Software

Pathicular

The Cytoscape plug-in ‘Pathicular’ identifies path motifs in integrated networks and arranges them in a modular structure. After the integrated network and the source network (deletion or overexpression in this case) are loaded into Cytoscape, Pathicular can be used to find all the paths of a given type in the source network using the integrated network. A p-value is provided to check the overrepresentation of the path of interest.

Pathicular can be installed by downloading and extracting the tar.gz file below and by copying the pathicular<version>.jar file into the Cytoscape plugins directory and placing the colt.jar library in the lib directory.

Alternatively, you can use the Cytoscape plugin manager:

• Plugins -> Manage plugins
• Change download site
• Edit sites
• Add BEG : http://bioinformatics.psb.ugent.be/cytoscape/downloadsite/beg.xml
• Select Analysis -> Pathicular from the download list.

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