![]() A smaller pathway (called sub-pathway) may be drawn in a bigger pathway, which has its own pathway diagram. Not all pathways have their own pathway diagrams. Open pathway diagram: Pathways in Reactome are organized in a hierarchical way.Follow the procedures to finish the installation. Choose the app, and then click the "Install" button at the bottom of the dialog. Note: The listed name of this app is "ReactomeFIPlugIn", which is the original name of the app.). You should see the ReactomeFIViz app listed in the middle panel (See the Figure below. After launching Cytoscape, use menu "Apps/App Manager" to open the "App Manager" dialog, and search for "ReactomeFI". If you have not installed Cytoscape 3.7.0 or above, please download it from Cytoscape's web site. ReactomeFIViz app 6 needs Cytoscape 3.7.0 or above. Recently we have also added features to help users visualize FDA-approved cancer drugs in the contexts of the FI network and Reactome pathways, and use Boolean network models directly built from Reactome pathways to investigate potential functional impacts of displayed cancer drugs.įor an example how we use Reactome FIs for cancer data analysis, please see our publication: A human functional protein interaction network and its application to cancer data analysis. The app can also access the Reactome Functional Interaction (FI) network, a highly reliable, manually curated pathway-based protein functional interaction network covering over 60% 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. This app 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 ReactomeFIViz app is designed to find pathways and network patterns related to cancer and other types of diseases. Perform scRNA-seq Data Analysis and Visualization Simulate Impact Drugs on Pathway Activities Visualize Cancer Drugs in Reactome Pathways Visualize Drugs in the Contexts of Reactome Pathways and FI Network Use the Reactome Functional Interaction (FI) Network Visualization of Structural Variants in the Context of Reactome Pathways Probabilistic Graphical Model Based Pathway Analysis Display Reactome Pathways in the FI Network View ![]()
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