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 01/5/2011 - Two versions of Release 1.0:

Compatible with cytoscape 2.8
- Enrichment Map Plugin (v1.0 Release)- cytoscape 2.8 compatible

Download the zipped file, move it to the Cytoscape plugin directory and unzip it.

Distributions with source code:

Compatible with Cytoscape 2.7, and 2.6
- Enrichment Map Plugin (v1.0 Release)- cytoscape 2.7/6 compatible

Download the zipped file, move it to the Cytoscape plugin directory and unzip it.

Distributions with source code:

Sample Data Download

Main analysis

Estradiol-treated MCF7 cells, 12 and 24hrs (Gene Expression Omnibus: GSE11352)
- GSEA format:
  - files: EM_EstrogenMCF7_TestData.zip
  - Guided tutorial to load the files into Enrichment Map
- Generic format:
  - files: EM_EstrogenMCF7_TestData_Generic.zip
  - note: the results should be the same as GSEA

Query-set analysis (aka Post-analysis)

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

User Guide

User Guide Link

Gene-sets for Enrichment Analysis

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

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-Updated at 11/16/2010

 * [[attachment:EnrichmentMapPlugin_v1.0.zip|Enrichment Map Plugin (v1.0 Release)]]
+Updated at 01/5/2011 - Two versions of Release 1.0:
 1. '''Compatible with cytoscape 2.8'''
   * [[attachment:EnrichmentMapPlugin_v1.0_28.zip|Enrichment Map Plugin (v1.0 Release)- cytoscape 2.8 compatible]]
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- * [[attachment:EnrichmentMapPlugin_v1.0_src.zip|Enrichment Map Plugin with source code (v1.0 Release)]]
 * [[attachment:EnrichmentMapPlugin_v1.0_src.tar.gz|Enrichment Map Plugin with source code, tar and gzipped (v1.0 Release)]]
+   * [[attachment:EnrichmentMapPlugin_v1.0_28_src.zip|Enrichment Map Plugin with source code (v1.0 Release)- cytoscape 2.8 compatible]]
   * [[attachment:EnrichmentMapPlugin_v1.0_28_src.tar.gz|Enrichment Map Plugin with source code, tar and gzipped (v1.0 Release)- cytoscape 2.8 compatible]]
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+. '''Compatible with Cytoscape 2.7, and 2.6'''
   * [[attachment:EnrichmentMapPlugin_v1.0_27.zip|Enrichment Map Plugin (v1.0 Release)- cytoscape 2.7/6 compatible]]
Download the zipped file, move it to the Cytoscape plugin directory and unzip it.

Distributions with source code:
   * [[attachment:EnrichmentMapPlugin_v1.0_27_src.zip|Enrichment Map Plugin with source code (v1.0 Release)- cytoscape 2.7/6 compatible]]
   * [[attachment:EnrichmentMapPlugin_v1.0_27_src.tar.gz|Enrichment Map Plugin with source code, tar and gzipped (v1.0 Release)- cytoscape 2.7/6 compatible]]
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-=== How to Cite ===
+=== Cite EM ===
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-=== Publications Using EM ===
 * '''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''', Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BH, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger Jr JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C<<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>>
+=== 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>>