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## page was renamed from Software/EnrichmentMaps
## IMPORTANT EDITING NOTE (by Daniele Merico, 12/10/2010)
## - links to this page and its subsection have been included in a book chapter
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{{attachment:Software/EnrichmentMap/UserManual/enrichmentmap_logo3.png|Enrichment Map Logo|align="right"}}<<BR>> 
= 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 [[Software/EnrichmentMap/Description|more details and an analysis example]]. 
== Plugin Download ==
Updated at 11/16/2010

 * [[attachment:EnrichmentMapPlugin_v1.0.zip|Enrichment Map Plugin (v1.0 Release)]]
Download the zipped file, move it to the Cytoscape plugin directory and unzip it.

Distributions with source code:
 * [[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)]]

== 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

=== Query-set analysis (aka Post-analysis) ===
 * [[attachment:estrogenTargetsLin2007.GMT|Estrogen targets]] (Lin CY et al 2007, Plos Genetics; PMID: 17542648)
== User Guide ==
[[Software/EnrichmentMap/UserManual|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
 [[GeneSetDB_02|download page]]
 * how to convert DAVID gene-sets to GMT: [[/DAVIDgs_R|R script]]
== Publications ==

 * 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

 * '''Merico D''', '''Isserlin R''', '''Stueker O''', Emili A, '''Bader GD'''<<BR>>'''Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation'''<<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>>