EnrichmentMap

Visualizes enrichments of pathways as an enrichment map, a network representing overlaps among enriched pathways.
Categories: automation, enrichment analysis, enrichment map, GO annotation, ontology analysis
*This App is part of the [https://apps.cytoscape.org/apps/enrichmentmappipelinecollection EnrichmentMap Collection].* The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network. It will operate on any generic enrichment results as well as specifically on Gene Set Enrichment Analysis (GSEA) results. Nodes represent gene-sets and edges represent mutual overlap; in this way, highly redundant gene-sets are grouped together as clusters, dramatically improving the capability to navigate and interpret enrichment results. Gene-set enrichment is a data analysis technique taking as input: * A (ranked) gene list, from a genomic experiment * Gene-sets, grouping genes on the basis of a-priori knowledge (e.g. Gene Ontology) or experimental data (e.g. co-expression modules) and generating as output the list of enriched gene-sets, i.e. best sets that summarizing the gene-list. It is common to refer to gene-set enrichment as functional enrichment because functional categories (e.g. Gene Ontology) are commonly used as gene-sets. Links: * [https://enrichmentmap.readthedocs.io User Guide] * [https://enrichmentmap.readthedocs.io/en/latest/Automating.html Automation Guide] * [https://github.com/BaderLab/EnrichmentMapApp Code Repository]
Authors:

3.5.0

Works with Cytoscape 3.7

Release Notes

* Heat Map panel usability improvements. * New option in EnrichmentMap Create dialog for running AutoAnnotate. * Bug fixes.

3.4.0

Works with Cytoscape 3.7

Release Notes

* New column, style mapping and chart for -log10(pvalue). * Better support for latest version of AutoAnnotate. * Default layout is now yFiles organic layout. * UI changes to the EnrichmentMap create dialog. * Bug fixes.

3.3.6

Works with Cytoscape 3.7

Release Notes

* Fixes a bug where the leading edge was not being rendered correctly in the heat map.

3.3.5

Works with Cytoscape 3.7

Release Notes

- The Heat Map works for AutoAnnotate summary networks created from EnrichmentMap networks. - New option to set edge color for multi-dataset networks. - Bug Fixes

3.3.4

Works with Cytoscape 3.7

Release Notes

* Created an options menu next to the Data Set list and moved all the buttons that used to be next to the Data Set list into this menu. * Added ability to synchronize data set list with network selection. * Bug fixes.

3.3.3

Works with Cytoscape 3.7

Release Notes

* Creating a subnetwork from an EnrichmentMap network will copy the EnrichmentMap data to the subnetwork. * Bug fixes.

3.3.2

Works with Cytoscape 3.7

Release Notes

* Bug fixes.

3.3.1

Works with Cytoscape 3.7

Release Notes

* Enhancements to 'build-table' command for app interoperability. * Bug fixes.

3.3.0

Works with Cytoscape 3.7

Release Notes

New in EnrichmentMap 3.3: * The colors used in the 'Color by DataSet' chart can be customized. * It is no longer a strict error when gene sets are missing from the GMT file. The user may choose to continue to create the network without the missing gene sets. * The Heat Map panel can sort ranks automatically based on the leading edge. * The Heat Map panel can filter Data Sets based on node/edge selection. * Support for importing Enrichr files when creating an EnrichmentMap network. * New "Create Command" button in the Create Enrichment Map Dialog shows equivalent command for automation. * New "Getting Started" section on the Create Enrichment Map Dialog to better help new users. * An EnrichmentMap network can now be created from a STRING or GeneMania network. * Bug Fixes

3.2.1

Works with Cytoscape 3.7

Release Notes

Minor features and bug fixes. - The Heat Map panel is now synchronized with the data set list in the Control Panel. When a data set is disabled the genes/expressions from that data set will be hidden in the Heat Map. This is consistent with how the data set list interacts with the network. - Added better documentation for commands (accessible via command line or swagger) - Added 'pattern' argument to mastermap command. - Bug fixes

3.2.0

Works with Cytoscape 3.7

Release Notes

- Integration with other tools - GeneMANIA - STRING - Pathway Commons - New Commands - export pdf - set chart options - show/hide datasets - create EM from data in a table (allows EM to be created from STRING) - New Column name prefixes (EnrichmentMap::name) - Uses new Column Namespace feature introduced in Cytoscape 3.7 - Scroll bar in main panel - Empty ranks always sorted to bottom of heat map - Drag and drop files onto the creation dialog - Many bug fixes - Requires Cytoscape 3.7

3.1.0

Works with Cytoscape 3.5

Apps that depend on this release

Release Notes

* Redesigned Post-Analysis UI * Ability to preview signature gene sets before import * Ability to import GMT files from the web (download.baderlab.org) * New Chart: Color by DataSet. * Support for g:profiler 2-phenotype analysis. * Heat Map: Compress expressions by class. * Export Legend to PDF. * Export Heat Map to PDF. * Ability to specify the name of the EnrichmentMap network. * Drag-and-Drop folders onto the Create EnrichmentMap Dialog. * Several bug fixes (https://github.com/BaderLab/EnrichmentMapApp/milestone/7?closed=1) * Requires Cytoscape 3.5.1

3.0.0

Works with Cytoscape 3.4

Release Notes

EnrichmentMap 3.0 is a major release, with the following new features: * EnrichmentMap networks can now be created from any number of enrichment data sets (EnrichmentMap 2.0 supported maximum 2 data sets). * New chart visualizations on nodes for visualizing NES scores, p-values or q-values. Three new charts are available: radial heat-map, linear heat-map and heat-strips. * New network creation dialog has the ability to scan a folder for files belonging to each dataset. In most cases this removes the need to manually enter the required files. * New control panel allows the contents and style of the network and charts to be updated dynamically. * New legend dialog. * New streamlined HeatMap panel has the ability to summarize expression data. * Several new commands that allow EnrichmentMap to be automated from external scripts and CyREST.

2.2.1

Works with Cytoscape 3.3

Apps that depend on this release

Release Notes

Bug fix release

2.2.0

Works with Cytoscape 3.3

Release Notes

Bug Fixes * Bug fixes listed here: https://github.com/BaderLab/EnrichmentMapApp/issues?q=is%3Aissue+is%3Aclosed+milestone%3A2.2_release Features: * New color scheme for network style. * Updated the UI to be cleaner and more modern looking. * Improved the performance of the gene-set similarity calculation, and made the task cancellable.

2.1.0

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

### Bug fixes and Added features in 2.1.0: Bug fixes: - Numerous bug fixes that are outlined here: https://github.com/BaderLab/EnrichmentMapApp/issues?q=is%3Aissue+is%3Aclosed+milestone%3A2.1_release Features: - Revamped post analysis interface and functionality.    - Post analysis can be run in known signature mode or signature discovery mode.  Known signature mode calculates post analysis edges for a small subset of sets.  Signature discovery mode allows for filtering of large set of potential signatures to help uncover most likely set. - Post analysis edges can be calculated using a two sided or one sided Mann whitney test using rank files from either dataset1 or dataset2 separately.  For example, this allows the user to look for pathways that contain a significant set of up-regulated miR targets only.   - Update g:profiler support so we no longer require a gmt file to be specified. - Add the ability to specify the set of genes associated with the geneset in the generic enrichment file. - Added “publication ready” button to legend panel so users can easily toggle between figure ready and normal view of network. 

2.0.1

Works with Cytoscape 3.1

Release Notes

### Bug Fixes and Added features in 2.0.1<BR> **Bug Fixes**<BR> * Fixed issue with building a two dataset network using edb or rpt because a missing reference to gmt file.<BR> * Fixed rank file load through heatmap panel<BR> * Added error message to say that PDF export is currently not available<BR> * Fixed issue creating heatmap with hiearchical clusters for some datatypes <BR> * Enabled input panel to be reopened after closed by the user.<BR> Fixed issue with GREAT file import(if a line was missing genes it would truncate the load and only load results prior to the line with missing genes)<BR> * GREAT export loads from TSV file instead of a TXT version of the TSV file downloaded.<BR> * Enable GMT only EM creation<BR> * Fixed issue with EM created from all genesets if nothing passed the thresholds<BR><BR> **Features**<BR> * Enabled EM creation from Bingo 3.0 output files.<BR> * P-value and Q-value can be set using precision of 10-12 or using scientific notation (no limit with scientific notation).<BR> * Added the ability to specify which p-value you want to filter by (hyper, binom, both or either) for GREAT results.<BR> * Enabled slliders to work with precision higher than 10-3. Now works for whatever the cutoff is with an additional range of precision 10-3 less than the cutoff value.<BR>

2.0.0

Works with Cytoscape 3.1

CYTOSCAPE 3

Version 3.5.0

Released 7 Oct 2024

Works with Cytoscape 3.7

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