Project co-funded by the European Commission within the Sixth Framework Programme (2002-2006)
Dissemination Level
PU	Public	X
PP	Restricted to other programme participants (including the Commission Services)	
RE	Restricted to a group specified by the consortium (including the Commission Services)	
CO	Confidential, only for members of the consortium (including the Commission Services)	

Project No. LSHG-CT-2005-518254

ENFIN

An Experimental Network for Functional Integration

Instrument: Network of Excellence

Thematic Priority: LSH-2004-1.1.4-1

D2.

Report on the export of Reactome pathways into Cytoscape

Due date of deliverable: 15.10.10

Actual submission date: 15.02.10

Start date of project:	13.11.2005	Duration: 60 months

Organisation name of lead contractor for this deliverable: EMBL-HERMJAKOB

Contributors
EMBL-HERMJAKOB

Introduction
D2. Report on the export of Reactome pathways into Cytoscape

Methods/Results
A plugin has been developed for Cytoscape which allows the user to view Reactome pathways in Cytoscape. Pathway layout is maintained as is much of the look and feel (though not all). As well as the standard Cytoscape features, a number of features specific to the Reactome plugin are available to the user. These can be found in the 'Reactome' tab of the Cytoscape control panel. Pathways: A drop down lists the pathways in Reactome that have a diagram associated with them. This list is automatically retrieved from the Reactome server everytime the plugin is activated. When a pathway is selected, it is displayed in the main panel of Cytoscape. Node shapes and colours correspond to the coding found on the Reactome website (for example, complexes are blue coloured rounded rectangles). This is a fully interactive network – layout can be changed manually or using one of the layout algorithms provided in Cytoscape. Due to limitations of the Cytoscape software it was not possible to completely replicate the appearance of pathway diagrams found at www.reactome.org. Figure 1: The Eukaryotic Translation Elongation pathway displayed in Cytoscape. Link Out: Clicking this button will open a browser window showing the pathway currently selected in the Pathway drop down in the 'Pathway Browser' tool at www.reactome.org Interaction Network: Using this feature the pathway currently selected in the Pathway drop down can be viewed as a network of interacting proteins. This network is generated by retrieving a list of all the proteins found in the current pathway (solitary proteins and those which are found in complexes, polymers and sets). Each of these are submitted as queries to the Reactome PSICQUIC service. Interactions where both interacting proteins are found in the current pathway are added to the network. Searching: A search box allows the user to search the Reactome database for a list of pathways containing queries. As the user types, the application will suggest phrases the typed text might match. Submitting a query will return a list of entities in Reactome that match that query. Selecting one of these will populate the Pathway drop down with pathways containing that entity.

Perspectives
The plugin provides the foundation that features such as the following could be built on: Context menu features: The Pathway Browser at www.reactome.org provides context sensitive menus providing features such as the ability to list other pathways an entity is found in, retrieve interactors from a data source and display components of entities such as complexes and polymers. This functionality could also be implemented in Cytoscape. Network expansion: Combine pathways (either from Reactome or other databases) into one network. Pathways could be combined using shared entities or through interactors shared between entities in each pathway.

Publications

References

Project deliverable: ENFIN

3

LOGO

Zoe Ketselidou

2009-10-06T10:52:00

Gavin O'Kelly