ReactomeFIPlugIn

Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
Categories: automation, Boolean Network, cancer data analysis, clustering, disease, enrichment analysis, Factor Graph, functional analysis, functional module detection, Fuzzy Logic, gene co-expression, GO annotation, graph analysis, interaction database, Interactive search, microarrays, mutation analysis, network analysis, network generation, network partitioning, pathway database, Probabilistic Graphical Model, prognostic network module, R, survival analysis, systems biology
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.
Authors:

8.0.9

Works with Cytoscape 3.8

Release Notes

Bug fix: The 2024 version of the FI network in release 8.0.8 points to the 2022 version of the FI network. This has been fixed now.

8.0.8

Works with Cytoscape 3.8

Release Notes

This release updates ReactomeFIViz to support Java 17, which is bundled with the latest version of Cytoscape, 3.10.2.

8.0.7

Works with Cytoscape 3.8

Release Notes

The 2024 version of the Reactome FI network is released in this update of ReactomeFIViz. FIs from KEGG are no longer included due to licensing issues. However, the pathway enrichment analysis still includes KEGG pathways to provide more functional insight into the constructed FI network for the uploaded gene sets.

8.0.6

Works with Cytoscape 3.8

Release Notes

The 2022 version of the Reactome FI network is released in this update of ReactomeFIViz. The workflow for constructing the FI network has been revamped by replacing the original Naive Bayesian Classifier with a random forest classifier trained using 106 protein/gene pairwise features in the place of . For more information about this new workflow, please refer to https://www.biorxiv.org/content/10.1101/2023.06.05.543335v1.

8.0.5

Works with Cytoscape 3.8

Release Notes

This is a maintenance release to fix a bug related to set the drug targets for pathway drug impact analysis after selecting a drug (For this feature, see https://reactome.org/userguide/reactome-fiviz#Simulate_Impact_of_Cancer_Drugs_on_Pathway_Activities).

8.0.4

Works with Cytoscape 3.8

Release Notes

1. Added the support to Reactome FI network version 2021 and Reactome release 78. 2. For Mac OS only: Added new features for pathway and transcription factor activity analysis using AUCell and ssGSEA for scRNA-seq data. The support to Windows will be released soon.

8.0.3

Works with Cytoscape 3.7

Release Notes

Another bug fix: After a pathway enrichment analysis, converting to FI network view fails because of the class cast exception. This bug has been fixed now.

8.0.2

Works with Cytoscape 3.7

Release Notes

This is a bug fix release: When linkers are used, the class cast exception causes the hang of the network construction. This bug has been fixed now.

8.0.1

Works with Cytoscape 3.7

Release Notes

This release updates the version of Reactome FI network to 2020, the latest release, and the release of Reactome pathways to release 75, released in December 2020. The Reacfoam view used for overview of Reactome pathways has been updated to a licensed version, which removes the commercial logo at the bottom-right corner.

8.0.0

Works with Cytoscape 3.7

Release Notes

Many new features have been added in this release for users to conduct scRNA-seq data analysis and visualization using ReactomeFIViz inside Cytoscape with GUIs: 1). Support Reactome pathways and the FI network for mouse. 2). A set of new features for scRNA-seq data analysis and visualization. See https://reactome.org/userguide/reactome-fiviz#scRNA_seq for details.

7.2.3

Works with Cytoscape 3.7

Release Notes

Added a new feature to visualize all Reactome pathways in the **Reactome Reacfoam** view. The user can open this view using a popup menu called "*Open Reactome Reacfoam*" in the pathway tree for the original pathways or pathways highlighted based on an enrichment analysis. The user can also download this view from the browser into an image file.

7.2.2

Works with Cytoscape 3.7

Release Notes

This release supports the Reactome FI network version 2019, constructed based on the Reactome release 71. The code in this release has been updated to support the upcoming Cytoscape 3.8.0.

7.2.1

Works with Cytoscape 3.7

Release Notes

This is a maintenance release having two bugs fixed: 1). Some pathway diagrams cannot be opened if they contain chemical drugs. 2). In GSEA analysis, the pathway size cutoff values (i.e. min and max values) are not used.

7.2.0

Works with Cytoscape 3.7

Release Notes

The following new features have been provided in this release: 1). Support the new version of Reactome FI network: version 2018. 2). The Reactome database has been updated to release 67, which was released in December, 2018. 3). For Boolean-network based constrained fuzzy logic simulation, users can choose a transfer function and specify parameters for Hill function if it is chosen. 4). The gene score distribution plot has been improved. It should be much faster now. 5). The backend server has been migrated to Amazon AWS to provide a faster and uninterrupted service. 6). The user guide, https://reactome.org/tools/reactome-fiviz, has been updated.

7.1.0

Works with Cytoscape 3.6

Apps that depend on this release

Release Notes

The following new features have been provided in this release: 1). Support the new version of Reactome FI network: version 2017. 2). The Reactome database has been updated to release 63, which was released in December, 2017. 3). Drugs collected in the DrugCentral database are now supported for visualizing in Reactome pathways and FI networks. The drug/target interactions are based on file, drug.target.interaction.08292017.tsv, downloaded from the DrugCentral web site. 4). The popular GSEA pathway enrichment analysis is now supported. However, the data is limited to a gene score file only. 5). Users can now overlay gene scores onto an opened pathway diagram from a file. For detailed, see our updated user guide: https://reactome.org/tools/reactome-fiviz.

7.0.2

Works with Cytoscape 3.6

Release Notes

This is a maintenance release to fix a bug related to Reactome pathway enrichment analysis for a set of genes in ReactomeFIViz CyREST API: if no gene can be mapped to Reactome pathways, results from previous positive Reactome enrichment analysis will be returned.

7.0.1

Works with Cytoscape 3.6

Release Notes

This is a maintenance release to fix a bug related to survival analysis result display.

7.0.0

Works with Cytoscape 3.6

Release Notes

The following new features have been added: 1). Support CyREST based automation. The following API has been provided: <br>a). Get a list of FI network versions. <br>b). Build a FI sub-network <br>c). Perform network clustering analysis <br>d). Perform functional enrichment analysis for the displayed FI network or network modules <br>e). Load Reactome pathways <br>f). Perform pathway enrichment analysis for a set of genes <br>g). Export pathway diagrams 2). Perform batch pathway impact analysis for a drug based on Reactome pathways. 3). A set of selected objects in pathway diagram view can be highlighted by changing the background color. 4). A new plot view showing all targets for one selected drug. 5). During FI network view for a pathway, an option is added so that only FIs converted from the selected reaction or complex can be displayed. 6). Preference setting for ReactomeFIViz Web Server port to avoid the firewall problem for some organizations. Bug fixes 1). Cannot show FI network after converting pathway diagram. 2). Auto-layout cannot be applied after a FI network is constructed.

6.1.0

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

In this release, we have made the following changes: 1). A new way to calculate the difference or perturbation of entity activities based on the Boolean network simulation has been implemented. 2). New GUIs have been added to control the total number of columns in the time course table to display Boolean network simulation results. 3). A new method is used to generate initial values for Boolean network simulation. You may see some 0 in the simulation set up table. 4). Attractor values are no longer displayed in the simulation set up table. Users should focus on their attention to the time course table.

6.0.0

Works with Cytoscape 3.2

Release Notes

This new release introduces the following two new features: 1). Boolean network-based pathway modeling. For details see: [https://wiki.reactome.org/index.php/ReactomeFIViz#Boolean_Network_based_Pathway_Analysis] 2). Visualize FDA approved cancer drugs in the contexts of Reactome pathways and its functional interaction network. For details see: [https://wiki.reactome.org/index.php/ReactomeFIViz#Visualize_Cancer_Drugs_in_Contexts_of_Reactome_Pathways_and_FI_Network]

5.2.0.beta

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

This version of ReactomeFIViz is released to support the latest version of the Reactome FI Network, version 2016. No new features have been released.

5.1.0.beta

Works with Cytoscape 3.2

Release Notes

In this minor release, we provide the following new features: 1). Pathway diagram view is supported for Cytoscape 3.4.0. It was broken because of the new network view implementation in Cytoscape 3.4.0. 2). Added a new feature to compare PGM inference results and observation data for two selected samples. 3). Several bug fixes related to gene list and pathway highlight and performance tunings.

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 8.0.9

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Released 13 Jul 2024

Works with Cytoscape 3.8

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