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.

Plugin Download

Updated at 07/06/2011 - Release 1.2 : Compatible with cytoscape 2.6,2.7,2.8
- Enrichment Map Plugin (v1.2 Release)
  Download the zipped file, move it to the Cytoscape plugin directory and unzip it.
  
  Distributions with source code:
- Enrichment Map Plugin with source code (v1.2 Release)
- Enrichment Map Plugin with source code, tar and gzipped (v1.2 Release)
- Added Features and Release Notes
Updated at 02/7/2011 - Release 1.1: Compatible with cytoscape 2.6,2.7,2.8
- Enrichment Map Plugin (v1.1 Release)
  Download the zipped file, move it to the Cytoscape plugin directory and unzip it.
  
  Distributions with source code:
- Enrichment Map Plugin with source code (v1.1 Release)
- Enrichment Map Plugin with source code, tar and gzipped (v1.1 Release)

Development Versions

Updated at 04/9/2014 - Release 1.3 - Release Candidate 6 : Compatible with cytoscape 2.6,2.7,2.8
- Added bug fix with missing leading edge on reloaded sessions files for down regulated gene sets.
- Added command tool support
- Added EDB support
- Added values to heat map
- Added ability to load GSEA class files directly
- fixed misc bugs
- Enrichment Map Plugin (v1.3 RC6)
  Download the zipped file, move it to the Cytoscape plugin directory and unzip it.
- Source code can be found on github: https://github.com/BaderLab/EnrichmentMapApp
Updated at 05/28/2014 - Release 2.0 - Release Candidate : Compatible with cytoscape 3.1
- Ported existing EM to Cytoscape 3.
- Enrichment Map Plugin (v2.0 RC1 build 400)
  Download the zipped file, install plugin from file in plugin manager.
- Source code can be found on github: https://github.com/BaderLab/EnrichmentMapApp (EM_Cyto_port branch)

Tutorials and Examples

data used for the tutorials: Estradiol-treated MCF7 cells, 12 and 24hrs (Gene Expression Omnibus: GSE11352)

GSEA format:
- Guided GSEA tutorial to load the filed into Enrichment Map
- Guided GSEA/EM tutorial to create EM directly from GSEA interface for single analysis (direct link from GSEA Reports frame).
- Guided GSEA/EM tutorial for multiple analyses to create an EM directly from GSEA interface for multiple analysis (from "Step in GSEA analysis frame)
Generic format:
- files: EM_EstrogenMCF7_TestData_Generic.zip
- note: the results should be the same as GSEA
DAVID format:
- files: EM_David_testData.zip
- Guided DAVID Tutorial to load the files into Enrichment Map
BiNGO format:
- files: EM_Bingo_testData.zip
- Guided BiNGO Tutorial to load the files into Enrichment Map
g:Profiler format:
- files: EM_gProfiler_testData.zip
- Guided g:Profiler Tutorial to load the files into Enrichment Map
Query-set analysis (aka Post-analysis)
- CTCF targets in MCF7 treated or not with Estrogen
- Guided Post Analysis Tutorial to load the files into Enrichment Map

User Guide

Link to User Guide (and FAQ)

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
For Feature requests please send to enrichmentmap-dev@googlegroups.com

-  ⇤ ← Revision 9 as of 2009-07-06 19:29:11 → 
  Size: 714
  Editor: OliverStueker
  Comment:
+   ← Revision 135 as of 2014-05-31 16:26:09 → ⇥
  Size: 9857
  Editor: VeroniqueVoisin
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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+#acl All:read
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-#acl All:read
+## IMPORTANT EDITING NOTE (by Daniele Merico, 12/10/2010)
## - links to this page and its subsection have been included in a book chapter
## - if the URL of this page needs to be changed, please keep the current URL and auto-direct to the new one

{{attachment:Software/EnrichmentMap/UserManual/enrichmentmap_logo3.png|Enrichment Map Logo|align="right"}}<<BR>>
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+<<TableOfContents(5)>>
== 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.
-Line 5:
+Line 14:
+Follow this link for [[Software/EnrichmentMap/Description|more details and an analysis example]].
-Line 6:
+Line 16:
+. Updated at 07/06/2011 - '''Release 1.2''' : '''Compatible with cytoscape 2.6,2.7,2.8'''
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-Updated at 01/07/2009 
 * attachment:EnrichmentMap.jar (v0.5 beta - Build: 97 from SVN: 279 by: revilo@REVILO-NB at: 2009/07/01)
+   * [[attachment:EnrichmentMapPlugin_v1.2.zip|Enrichment Map Plugin (v1.2 Release)]]<<BR>>
   Download the zipped file, move it to the Cytoscape plugin directory and unzip it.<<BR>>
-Line 10:
+Line 21:
-Older Version (classic user-Interface):
 * attachment:EnrichmentMapPlugin_0.4_beta.zip (v0.4 beta - Build: 70 from SVN: 254 by: revilo@!MacPro14 at: 2009/06/18)
+   Distributions with source code:<<BR>>
   * [[attachment:EnrichmentMapPlugin_v1.2_src.zip|Enrichment Map Plugin with source code (v1.2 Release)]]
   * [[attachment:EnrichmentMapPlugin_v1.2_src.tar.gz|Enrichment Map Plugin with source code, tar and gzipped (v1.2 Release)]]
-Line 13:
+Line 25:
-== Sample Data Download ==
+   * [[EnrichmentMap/ReleaseNotesv1.2 | Added Features and Release Notes]]
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-Estradiol-treated MCF7 breast cancer cells, 12hrs and 24hrs: attachment:EM_EBC_TestData.zip
 * Guided tutorial for the test data: [:EnrichmentMap/Background/Tutorial: here]
+. 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 18:
+Line 32:
+   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)]]

== Development Versions ==

 1. Updated at 04/9/2014 - '''Release 1.3 - Release Candidate 6''' : '''Compatible with cytoscape 2.6,2.7,2.8'''
   * Added bug fix with missing leading edge on reloaded sessions files for down regulated gene sets.
   * Added command tool support
   * Added EDB support
   * Added values to heat map
   * Added ability to load GSEA class files directly
   * fixed misc bugs

   * [[attachment:EnrichmentMap-1.3.0-SNAPSHOT_v1.30_RC6.zip|Enrichment Map Plugin (v1.3 RC6)]]<<BR>>
   Download the zipped file, move it to the Cytoscape plugin directory and unzip it.<<BR>>
   * Source code can be found on github: https://github.com/BaderLab/EnrichmentMapApp

 1. Updated at 05/28/2014 - '''Release 2.0 - Release Candidate''' : '''Compatible with cytoscape 3.1'''
   * Ported existing EM to Cytoscape 3.

   * [[attachment:EnrichmentMapPlugin_v2.0-RC1.zip|Enrichment Map Plugin (v2.0 RC1 build 400)]]<<BR>>
   Download the zipped file, install plugin from file in plugin manager.<<BR>>

   * Source code can be found on github: https://github.com/BaderLab/EnrichmentMapApp (EM_Cyto_port branch)

== Tutorials and Examples ==
data used for the tutorials: Estradiol-treated MCF7 cells, 12 and 24hrs (Gene Expression Omnibus: GSE11352)
   * ''GSEA format:'' 
     * [[Software/EnrichmentMap/Tutorial| Guided GSEA tutorial]] to load the filed into Enrichment Map
     * [[Software/EnrichmentMap/AutoEMFromGSEA| Guided GSEA/EM tutorial]] to create EM directly from GSEA interface for single analysis (direct link from GSEA Reports frame).
     * [[Software/EnrichmentMap/AutoMultiEMFromGSEA| Guided GSEA/EM tutorial for multiple analyses]] to create an EM directly from GSEA interface for multiple analysis (from "Step in GSEA analysis frame)
   * ''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
   * ''BiNGO format:''
     * files: [[attachment:EM_Bingo_testData.zip]]
     * [[Software/EnrichmentMap/BingoTutorial|Guided BiNGO Tutorial]] to load the files into Enrichment Map
   * ''g:Profiler format:''
     * files: [[attachment:EM_gProfiler_testData.zip]]
     * [[Software/EnrichmentMap/GProfilerTutorial|Guided g:Profiler Tutorial]] to load the files into Enrichment Map
   * ''Query-set analysis (aka Post-analysis)''
     * [[attachment:EM_PostAnalysis_TesData.zip|CTCF targets in MCF7 treated or not with Estrogen]] 
     * [[Software/EnrichmentMap/PostAnalysisTutorial|Guided Post Analysis Tutorial]] to load the files into Enrichment Map
-Line 19:
+Line 80:
+[[Software/EnrichmentMap/UserManual|Link to User Guide (and FAQ)]]
-Line 20:
+Line 82:
-[:Software/EnrichmentMaps/UserManual: User Guide Link]
+== Gene-sets for Enrichment Analysis ==
 * 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]]
 * 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
 [[GeneSetDB_02|download page]]
 * how to convert DAVID gene-sets to GMT: [[/DAVIDgs_R|R script]]
== Publications ==
=== Cite EM ===
 * '''Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation'''<<BR>> '''Merico D''', '''Isserlin R''', '''Stueker O''', Emili A, '''Bader GD'''<<BR>>[[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013984|PLoS One. 2010 Nov 15;5(11):e13984]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21085593|PubMed Abstract]] -[[attachment:2010_MericoIsserlinStuekerBader-EnrichmentMap_PLoSOne.pdf|PDF]]<<BR>>

=== Examples of Use ===
 * '''Functional impact of global rare copy number variation in autism spectrum disorders.'''<<BR>>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.''<<BR>>[[http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature09146.html|Nature. 2010 Jun 9 (Epub ahead of print)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20531469|PubMed Abstract]] - [[attachment:Publications/2010_AutismNature.pdf|PDF]]<<BR>>[[http://blogs.nature.com/news/thegreatbeyond/2010/06/rare_genetic_variants_linked_t.html|Nature Blogs]] - [[http://www.theglobeandmail.com/news/national/autism-caused-by-wide-array-of-rare-gene-changes-study/article1597861/|In the news (The Globe and Mail)]]<<BR>>

 * '''Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps'''<<BR>>'''Isserlin R''', '''Merico D''', Alikhani-Koupaei R, Gramolini A, '''Bader GD''', Emili A.<<BR>>[[http://www3.interscience.wiley.com/journal/123269335/abstract|Proteomics 2010, March 10(6):1316-27]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20127684|Pubmed Abstract]] - [[attachment:Publications/2010_EM_proteomics.pdf|PDF]]<<BR>>


== 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>>

== Report a Bug or a Problem ==
 1. please make sure you don't have formatting issues (have a look at the [[Software/EnrichmentMap/UserManual|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
 1. 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
 1. For Feature requests please send to enrichmentmap-dev@googlegroups.com