapes and labels. An example of how this could look in the end can be found as attachement

Note that the literature references are copied along to the WikiPathways page.

Imagine you did a microarray experiment and found a set of rhytmically expressed genes that may be relevant to the circadian rhythm pathway. We want to know how and where these genes are functional and display this in our pathway. One way to place the gene list in biological context is to apply a functional layout using BubbleRouter.

Copy the genes from the GPML pathway to Cytoscape. Create a new Bubblerouter region by holding "Shift" and dragging a rectangle with your mouse. In the dialog, select the attribute "Bubblerouter-CellularComponents" and mark a cellular component (e.g. cytoplasm).

The genes that are associated to the celllular component you selected will be routed to the region.

We can create several regions representing different cellular locations to get an idea where the genes play a role.

Create regions for various organelles.

See the screenshots for an example of the end result.

Now we can export everything back to the GPML pathway, adjust the layout and add annotations

Switch to PathVisio or the WikiPathways applet and remove the genes that you copied to Cytoscape before. Switch back to Cytosccape, select all nodes and copy them to the WikiPathways applet. You can rearrange the genes to give it a better look. This workflow can be repeated,

Note that the regions don't look exactly the same as in Cytoscape. You can rearrange the genes to make it look similar (see screenshot). If you also want to get an idea about how the genes interact, you can again use the Agilent Literature Search plugin, or merge the nodes with an interaction network.

Data / Session Files:

Presentation: presentation

Webstart: Attach a webstart

Video: Attach a video link

WikiPathwaysRecipe (last edited 2009-02-12 01:04:01 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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