EnrichmentMap

Visualizes enrichment of specific functions (GO terms) by interactions between functions.
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.

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 2.2.0

Released 16 Jan 2017

Works with Cytoscape 3.3

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CYTOSCAPE 2

Version 1.3

Released 21 Jul 2014

Works with Cytoscape 2.6, 2.7, 2.8

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