ReactomeFIPlugIn

Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
ReactomeFIViz (also called Reactome Cytoscape Plugin or ReactomeFIPlugIn) 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.

5.0.0.beta

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

In this major release, we provide the following new features: 1). We have developed a new MRF (Markov random field)-based PGM model for the Reactome FI network to perform functional impact analysis based on multiple omics data types. 2). We have implemented visualization features for users to investigate inference results and omics data for individual samples coming from PGMs for both pathways and the FI network. These new features will help users to perform personal genomic data analysis. 3). We have added a way for users to perform gene set analysis without going through a file: Finally users can enter or copy/paste a list of genes directly into ReactomeFIVz. 4). We have implemented a quick way for users to perform gene enrichment analysis for a set of genes displayed in the network view: The user can select displayed genes and then use a popup menu to analyze their functions. 5). In this version, we have chosen Benjamini-Hochberg method to calculate FDR values for functional enrichment analysis for extremely quick performance and easy understanding of results. 5). Many bug fixes. For details, please see our tutorial page: [http://wiki.reactome.org/index.php/ReactomeFIViz]

4.2.0.beta

Works with Cytoscape 3.0

Release Notes

We have completely re-implemented features related to pathway analysis based on probabilistic graphical models (PGMs) in this release. Please see our updated user guide http://wiki.reactome.org/index.php/Reactome_FI_Cytoscape_Plugin#Probabilistic_Graphical_Model_based_Pathway_Analysis for these new features. Also in this release, we introduced the latest version of the Reactome functional interaction network, which is version 2014.

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 5.0.0.beta

License Click here

Released 17 Mar 2016

Works with Cytoscape 3.2

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