ReactomeFIPlugIn

Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
Reactome Cytoscape Plugin is designed to find pathways and network patterns related to cancer and other types of diseases. This plugin accesses the Reactome pathways stored in the database, help you to do pathway enrichment analysis for a set of genes, visualize hit pathways using manually laid-out pathway diagrams directly in Cytoscape, and investigate functional relationships among genes in hit pathways. The plugin can also access the Reactome Functional Interaction (FI) network, a highly reliable, manually curated pathway-based protein functional interaction network covering over 50% of human proteins, and allows you to construct a FI sub-network based on a set of genes, query the FI data source for the underlying evidence for the interaction, build and analyze network modules of highly-interacting groups of genes, perform functional enrichment analysis to annotate the modules, expand the network by finding genes related to the experimental data set, display pathway diagrams, and overlay with a variety of information sources such as cancer gene index annotations.

4.1.1.beta

Works with Cytoscape 3.0

Release Notes

Changes in this new release are mainly related to features related to probabilistic graphical models (PGMs): 1). Entity names are used in the factor graphs converted from Reactome pathways. Originally interaction DB_IDs were used. 2). When a pathway is converted into a factor graph, outputs from BlackBoxEvents for gene regulatory interactions are augmented for observation data. 3). Bug fix: the feature of exporting annotations for functional enrichment analysis results has been fixed now.

4.1.0.beta

Works with Cytoscape 3.0

Release Notes

Added a new feature to use probabilistic graphical models for doing pathway analysis. For details, see [http://wiki.reactome.org/index.php/Reactome_FI_Cytoscape_Plugin#Probabilistic_Graphical_Model_based_Pathway_Analysis].

4.0.1.beta

Works with Cytoscape 3.0

Release Notes

1). Bug fix: unable to load a text file for pathway enrichment analysis using a popup menu in the loaded Reactome pathway tree for Windows. 2). New features: fetch FIs for a selected entity in a pathway diagram; In-Cytoscape Reactome source view to avoid loading a Reactome web page from an unstable Reactome dev server.

4.0.0.beta

Works with Cytoscape 3.0


3.0.2.beta

Works with Cytoscape 3.0


3.0.1.beta

Works with Cytoscape 3.0


3.0.0.beta

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 4.1.1.beta

License Click here

Released 19 Aug 2014

Works with Cytoscape 3.0

Download Stats Click here