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 10/17/2013 - Release 1.3 - DEVELOPMENT Release : 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 DEV)
  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 08/05/2011 - Release 1.3 - DEVELOPMENT Release : 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.
- Enrichment Map Plugin (v1.3 DEV)
  Download the zipped file, move it to the Cytoscape plugin directory and unzip it.
  
  Distributions with source code:
- Enrichment Map Plugin with source code (v1.3 DEV)
- Enrichment Map Plugin with source code, tar and gzipped (v1.3 DEV)

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)
- Estrogen targets (Lin CY et al 2007, Plos Genetics; PMID: 17542648)

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 32 as of 2010-04-12 23:41:49 → 
  Size: 1646
  Editor: OliverStueker
  Comment:
+   ← Revision 125 as of 2013-10-17 19:40:38 → ⇥
  Size: 10006
  Editor: RuthIsserlin
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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+#acl All:read
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+Line 4:
-#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
-Line 5:
+Line 10:
+<<TableOfContents(5)>>
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+Line 16:
-Updated at 12/04/2010
+. Updated at 07/06/2011 - '''Release 1.2''' : '''Compatible with cytoscape 2.6,2.7,2.8'''
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+Line 18:
- * [[attachment:EnrichmentMapPlugin_v1.00-RC2.zip|Enrichment Map Plugin (v1.00 Release Candidate 2)]]
Download the zipped file, move it to the Cytoscape plugin directory and unzip it.
== Sample Data Download ==
Estradiol-treated MCF7 breast cancer cells, 12hrs and 24hrs: [[attachment:EM_EBC_TestData.zip]]
+   * [[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 17:
+Line 21:
- * [[Software/EnrichmentMap/Tutorial|Guided tutorial]] to load the test data into Enrichment Map
+   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 19:
+Line 25:
+   * [[EnrichmentMap/ReleaseNotesv1.2 | Added Features and Release Notes]]

 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>>

   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 10/17/2013 - '''Release 1.3 - DEVELOPMENT Release''' : '''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:EnrichmentMapPlugin_v1.3-DEV-reebf77f_44_EMrefactor.zip|Enrichment Map Plugin (v1.3 DEV)]]<<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 08/05/2011 - '''Release 1.3 - DEVELOPMENT Release''' : '''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.

   * [[attachment:EnrichmentMapPlugin_v1.3-DEV.zip|Enrichment Map Plugin (v1.3 DEV)]]<<BR>>
   Download the zipped file, move it to the Cytoscape plugin directory and unzip it.<<BR>>

   Distributions with source code:<<BR>>
   * [[attachment:EnrichmentMapPlugin_v1.3-DEV_src.zip|Enrichment Map Plugin with source code (v1.3 DEV)]]
   * [[attachment:EnrichmentMapPlugin_v1.3-DEV_src.tar.gz|Enrichment Map Plugin with source code, tar and gzipped (v1.3 DEV)]]

== 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:estrogenTargetsLin2007.GMT|Estrogen targets]] (Lin CY et al 2007, Plos Genetics; PMID: 17542648)
-Line 20:
+Line 81:
-[[Software/EnrichmentMap/UserManual|User Guide Link]]
+[[Software/EnrichmentMap/UserManual|Link to User Guide (and FAQ)]]
-Line 22:
+Line 83:
+== 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]]
-Line 23:
+Line 89:
+=== 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>>
-Line 24:
+Line 92:
- * Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A. <<BR>>
 '''''Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps.''''' <<BR>>
 Proteomics. '''''2010''''' Feb 1. <<BR>>
 PMID: 20127684
+=== 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