Enrichment Map Plugin Download Page

Contents

Enrichment Map Plugin Download Page

Brief Description

Enrichment Map is a Cytoscape plugin for functional enrichment visualization. Enrichment results have to be generated outside Enrichment Map, using any of the available methods. Gene-sets, such as pathways and Gene Ontology terms, are organized into a network (i.e. the "enrichment map"). In this way, mutually overlapping gene-sets cluster together, making interpretation easier. Enrichment Map also enables the comparison of two different enrichment results in the same map.

Follow this link for more details and an analysis example.

Legends

For easier figure creation download our template legends that contains all the visual properties used in a standard enrichment map. Download and customize legend to fit your network

Downloads

Cytoscape can be downloaded from: http://cytoscape.org/

EnrichmentMap is available on the Cytoscape App Store: http://apps.cytoscape.org/apps/enrichmentmap

Alternatively download the EnrichmentMap Pipeline Collection. This will install EnrichmentMap as well as a suite of other apps that work well with EnrichmentMap, including AutoAnnotate, WordCloud and clusterMaker2: http://apps.cytoscape.org/apps/enrichmentmappipelinecollection

Tutorials and Examples

Tuturials and protocols for EnrichmentMap 3.0 are here: https://baderlab.github.io/Cytoscape_workflows/EnrichmentMapPipeline/

Tutorials for the older 2.2 version of EnrichmentMap are here: http://enrichmentmap.readthedocs.io/en/docs-2.2/Tutorials.html

User Guide

The EnrichmentMap User Guide has been moved to: http://enrichmentmap.readthedocs.io

User Guide for older 2.2 version of EnrichmentMap (including tutorials) is here: http://enrichmentmap.readthedocs.io/en/docs-2.2/

Gene-sets for Enrichment Analysis

directly downloading our monthly updated gene-set collections from Baderlab genesets collections. Description of sources and methods used to create collection can be found here
we generate gene-set files for enrichment analysis (e.g. GSEA) by querying public resources such as Gene Ontology and KEGG, and using Entrez-Gene ID for genes
download page
how to convert DAVID gene-sets to GMT: R script

Publications

Cite EM

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
Merico D, Isserlin R, Stueker O, Emili A, Bader GD
PLoS One. 2010 Nov 15;5(11):e13984
PubMed Abstract -PDF

Examples of Use

Functional impact of global rare copy number variation in autism spectrum disorders.
Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, et al.
Nature. 2010 Jun 9 (Epub ahead of print)
PubMed Abstract - PDF
Nature Blogs - In the news (The Globe and Mail)
Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps
Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A.
Proteomics 2010, March 10(6):1316-27
Pubmed Abstract - PDF

Papers Citing Enrichment Map

Citations in Pubmed Central
Pathway analysis of expression data: deciphering functional building blocks of complex diseases.
Emmert-Streib F, Glazko GV.
PLoS Comput Biol. 2011 May;7(5):e1002053.
PubMed
Inflammasome is a central player in the induction of obesity and insulin resistance.
Stienstra R, van Diepen JA, Tack CJ, Zaki MH, van de Veerdonk FL, Perera D, Neale GA, Hooiveld GJ, Hijmans A, Vroegrijk I, van den Berg S, Romijn J, Rensen PC, Joosten LA, Netea MG, Kanneganti TD.
Proc Natl Acad Sci U S A. 2011 Aug 29.
PubMed
Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma
Witt H, Mack SC, Ryzhova M, Bender S, Sill M, Isserlin R, Benner A, Hielscher T, Milde T, Remke M, Jones DTW, Northcott PA, Garzia L, Bertrand KC, Wittmann A, Yao Y, Roberts SS, Massimi L, Van Meter T, Weiss WA, Gupta N, Grajkowska W, Lach B, Cho YJ, von Deimling A, Kulozik AE, Witt O, Bader GD, Hawkins CE, Tabori U, Guha A, Rutka JT, Lichter P, Korshunov A, Taylor MD, Pfister SM
Cancer Cell, Volume 20, Issue 2, 143-157, 16 August 2011
PubMed Abstract - PDF

Report a Bug or a Problem

please make sure you don't have formatting issues (have a look at the User Guide (and FAQ))
- if you are still not sure how to handle formats,
- or you don't know what's the best suitable analysis for you,
- please send an email to: daniele[AT]merico[DOT]gmail.com
please check what's your
- plugin version and build (from the Cytoscape menu / Plugins / Enrichment Map / About)
- Cytoscape version (from the Cytoscape menu / Cytoscape)
- Operating System (e.g. Windows Vista)
and send your bug report to ruth[DOT]isserlin[AT]utoronto.ca
OR
report the bug to the Enrichment map issue tracker:
1. go to https://github.com/BaderLab/EnrichmentMapApp
2. click on "Issues"
3. click on "New Issue"
4. write a short description of the issue
5. attached session file (.cys) file or example input files if applicable
6. Make sure to enter plugin version and build, cytoscape version and operating system.
7. click on "Submit new issue"
For Feature requests please send to enrichmentmap-dev@googlegroups.com

-  ⇤ ← Revision 86 as of 2011-07-05 22:19:37 → 
  Size: 6862
  Editor: RuthIsserlin
  Comment:
+   ← Revision 178 as of 2018-04-19 18:08:18 → ⇥
  Size: 7567
  Editor: MikeKucera
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-{{attachment:Software/EnrichmentMap/UserManual/enrichmentmap_logo3.png|Enrichment Map Logo|align="right"}}<<BR>>
+{{attachment:Software/EnrichmentMap/UserManual/enrichmentmap_logo_mini.png|Enrichment Map Logo|align="right"}}<<BR>>
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+<<TableOfContents(5)>>
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+Line 15:
-== Plugin Download ==
 1. Updated at 02/7/2011 - '''Release 1.1''':
 '''Compatible with cytoscape 2.6,2.7,2.8'''
   * [[attachment:EnrichmentMapPlugin_v1.1.zip|Enrichment Map Plugin (v1.1 Release)]]<<BR>>
   Download the zipped file, move it to the Cytoscape plugin directory and unzip it.<<BR>>
-Line 20:
+Line 16:
-   Distributions with source code:<<BR>>
   * [[attachment:EnrichmentMapPlugin_v1.1_src.zip|Enrichment Map Plugin with source code (v1.1 Release)]]
   * [[attachment:EnrichmentMapPlugin_v1.1_src.tar.gz|Enrichment Map Plugin with source code, tar and gzipped (v1.1 Release)]]
+== Legends ==
For easier figure creation download our template legends that contains all the visual properties used in a standard enrichment map.  Download and customize legend to fit your network
  * [[attachment:em_legend.pdf|PDF File]]
  * [[attachment:em_legend.svg|SVG File]]
  * {{attachment:em_example_legend.png|Enrichment Map Example Legend|width=500}}<<BR>>
-Line 24:
+Line 22:
-. Updated at 07/05/2011 - '''DEVELOPMENT Release 1.2''' (SVN 580):
 '''Compatible with cytoscape 2.6,2.7,2.8'''<<BR>>
  '''Added Features in DEV version'''
    1. Bulk Enrichment map creation - designed for multiple GSEA results where an EM is wanted for each GSEA run.  Using the rpt file of each GSEA result a cytoscape session with the EM and a pdf of each network is generated.
    1. Ability to compare two different species or enrichment results from two different expression platforms.  Overlaps are created for each expression set separately.
    1. Creation of Enrichment maps based solely on a gene set file (for large gmt files requires a lot of memory)
    1. New similarity metric using combined overlap and jaccard coefficient based on a constant K defined by the user.
    1. Added Bingo file support
    1. Added ability view gene in each geneset even if an expression file has not been loaded.
    1. Added elementary support for exporting expression files as pdf (in addition to being able to export a text file).
    1. (added bug fix for post-analysis edges missing overlap data) 
  * [[attachment:EnrichmentMapPlugin_v1.2_DEV.zip|Enrichment Map Plugin (v1.2  DEV Release)]]<<BR>>
   Download the zipped file, move it to the Cytoscape plugin directory and unzip it.<<BR>>
+== Downloads ==
-Line 38:
+Line 24:
-   Distributions with source code:<<BR>>
  * [[attachment:EnrichmentMapPlugin_v1.2_DEV_src.zip|Enrichment Map Plugin with source code (v1.2 DEV Release)]]
  * [[attachment:EnrichmentMapPlugin_v1.2_DEV_src.tar.gz|Enrichment Map Plugin with source code, tar and gzipped (v1.2 DEV Release)]]
 
== Sample Data Download ==
=== Main analysis ===
 * Estradiol-treated MCF7 cells, 12 and 24hrs (Gene Expression Omnibus: GSE11352)
   * ''GSEA format:'' 
     * files: [[attachment:EM_EstrogenMCF7_TestData.zip]] 
     * [[Software/EnrichmentMap/Tutorial|Guided tutorial]] to load the files into Enrichment Map
   * ''Generic format:''
     * files: [[attachment:EM_EstrogenMCF7_TestData_Generic.zip]]
     * note: the results should be the same as GSEA
   * ''DAVID format:''
     * files: [[attachment:EM_David_testData.zip]]
     * [[Software/EnrichmentMap/DavidTutorial|Guided DAVID Tutorial]] to load the files into Enrichment Map
+Cytoscape can be downloaded from: http://cytoscape.org/
-Line 55:
+Line 26:
-=== Query-set analysis (aka Post-analysis) ===
 * [[attachment:estrogenTargetsLin2007.GMT|Estrogen targets]] (Lin CY et al 2007, Plos Genetics; PMID: 17542648)
+EnrichmentMap is available on the Cytoscape App Store: http://apps.cytoscape.org/apps/enrichmentmap

Alternatively download the EnrichmentMap Pipeline Collection. This will install EnrichmentMap as well as a suite of other apps that work well with EnrichmentMap, including AutoAnnotate, WordCloud and clusterMaker2: http://apps.cytoscape.org/apps/enrichmentmappipelinecollection

== Tutorials and Examples ==

Tuturials and protocols for EnrichmentMap 3.0 are here: https://baderlab.github.io/Cytoscape_workflows/EnrichmentMapPipeline/

Tutorials for the older 2.2 version of EnrichmentMap are here: http://enrichmentmap.readthedocs.io/en/docs-2.2/Tutorials.html
-Line 58:
+Line 37:
-[[Software/EnrichmentMap/UserManual|User Guide (and FAQ)]]
+The EnrichmentMap User Guide has been moved to: http://enrichmentmap.readthedocs.io

User Guide for older 2.2 version of EnrichmentMap (including tutorials) is here: http://enrichmentmap.readthedocs.io/en/docs-2.2/
-Line 61:
+Line 43:
+ * directly downloading our monthly updated gene-set collections from [[http://download.baderlab.org/EM_Genesets/current_release/|Baderlab genesets]] collections. Description of sources and methods used to create collection can be found [[http://baderlab.org/GeneSets|here]]
-Line 73:
+Line 56:
+== Papers Citing Enrichment Map ==

 * [[http://www.ncbi.nlm.nih.gov/pubmed?db=pubmed&cmd=link&linkname=pubmed_pubmed_citedin&uid=21085593|Citations in Pubmed Central]]


 * '''Pathway analysis of expression data: deciphering functional building blocks of complex diseases.'''<<BR>> Emmert-Streib F, Glazko GV.<<BR>> PLoS Comput Biol. 2011 May;7(5):e1002053.<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/21637797|PubMed]]

 * '''Inflammasome is a central player in the induction of obesity and insulin resistance.'''<<BR>> Stienstra R, van Diepen JA, Tack CJ, Zaki MH, van de Veerdonk FL, Perera D, Neale GA, Hooiveld GJ, Hijmans A, Vroegrijk I, van den Berg S, Romijn J, Rensen PC, Joosten LA, Netea MG, Kanneganti TD.<<BR>> Proc Natl Acad Sci U S A. 2011 Aug 29.<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21637797|PubMed]]

 * '''Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma'''<<BR>> Witt H, Mack SC, Ryzhova M, Bender S, Sill M, '''Isserlin R''', Benner A, Hielscher T, Milde T, Remke M, Jones DTW, Northcott PA, Garzia L, Bertrand KC, Wittmann A, Yao Y, Roberts SS, Massimi L, Van Meter T, Weiss WA, Gupta N, Grajkowska W, Lach B, Cho YJ, von Deimling A, Kulozik AE, Witt O, '''Bader GD''', Hawkins CE, Tabori U, Guha A, Rutka JT, Lichter P, Korshunov A, Taylor MD, Pfister SM <<BR>> [[http://www.sciencedirect.com/science/article/pii/S1535610811002625|Cancer Cell, Volume 20, Issue 2, 143-157, 16 August 2011]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21840481|PubMed Abstract]] - [[attachment:Publications/ependymoma.pdf|PDF]]<<BR>>
-Line 82:
+Line 77:
- and send your bug report to ruth[DOT]isserlin[AT]utoronto.ca
+ and send your bug report to ruth[DOT]isserlin[AT]utoronto.ca<<BR>> OR <<BR>> report the bug to the Enrichment map issue tracker:
   1. go to https://github.com/BaderLab/EnrichmentMapApp
   1. click on "Issues"
   1. click on "New Issue"
   1. write a short description of the issue
   1. attached session file (.cys) file or example input files if applicable
   1. Make sure to enter plugin version and build, cytoscape version and operating system.
   1. click on "Submit new issue"
 1. For Feature requests please send to enrichmentmap-dev@googlegroups.com